General information
PDB ID 5OQM
Title STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR
PDB header TRANSCRIPTION
Date 2017-08-13
Experimental method ELECTRON MICROSCOPY
Resolution (A) 5.8
Kind dna
Organism SYNTHETIC CONSTRUCT
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb5oqm.pdb ABCDEFGHIJKLMOQRUVWX01234567Zabcdefghijklmno NT 0
Biounits:
5oqm.pdb1.pdb ABCDEFGHIJKLMOQRUVWX01234567Zabcdefghijklmno NT 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Helicase_C_2 Domain P06839_526-699 1.3e-44 1 CL0023 0 526 700   
HBB Domain P06839_270-415 1.8e-28 1 No_clan 0 270 415   
PH_TFIIH Domain P32776_8-105 3.4e-19 1 CL0266 1 8 105   
BSD Domain P32776_243-300 2.8e-08 1 No_clan 1 248 298   
BSD Domain P32776_177-226 4.6e-05 0 No_clan 1 174 222   
Tfb2_C Domain Q02939_439-506 3.9e-22 1 No_clan 2 439 506   
zf-C3HC4_5 Domain Q03290_10-60 1.9e-28 1 CL0229 3 10 60   
Tfb4 Domain Q12004_23-309 8.4e-93 1 CL0128 4 23 309   
C1_4 Domain Q04673_402-456 1.7e-20 1 CL0006 6 402 456   
ERCC3_RAD25_C Domain Q00578_543-770 5.5e-127 1 CL0023 7 543 770 N   
RNA_pol_Rpb1_1 Domain P04050_11-340 1e-113 1 No_clan A 11 340 T   
RNA_pol_Rpb1_5 Domain P04050_807-1397 2.2e-90 1 No_clan A 807 1397 T   
RNA_pol_Rpb1_2 Domain P04050_342-507 1.9e-77 1 No_clan A 342 507   
RNA_pol_Rpb1_6 Domain P04050_873-1056 6.6e-65 1 No_clan A 873 1056   
RNA_pol_Rpb1_3 Domain P04050_510-669 7.3e-47 1 No_clan A 510 669   
RNA_pol_Rpb1_7 Domain P04050_1141-1274 3.9e-37 1 No_clan A 1141 1274   
RNA_pol_Rpb1_4 Domain P04050_693-800 6.3e-35 1 No_clan A 693 800   
RNA_pol_Rpb2_6 Domain P08518_752-1124 7.6e-127 1 CL0410 B 752 1124   
RNA_pol_Rpb2_2 Domain P08518_219-407 2.7e-51 1 No_clan B 219 407   
RNA_pol_Rpb2_7 Domain P08518_1126-1219 1.6e-33 1 No_clan B 1126 1219   
RNA_pol_Rpb2_4 Domain P08518_580-641 2e-25 1 No_clan B 580 641   
RNA_pol_Rpb2_3 Domain P08518_481-545 2.2e-20 1 No_clan B 481 545   
RNA_pol_Rpb2_5 Domain P08518_681-745 9.2e-19 1 No_clan B 681 745   
RNA_pol_A_bac Domain P16370_49-171 8e-32 1 No_clan C 49 171   
RNA_pol_L Domain P16370_19-255 3.7e-20 1 CL0509 C 19 255   
Med18 Domain P32585_3-299 5.7e-47 1 CL0273 e 3 299 N   
RNA_pol_Rpb5_C Domain P20434_142-214 1.4e-30 1 No_clan E 142 214   
RNA_pol_Rpb5_N Domain P20434_6-100 3.3e-29 1 CL0236 E 6 100   
S1 Domain P34087_80-161 5.5e-18 1 CL0021 G 80 161   
SHS2_Rpb7-N Domain P34087_8-66 3.3e-12 1 CL0319 G 8 66   
RNA_POL_M_15KD Domain P27999_4-41 1.3e-17 1 CL0167 I 4 41   
TFIIS_C Domain P27999_73-111 1.2e-14 1 CL0167 I 73 111   
RNA_pol_N Domain P22139_2-60 8.1e-29 1 No_clan J 2 60   
RNA_pol_L_2 Domain P38902_30-104 4.7e-25 1 CL0509 K 30 104   
DNA_RNApol_7kD Domain P40422_29-60 9.6e-17 1 CL0167 L 29 60   
TFIIB Domain P29055_122-213 7.2e-32 1 CL0065 M 122 213   
TFIIB Domain P29055_233-319 1.7e-16 1 CL0065 M 216 319   
TF_Zn_Ribbon Domain P29055_22-66 5.9e-13 1 CL0167 M 22 66   
TBP Domain P13393_154-237 6e-33 1 CL0407 O 154 237 NT   
TBP Domain P13393_64-146 6.8e-33 1 CL0407 O 64 146 NT   
TFIIF_beta Domain P41896_294-351 5.3e-23 1 CL0123 R 279 351   
TFIIA_gamma_C Domain P32774_63-118 2.3e-22 1 No_clan V 63 118   
TFIIA_gamma_N Domain P32774_6-52 6.7e-22 1 No_clan V 6 52   
TF_Zn_Ribbon Domain P36100_122-171 3.5e-11 1 CL0167 W 122 171   
TFA2_Winged_2 Domain P36145_187-247 3.5e-21 1 CL0123 X 187 247   
TFIIE_beta Domain P36145_125-186 1.2e-15 1 CL0123 X 124 186   
DEAD_2 Family P06839_71-257 2.2e-57 1 CL0023 0 71 257   
Tfb2 Family Q02939_12-281 7.1e-35 1 No_clan 2 147 409   
Tfb2 Family Q02939_11-129 5.2e-29 1 No_clan 2 12 130   
MAT1 Family Q03290_63-145 4.3e-39 1 No_clan 3 63 145   
