General information
PDB ID 4V1N
Title ARCHITECTURE OF THE RNA POLYMERASE II-MEDIATOR CORE TRANSCRIPTION INITIATION COMPLEX
PDB header TRANSCRIPTION
Date 2014-09-29
Experimental method ELECTRON MICROSCOPY
Resolution (A) 7.8
Kind hybrid
Organism SACCHAROMYCES CEREVISIAE, SYNTHETIC CONSTRUCT, SACCHAROMYCES MIKATAE
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
PRIDB
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb4v1n.pdb ABCDEFGHIJKLMOQR NT P 0
Biounits:
4v1n.pdb1.pdb ABCDEFGHIJKLMOQR NT P 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
RNA_pol_Rpb1_1 Domain P04050_11-340 3.6e-114 1 No_clan A 11 340   
RNA_pol_Rpb1_5 Domain P04050_807-1397 3.1e-92 1 No_clan A 807 1397 NT  L-Bb L-Mn 
RNA_pol_Rpb1_2 Domain P04050_342-507 1.9e-77 1 No_clan A 342 507 PT   
RNA_pol_Rpb1_6 Domain P04050_873-1056 6.7e-65 1 No_clan A 873 1056   
RNA_pol_Rpb1_3 Domain P04050_510-669 7.5e-47 1 No_clan A 510 669   
RNA_pol_Rpb1_7 Domain P04050_1141-1274 9.5e-38 1 No_clan A 1141 1274   
RNA_pol_Rpb1_4 Domain P04050_693-800 6.4e-35 1 No_clan A 693 800   
RNA_pol_Rpb2_6 Domain P08518_752-1124 1.7e-122 1 CL0410 B 752 1124 PT   
RNA_pol_Rpb2_2 Domain P08518_219-407 2.8e-51 1 No_clan B 219 407   
RNA_pol_Rpb2_7 Domain P08518_1126-1219 1.6e-33 1 No_clan B 1126 1219 T   
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 P   
RNA_pol_Rpb2_5 Domain P08518_681-745 2.7e-19 1 No_clan B 681 745   
RNA_pol_A_bac Domain P16370_49-171 8.4e-32 1 No_clan C 49 171   
RNA_pol_L Domain P16370_19-255 3.9e-20 1 CL0509 C 19 255   
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 1.4e-17 1 CL0167 I 4 41   
TFIIS_C Domain P27999_73-111 1.3e-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 4.9e-25 1 CL0509 K 30 104   
DNA_RNApol_7kD Domain P40422_29-60 1e-16 1 CL0167 L 29 60   
TFIIB Domain P29055_122-213 7.7e-32 1 CL0065 M 122 213   
TFIIB Domain P29055_233-319 1.4e-16 1 CL0065 M 211 319 T  H-Bb H-Mj L-Bb L-Mj 
TF_Zn_Ribbon Domain P29055_22-66 6.5e-13 1 CL0167 M 22 66 T   
TBP Domain P13393_154-237 6e-33 1 CL0407 O 154 237 NT  S-Bb S-Mn L-Bb L-Mj L-Mn 
TBP Domain P13393_64-146 6.8e-33 1 CL0407 O 64 146 NT  S-Bb S-Mn L-Bb L-Mn 
RNA_pol_Rpb2_1 Family P08518_42-455 2.1e-74 1 No_clan B 42 455   
RNA_pol_Rpb4 Family P20433_49-218 3e-40 1 CL0426 D 49 218   
RNA_pol_Rpb6 Family P20435_79-132 2.7e-14 1 No_clan F 79 132   
RNA_pol_Rpb8 Family P20436_7-146 1.1e-42 1 CL0021 H 7 146   
TFIIF_alpha Family A0A0H2UKZ8_343-412 9.9e-10 1 CL0123 Q 133 412   
TFIIF_beta_N Family P41896_65-227 6.3e-24 1 CL0662 R 65 211   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
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
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
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
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
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
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
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
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
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
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
O=61-240 C nucleoplasm
O=61-240 C nucleus
O=61-240 C protein-containing complex
O=61-240 C transcription factor TFIIA complex
O=61-240 C transcription factor TFIID complex
O=61-240 C transcription factor TFIIIB complex
O=61-240 C transcription regulator complex
O=61-240 F chromatin binding
O=61-240 F disordered domain specific binding
O=61-240 F DNA binding, bending
O=61-240 F DNA-binding transcription factor activity
O=61-240 F RNA polymerase I general transcription initiation factor binding
O=61-240 F RNA polymerase II activating transcription factor binding
O=61-240 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
O=61-240 F RNA polymerase II core promoter sequence-specific DNA binding
O=61-240 F RNA polymerase II general transcription initiation factor activity
O=61-240 F RNA polymerase III general transcription initiation factor activity
O=61-240 F RNA polymerase III transcription regulatory region sequence-specific DNA binding
O=61-240 F TFIIA-class transcription factor complex binding
O=61-240 F transcription factor binding
O=61-240 P nucleolar large rRNA transcription by RNA polymerase I
O=61-240 P RNA polymerase I preinitiation complex assembly
O=61-240 P RNA polymerase II preinitiation complex assembly
O=61-240 P RNA polymerase III preinitiation complex assembly
O=61-240 P transcription by RNA polymerase II
O=61-240 P transposon integration
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
Sequences
Download file with secondary structure created by Stride  
4v1n.pdb1.pdb:   [ download sequences in FASTA format ]
N (dna): 
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T (dna): 
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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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O (protein): 
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Q (protein): 
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R (protein): 
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P (rna): 
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