Tfb5 Family Q3E7C1_2-64 2.4e-25 1 No_clan 5 2 66   
Ssl1 Family Q04673_129-325 8.4e-84 1 CL0128 6 129 317   
ResIII Family Q00578_359-519 3.3e-11 1 CL0023 7 363 519 N   
Med6 Family P38782_9-195 1.8e-49 1 No_clan a 10 195   
RNA_pol_Rpb2_1 Family P08518_42-455 8e-72 1 No_clan B 42 455   
Med8 Family P38304_31-210 4.7e-16 1 No_clan b 31 171   
Med11 Family Q99278_7-109 1.6e-12 1 No_clan c 7 104   
Med17 Family P32569_99-569 1.6e-111 1 No_clan d 106 569   
RNA_pol_Rpb4 Family P20433_49-218 1.9e-40 1 CL0426 D 49 218   
Med20 Family P34162_2-209 5.8e-40 1 CL0273 f 3 209   
RNA_pol_Rpb6 Family P20435_79-132 2.6e-14 1 No_clan F 79 132   
Med22 Family P32570_8-117 1.1e-13 1 No_clan g 8 115   
RNA_pol_Rpb8 Family P20436_7-146 8.4e-44 1 CL0021 H 7 146   
Med4 Family Q12343_67-200 4.2e-13 1 No_clan h 67 181   
Med7 Family Q08278_15-203 6.4e-32 1 No_clan i 62 203   
Med9 Family P33308_64-145 1.2e-12 1 No_clan j 64 145   
Med10 Family Q06213_19-142 8.8e-36 1 No_clan k 19 142   
Med14 Family P19263_89-292 1.8e-52 1 No_clan l 89 292   
Rox3 Family P25046_25-156 1.9e-23 1 No_clan m 25 156   
Med21 Family P47822_3-131 2.9e-43 1 No_clan n 3 131   
Med9 Family P47822_42-106 0.00066 0 No_clan n 43 107   
Med31 Family P38633_20-91 5.4e-25 1 No_clan o 23 102 TN   
TFIIF_beta_N Family P41896_65-227 2.2e-11 1 CL0662 R 65 207   
TFIIA Family P32773_241-285 4.6e-22 1 No_clan U 47 285 NT   
TFIIA Family P32773_9-48 3.3e-14 1 No_clan U 9 242   
TFIIE_alpha Family P36100_11-118 7.4e-38 1 CL0123 W 11 118 N   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
0=1-778 C cytosol
0=1-778 C nucleotide-excision repair factor 3 complex
0=1-778 C nucleus
0=1-778 C transcription factor TFIIH core complex
0=1-778 C transcription factor TFIIH holo complex
0=1-778 F 4 iron, 4 sulfur cluster binding
0=1-778 F 5'-3' DNA helicase activity
0=1-778 F ATP binding
0=1-778 F damaged DNA binding
0=1-778 F DNA helicase activity
0=1-778 F DNA-dependent ATPase activity
0=1-778 F metal ion binding
0=1-778 P nucleotide-excision repair
0=1-778 P nucleotide-excision repair, DNA duplex unwinding
0=1-778 P nucleotide-excision repair, DNA incision
0=1-778 P phosphorylation of RNA polymerase II C-terminal domain
0=1-778 P positive regulation of mitotic recombination
0=1-778 P positive regulation of transcription, DNA-templated
0=1-778 P regulation of mitotic recombination
0=1-778 P regulation of transposition, RNA-mediated
0=1-778 P response to oxidative stress
0=1-778 P response to UV
0=1-778 P transcription by RNA polymerase II
1=1-642 C cytosol
1=1-642 C nucleotide-excision repair factor 3 complex
1=1-642 C nucleus
1=1-642 C transcription factor TFIIH core complex
1=1-642 C transcription factor TFIIH holo complex
1=1-642 F phosphatidylinositol-3-phosphate binding
1=1-642 F phosphatidylinositol-5-phosphate binding
1=1-642 P DNA repair
1=1-642 P nucleotide-excision repair
1=1-642 P phosphorylation of RNA polymerase II C-terminal domain
1=1-642 P transcription by RNA polymerase I
1=1-642 P transcription by RNA polymerase II
2=1-513 C nucleotide-excision repair factor 3 complex
2=1-513 C transcription factor TFIIH core complex
2=1-513 C transcription factor TFIIH holo complex
2=1-513 F ATPase activator activity
2=1-513 F double-stranded DNA binding
2=1-513 P nucleotide-excision repair
2=1-513 P phosphorylation of RNA polymerase II C-terminal domain
2=1-513 P transcription by RNA polymerase II
3=1-321 C transcription factor TFIIH holo complex
3=1-321 C transcription factor TFIIK complex
3=1-321 F cyclin-dependent protein serine/threonine kinase activator activity
3=1-321 F metal ion binding
3=1-321 P DNA repair
3=1-321 P nucleotide-excision repair
3=1-321 P phosphorylation of RNA polymerase II C-terminal domain
3=1-321 P regulation of cyclin-dependent protein serine/threonine kinase activity
3=1-321 P regulation of transcription by RNA polymerase II
3=1-321 P transcription by RNA polymerase II
4=1-338 C nucleotide-excision repair factor 3 complex
4=1-338 C transcription factor TFIIH core complex
4=1-338 C transcription factor TFIIH holo complex
4=1-338 F metal ion binding
4=1-338 P nucleotide-excision repair
4=1-338 P phosphorylation of RNA polymerase II C-terminal domain
4=1-338 P transcription by RNA polymerase II
5=1-72 C cytosol
5=1-72 C nucleus
5=1-72 C transcription factor TFIID complex
5=1-72 C transcription factor TFIIH core complex
5=1-72 C transcription factor TFIIH holo complex
5=1-72 P nucleotide-excision repair
5=1-72 P nucleotide-excision repair, preincision complex assembly
5=1-72 P phosphorylation of RNA polymerase II C-terminal domain
5=1-72 P transcription by RNA polymerase II
5=1-72 P transcription initiation from RNA polymerase II promoter
6=1-461 C nucleotide-excision repair factor 3 complex
6=1-461 C transcription factor TFIIH core complex
6=1-461 C transcription factor TFIIH holo complex
6=1-461 F ubiquitin protein ligase activity
6=1-461 F zinc ion binding
6=1-461 P nucleotide-excision repair
6=1-461 P phosphorylation of RNA polymerase II C-terminal domain
6=1-461 P regulation of transcription by RNA polymerase II
6=1-461 P transcription by RNA polymerase II
7=1-843 C cytosol
7=1-843 C nucleotide-excision repair factor 3 complex
7=1-843 C nucleus
7=1-843 C transcription factor TFIIH core complex
7=1-843 C transcription factor TFIIH holo complex
7=1-843 C transcription preinitiation complex
7=1-843 F 3'-5' DNA helicase activity
7=1-843 F ATP binding
7=1-843 F DNA binding
7=1-843 F DNA helicase activity
7=1-843 F DNA translocase activity
7=1-843 F transcription factor binding
7=1-843 P DNA duplex unwinding
7=1-843 P nucleotide-excision repair, DNA incision
7=1-843 P phosphorylation of RNA polymerase II C-terminal domain
7=1-843 P poly(A)+ mRNA export from nucleus
7=1-843 P promoter clearance from RNA polymerase II promoter
7=1-843 P regulation of mitotic recombination
7=1-843 P regulation of transposition, RNA-mediated
7=1-843 P response to UV
7=1-843 P transcription by RNA polymerase II
7=1-843 P transcription initiation from RNA polymerase II promoter
7=1-843 P transcription open complex formation at RNA polymerase II promoter
A=1-1733 C cytoplasmic stress granule
A=1-1733 C mitochondrion
A=1-1733 C nucleus
A=1-1733 C RNA polymerase II, core complex
A=1-1733 F DNA binding
A=1-1733 F DNA-directed 5'-3' RNA polymerase activity
A=1-1733 F metal ion binding
A=1-1733 P transcription by RNA polymerase II
A=1-1733 P transcription, RNA-templated
A=1-1733 P translesion synthesis
a=1-295 C core mediator complex
a=1-295 C mediator complex
a=1-295 F transcription coactivator activity
a=1-295 P positive regulation of transcription by RNA polymerase II
a=1-295 P regulation of transcription by RNA polymerase II
a=1-295 P RNA polymerase II preinitiation complex assembly
B=1-1224 C cytoplasmic stress granule
B=1-1224 C mitochondrion
B=1-1224 C nucleus
B=1-1224 C RNA polymerase II, core complex
B=1-1224 F DNA binding
B=1-1224 F DNA-directed 5'-3' RNA polymerase activity
B=1-1224 F metal ion binding
B=1-1224 F mRNA binding
B=1-1224 F ribonucleoside binding
B=1-1224 P transcription by RNA polymerase II
B=1-1224 P transcription, RNA-templated
b=1-223 C core mediator complex
b=1-223 C mediator complex
b=1-223 F protein-macromolecule adaptor activity
b=1-223 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
b=1-223 F TBP-class protein binding
b=1-223 F transcription coregulator activity
b=1-223 F transcription corepressor activity
b=1-223 P negative regulation of transcription by RNA polymerase II
b=1-223 P positive regulation of transcription by RNA polymerase II
b=1-223 P regulation of transcription by RNA polymerase II
c=1-115 C core mediator complex
c=1-115 C mediator complex
c=1-115 F TFIIH-class transcription factor complex binding
c=1-115 F transcription coactivator activity
c=1-115 P negative regulation of transcription by RNA polymerase II
c=1-115 P positive regulation of transcription by RNA polymerase II
c=1-115 P RNA polymerase II preinitiation complex assembly
C=1-318 C nucleoplasm
C=1-318 C RNA polymerase II, core complex
C=1-318 F DNA binding
C=1-318 F DNA-directed 5'-3' RNA polymerase activity
C=1-318 F metal ion binding
C=1-318 F protein dimerization activity
C=1-318 P termination of RNA polymerase II transcription
C=1-318 P transcription by RNA polymerase II
C=1-318 P transcription, RNA-templated
D=1-221 C cytoplasm
D=1-221 C nucleus
D=1-221 C P-body
D=1-221 C RNA polymerase II, core complex
D=1-221 F DNA-directed 5'-3' RNA polymerase activity
D=1-221 F nucleotide binding
D=1-221 F translation initiation factor binding
D=1-221 P mRNA export from nucleus in response to heat stress
D=1-221 P nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
D=1-221 P positive regulation of translational initiation
D=1-221 P recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
D=1-221 P transcription by RNA polymerase II
D=1-221 P transcription initiation from RNA polymerase II promoter
D=1-221 P transcription, RNA-templated
d=1-687 C core mediator complex
d=1-687 C mediator complex
d=1-687 F activating transcription factor binding
d=1-687 F RNA polymerase II complex recruiting activity
d=1-687 F RNA polymerase II core promoter sequence-specific DNA binding
d=1-687 F transcription coregulator activity
d=1-687 P positive regulation of transcription by RNA polymerase II
d=1-687 P regulation of transcription by RNA polymerase II
d=1-687 P transcription initiation from RNA polymerase II promoter
E=1-215 C host cell nucleus
E=1-215 C nucleoplasm
E=1-215 C RNA polymerase I complex
E=1-215 C RNA polymerase II, core complex
E=1-215 C RNA polymerase III complex
E=1-215 F DNA binding
E=1-215 F RNA polymerase I activity
E=1-215 P ribosome biogenesis
E=1-215 P termination of RNA polymerase III transcription
E=1-215 P transcription by RNA polymerase I
E=1-215 P transcription by RNA polymerase II
E=1-215 P transcription by RNA polymerase III
E=1-215 P transcription, RNA-templated
E=1-215 P tRNA transcription by RNA polymerase III
e=1-307 C core mediator complex
e=1-307 C mediator complex
e=1-307 F RNA polymerase II core promoter sequence-specific DNA binding
e=1-307 F transcription coactivator activity
e=1-307 F transcription coregulator activity
e=1-307 P positive regulation of transcription by RNA polymerase II
e=1-307 P regulation of transcription by RNA polymerase II
e=1-307 P RNA polymerase II preinitiation complex assembly
e=1-307 P termination of RNA polymerase II transcription
e=1-307 P transcription open complex formation at RNA polymerase II promoter
F=1-155 C cytoplasm
F=1-155 C nucleoplasm
F=1-155 C RNA polymerase I complex
F=1-155 C RNA polymerase II, core complex
F=1-155 C RNA polymerase III complex
F=1-155 F DNA binding
F=1-155 F RNA polymerase I activity
F=1-155 P ribosome biogenesis
F=1-155 P termination of RNA polymerase III transcription
F=1-155 P transcription by RNA polymerase I
F=1-155 P transcription by RNA polymerase II
F=1-155 P transcription by RNA polymerase III
F=1-155 P transcription, RNA-templated
F=1-155 P tRNA transcription by RNA polymerase III
f=1-210 C core mediator complex
f=1-210 C mediator complex
f=1-210 F protein domain specific binding
f=1-210 F TFIID-class transcription factor complex binding
f=1-210 F transcription coactivator activity
f=1-210 P negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to chemical stimulus
f=1-210 P negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels
f=1-210 P positive regulation of transcription by RNA polymerase II
f=1-210 P regulation of transcription by RNA polymerase II
f=1-210 P RNA polymerase II preinitiation complex assembly
g=1-121 C core mediator complex
g=1-121 C mediator complex
g=1-121 F transcription coregulator activity
g=1-121 P positive regulation of transcription by RNA polymerase II
G=1-171 C cytoplasm
G=1-171 C nucleus
G=1-171 C P-body
G=1-171 C RNA polymerase II, core complex
G=1-171 F DNA-directed 5'-3' RNA polymerase activity
G=1-171 F single-stranded DNA binding
G=1-171 F single-stranded RNA binding
G=1-171 F translation initiation factor binding
G=1-171 P nuclear-transcribed mRNA catabolic process, exonucleolytic
G=1-171 P positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
G=1-171 P positive regulation of translational initiation
G=1-171 P transcription by RNA polymerase II
G=1-171 P transcription initiation from RNA polymerase II promoter
G=1-171 P transcription, RNA-templated
H=1-146 C nucleoplasm
H=1-146 C RNA polymerase I complex
H=1-146 C RNA polymerase II, core complex
H=1-146 C RNA polymerase III complex
H=1-146 F DNA binding
H=1-146 F RNA polymerase I activity
H=1-146 P ribosome biogenesis
H=1-146 P termination of RNA polymerase III transcription
H=1-146 P transcription by RNA polymerase I
H=1-146 P transcription by RNA polymerase II
H=1-146 P transcription by RNA polymerase III
H=1-146 P transcription, RNA-templated
H=1-146 P tRNA transcription by RNA polymerase III
h=1-284 C core mediator complex
h=1-284 C mediator complex
h=1-284 F RNA polymerase II core promoter sequence-specific DNA binding
h=1-284 F transcription coregulator activity
h=1-284 P regulation of transcription by RNA polymerase II
h=1-284 P transcription by RNA polymerase II
I=1-122 C nucleolus
I=1-122 C RNA polymerase II, core complex
I=1-122 F DNA-directed 5'-3' RNA polymerase activity
I=1-122 F nucleic acid binding
I=1-122 F zinc ion binding
I=1-122 P maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter
I=1-122 P mRNA cleavage
I=1-122 P transcription by RNA polymerase II
I=1-122 P transcription initiation from RNA polymerase II promoter
I=1-122 P transcription, RNA-templated
I=1-122 P transcription-coupled nucleotide-excision repair
i=1-222 C core mediator complex
i=1-222 C mediator complex
i=1-222 F transcription coregulator activity
i=1-222 P negative regulation of transcription by RNA polymerase II
i=1-222 P positive regulation of transcription by RNA polymerase II
i=1-222 P regulation of transcription by RNA polymerase II
j=1-149 C core mediator complex
j=1-149 C cytosol
j=1-149 C mediator complex
j=1-149 C nucleus
j=1-149 F structural molecule activity
j=1-149 F transcription coactivator activity
j=1-149 P negative regulation of transcription by RNA polymerase II
j=1-149 P positive regulation of transcription by RNA polymerase II
j=1-149 P RNA polymerase II preinitiation complex assembly
J=1-70 C nucleoplasm
J=1-70 C RNA polymerase I complex
J=1-70 C RNA polymerase II, core complex
J=1-70 C RNA polymerase III complex
J=1-70 F DNA binding
J=1-70 F RNA polymerase I activity
J=1-70 F zinc ion binding
J=1-70 P ribosome biogenesis
J=1-70 P termination of RNA polymerase III transcription
J=1-70 P transcription by RNA polymerase I
J=1-70 P transcription by RNA polymerase II
J=1-70 P transcription by RNA polymerase III
J=1-70 P transcription, RNA-templated
J=1-70 P tRNA transcription by RNA polymerase III
K=1-120 C RNA polymerase II, core complex
K=1-120 F DNA binding
K=1-120 F protein dimerization activity
K=1-120 F RNA polymerase II activity
K=1-120 P termination of RNA polymerase II transcription
K=1-120 P transcription by RNA polymerase II
K=1-120 P transcription, RNA-templated
k=1-157 C core mediator complex
k=1-157 C mediator complex
k=1-157 C nucleus
k=1-157 F transcription coregulator activity
k=1-157 P negative regulation of transcription by RNA polymerase II
k=1-157 P positive regulation of transcription by RNA polymerase II
k=1-157 P regulation of transcription by RNA polymerase II
k=1-157 P RNA polymerase II preinitiation complex assembly
L=1-70 C cytoplasm
L=1-70 C nucleolus
L=1-70 C nucleoplasm
L=1-70 C nucleus
L=1-70 C RNA polymerase I complex
L=1-70 C RNA polymerase II, core complex
L=1-70 C RNA polymerase III complex
L=1-70 F DNA binding
L=1-70 F RNA polymerase I activity
L=1-70 F zinc ion binding
L=1-70 P ribosome biogenesis
L=1-70 P termination of RNA polymerase III transcription
L=1-70 P transcription by RNA polymerase I
L=1-70 P transcription by RNA polymerase II
L=1-70 P transcription by RNA polymerase III
L=1-70 P transcription, RNA-templated
L=1-70 P tRNA transcription by RNA polymerase III
l=1-745 C core mediator complex
l=1-745 C mediator complex
l=1-745 F RNA polymerase II repressing transcription factor binding
l=1-745 F TFIIB-class transcription factor binding
l=1-745 F transcription coregulator activity
l=1-745 P negative regulation of transcription by RNA polymerase II
l=1-745 P positive regulation of transcription by RNA polymerase II
l=1-745 P regulation of transcription by RNA polymerase II
m=1-220 C core mediator complex
m=1-220 C mediator complex
m=1-220 C nucleus
m=1-220 F transcription coactivator activity
m=1-220 F transcription coregulator activity
m=1-220 P negative regulation of transcription by RNA polymerase II
m=1-220 P positive regulation of transcription by RNA polymerase II
m=1-220 P regulation of transcription by RNA polymerase II
m=1-220 P RNA polymerase II preinitiation complex assembly
m=1-220 P transcription open complex formation at RNA polymerase II promoter
M=1-345 C nucleus
M=1-345 C transcription preinitiation complex
M=1-345 F metal ion binding
M=1-345 F RNA polymerase II complex binding
M=1-345 F RNA polymerase II complex recruiting activity
M=1-345 F RNA polymerase II core promoter sequence-specific DNA binding
M=1-345 F TBP-class protein binding
M=1-345 F transcription factor binding
M=1-345 P DNA-templated transcription, initiation
M=1-345 P positive regulation of transcription regulatory region DNA binding
M=1-345 P RNA polymerase II preinitiation complex assembly
M=1-345 P transcription open complex formation at RNA polymerase II promoter
M=1-345 P transcriptional start site selection at RNA polymerase II promoter
n=1-140 C core mediator complex
n=1-140 C mediator complex
n=1-140 F RNA polymerase II repressing transcription factor binding
n=1-140 F transcription coactivator activity
n=1-140 F transcription coregulator activity
n=1-140 F transcription corepressor activity
n=1-140 P negative regulation of transcription by RNA polymerase II
n=1-140 P positive regulation of transcription by RNA polymerase II
n=1-140 P regulation of transcription by RNA polymerase II
o=1-127 C core mediator complex
o=1-127 C mediator complex
o=1-127 C nucleus
o=1-127 F transcription coregulator activity
o=1-127 P DNA recombination
o=1-127 P DNA repair
o=1-127 P meiotic gene conversion
o=1-127 P meiotic sister chromatid segregation
o=1-127 P regulation of transcription by RNA polymerase II
o=1-127 P transcription by RNA polymerase II
O=1-240 C nucleoplasm
O=1-240 C nucleus
O=1-240 C protein-containing complex
O=1-240 C transcription factor TFIIA complex
O=1-240 C transcription factor TFIID complex
O=1-240 C transcription factor TFIIIB complex
O=1-240 C transcription regulator complex
O=1-240 F chromatin binding
O=1-240 F disordered domain specific binding
O=1-240 F DNA binding, bending
O=1-240 F DNA-binding transcription factor activity
O=1-240 F RNA polymerase I general transcription initiation factor binding
O=1-240 F RNA polymerase II activating transcription factor binding
O=1-240 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
O=1-240 F RNA polymerase II core promoter sequence-specific DNA binding
O=1-240 F RNA polymerase II general transcription initiation factor activity
O=1-240 F RNA polymerase III general transcription initiation factor activity
O=1-240 F RNA polymerase III transcription regulatory region sequence-specific DNA binding
O=1-240 F TFIIA-class transcription factor complex binding
O=1-240 F transcription factor binding
O=1-240 P nucleolar large rRNA transcription by RNA polymerase I
O=1-240 P RNA polymerase I preinitiation complex assembly
O=1-240 P RNA polymerase II preinitiation complex assembly
O=1-240 P RNA polymerase III preinitiation complex assembly
O=1-240 P transcription by RNA polymerase II
O=1-240 P transposon integration
Q=1-735 C transcription factor TFIIF complex
Q=1-735 F DNA binding
Q=1-735 F protein phosphatase activator activity
Q=1-735 F RNA polymerase II general transcription initiation factor activity
Q=1-735 F TFIIF-class transcription factor complex binding
Q=1-735 P dephosphorylation of RNA polymerase II C-terminal domain
Q=1-735 P positive regulation of transcription by RNA polymerase II
Q=1-735 P positive regulation of transcription elongation from RNA polymerase II promoter
Q=1-735 P promoter clearance from RNA polymerase II promoter
Q=1-735 P regulation of protein serine/threonine phosphatase activity
Q=1-735 P RNA polymerase II preinitiation complex assembly
Q=1-735 P transcription elongation from RNA polymerase II promoter
Q=1-735 P transcription initiation from RNA polymerase II promoter
Q=1-735 P transcriptional start site selection at RNA polymerase II promoter
R=1-400 C transcription factor TFIIF complex
R=1-400 F DNA binding
R=1-400 F nucleotide binding
R=1-400 F RNA polymerase II complex binding
R=1-400 P positive regulation of transcription elongation from RNA polymerase II promoter
R=1-400 P positive regulation of transcription initiation from RNA polymerase II promoter
R=1-400 P promoter clearance from RNA polymerase II promoter
R=1-400 P RNA polymerase II preinitiation complex assembly
R=1-400 P transcription elongation from RNA polymerase II promoter
R=1-400 P transcription initiation from RNA polymerase II promoter
R=1-400 P transcriptional start site selection at RNA polymerase II promoter
U=1-286 C cytoplasm
U=1-286 C transcription factor TFIIA complex
U=1-286 F RNA polymerase II core promoter sequence-specific DNA binding
U=1-286 F TBP-class protein binding
U=1-286 F transcription coregulator activity
U=1-286 P RNA polymerase II preinitiation complex assembly
U=1-286 P transcription by RNA polymerase II
U=1-286 P transcription initiation from RNA polymerase II promoter
V=1-122 C cytoplasm
V=1-122 C transcription factor TFIIA complex
V=1-122 F RNA polymerase II core promoter sequence-specific DNA binding
V=1-122 F TBP-class protein binding
V=1-122 F transcription coactivator activity
V=1-122 P positive regulation of DNA-binding transcription factor activity
V=1-122 P positive regulation of transcription by RNA polymerase II
V=1-122 P RNA polymerase II preinitiation complex assembly
V=1-122 P transcription initiation from RNA polymerase II promoter
W=332-482 C mitochondrion
W=332-482 C transcription factor TFIIE complex
W=332-482 C transcription preinitiation complex
W=332-482 F metal ion binding
W=332-482 F RNA polymerase II complex binding
W=332-482 F TFIIH-class transcription factor complex binding
W=332-482 P regulation of transcription by RNA polymerase II
W=332-482 P transcription by RNA polymerase II
W=332-482 P transcription open complex formation at RNA polymerase II promoter
X=1-328 C transcription factor TFIIE complex
X=1-328 C transcription preinitiation complex
X=1-328 F DNA binding
X=1-328 P transcription by RNA polymerase II
X=1-328 P transcription initiation from RNA polymerase II promoter
Sequences
Download file with secondary structure created by Stride  
5oqm.pdb1.pdb:   [ download sequences in FASTA format ]
T (dna): 
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0 (protein): 
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1 (protein): 
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2 (protein): 
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3 (protein): 
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4 (protein): 
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5 (protein): 
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6 (protein): 
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7 (protein): 
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A (protein): 
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b (protein): 
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c (protein): 
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D (protein): 
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E (protein): 
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f (protein): 
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G (protein): 
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h (protein): 
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I (protein): 
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J (protein): 
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K (protein): 
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L (protein): 
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m (protein): 
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n (protein): 
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O (protein): 
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Q (protein): 
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R (protein): 
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U (protein): 
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V (protein): 
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W (protein): 
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X (protein): 
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Z (protein): 
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