General information
PDB ID 2JA7
Title CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX C
PDB header TRANSFERASE
Date 2006-11-23
Experimental method X-RAY DIFFRACTION
Resolution (A) 3.8
Kind hybrid
Organism SACCHAROMYCES CEREVISIAE, SYNTHETIC CONSTRUCT
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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:
pdb2ja7.pdb ABCDEFGHIJKLMNOPQRSTUVWX 1245 36 0
Biounits:
2ja7.pdb1.pdb ABCDEFGHIJKL 12 3 1
2ja7.pdb2.pdb MNOPQRSTUVWX 45 6 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 2.7e-115 1 No_clan A 11 340 3   
RNA_pol_Rpb1_5 Domain P04050_807-1397 1.6e-93 1 No_clan A 807 1397 2  L-Mn 
RNA_pol_Rpb1_2 Domain P04050_342-507 1.7e-77 1 No_clan A 342 507 3   
RNA_pol_Rpb1_6 Domain P04050_873-1056 2.4e-63 1 No_clan A 873 1056   
RNA_pol_Rpb1_3 Domain P04050_510-669 7.9e-47 1 No_clan A 510 669   
RNA_pol_Rpb1_7 Domain P04050_1141-1274 3e-38 1 No_clan A 1141 1274   
RNA_pol_Rpb1_4 Domain P04050_693-800 5.3e-35 1 No_clan A 693 800   
RNA_pol_Rpb2_6 Domain P08518_752-1124 1.5e-122 1 CL0410 B 752 1124 23   
RNA_pol_Rpb2_2 Domain P08518_219-407 2.3e-51 1 No_clan B 219 407   
RNA_pol_Rpb2_7 Domain P08518_1126-1219 1.7e-33 1 No_clan B 1126 1219   
RNA_pol_Rpb2_4 Domain P08518_580-641 1.5e-25 1 No_clan B 580 641   
RNA_pol_Rpb2_3 Domain P08518_481-545 9.4e-20 1 No_clan B 481 545   
RNA_pol_Rpb2_5 Domain P08518_681-745 1.4e-19 1 No_clan B 681 745   
RNA_pol_A_bac Domain P16370_49-171 7.3e-32 1 No_clan C 49 171   
RNA_pol_L Domain P16370_19-255 6.7e-19 1 CL0509 C 19 255   
RNA_pol_Rpb5_C Domain P20434_142-214 1.6e-31 1 No_clan E 142 214   
RNA_pol_Rpb5_N Domain P20434_6-100 1.1e-29 1 CL0236 E 6 100   
S1 Domain P34087_80-161 6.2e-18 1 CL0021 G 80 161   
SHS2_Rpb7-N Domain P34087_8-66 2.6e-16 1 CL0319 G 8 79   
RNA_POL_M_15KD Domain P27999_4-41 1.2e-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_1-60 5.4e-30 1 No_clan J 1 60   
RNA_pol_L_2 Domain P38902_30-104 1.6e-24 1 CL0509 K 30 104   
DNA_RNApol_7kD Domain P40422_29-60 1.9e-16 1 CL0167 L 29 60   
RNA_pol_Rpb1_1 Domain P04050_11-340 2.7e-115 1 No_clan M 11 340 56   
RNA_pol_Rpb1_5 Domain P04050_807-1397 1.6e-93 1 No_clan M 807 1397 5  L-Mn 
RNA_pol_Rpb1_2 Domain P04050_342-507 1.7e-77 1 No_clan M 342 507 6   
RNA_pol_Rpb1_6 Domain P04050_873-1056 2.4e-63 1 No_clan M 873 1056   
RNA_pol_Rpb1_3 Domain P04050_510-669 7.9e-47 1 No_clan M 510 669   
RNA_pol_Rpb1_7 Domain P04050_1141-1274 3e-38 1 No_clan M 1141 1274   
RNA_pol_Rpb1_4 Domain P04050_693-800 5.3e-35 1 No_clan M 693 800   
RNA_pol_Rpb2_6 Domain P08518_752-1124 1.5e-122 1 CL0410 N 752 1124 56   
RNA_pol_Rpb2_2 Domain P08518_219-407 2.3e-51 1 No_clan N 219 407   
RNA_pol_Rpb2_7 Domain P08518_1126-1219 1.7e-33 1 No_clan N 1126 1219   
RNA_pol_Rpb2_4 Domain P08518_580-641 1.5e-25 1 No_clan N 580 641   
RNA_pol_Rpb2_3 Domain P08518_481-545 9.4e-20 1 No_clan N 481 545   
RNA_pol_Rpb2_5 Domain P08518_681-745 1.4e-19 1 No_clan N 681 745   
RNA_pol_A_bac Domain P16370_49-171 7.3e-32 1 No_clan O 49 171   
RNA_pol_L Domain P16370_19-255 6.7e-19 1 CL0509 O 19 255   
RNA_pol_Rpb5_C Domain P20434_142-214 1.6e-31 1 No_clan Q 142 214   
RNA_pol_Rpb5_N Domain P20434_6-100 1.1e-29 1 CL0236 Q 6 100   
S1 Domain P34087_80-161 6.2e-18 1 CL0021 S 80 161   
SHS2_Rpb7-N Domain P34087_8-66 2.6e-16 1 CL0319 S 8 79   
RNA_POL_M_15KD Domain P27999_4-41 1.2e-17 1 CL0167 U 4 41   
TFIIS_C Domain P27999_73-111 1.3e-14 1 CL0167 U 73 111   
RNA_pol_N Domain P22139_1-60 5.4e-30 1 No_clan V 1 60   
RNA_pol_L_2 Domain P38902_30-104 1.6e-24 1 CL0509 W 30 104   
DNA_RNApol_7kD Domain P40422_29-60 1.9e-16 1 CL0167 X 29 60   
RNA_pol_Rpb2_1 Family P08518_42-455 8.6e-54 1 No_clan B 42 455 2   
RNA_pol_Rpb4 Family P20433_49-218 8.5e-39 1 CL0426 D 49 218   
RNA_pol_Rpb6 Family P20435_79-132 8e-18 1 No_clan F 79 132   
RNA_pol_Rpb8 Family P20436_7-146 3e-43 1 CL0021 H 7 146   
RNA_pol_Rpb2_1 Family P08518_42-455 8.6e-54 1 No_clan N 42 455 5   
RNA_pol_Rpb4 Family P20433_49-218 8.5e-39 1 CL0426 P 49 218   
RNA_pol_Rpb6 Family P20435_79-132 8e-18 1 No_clan R 79 132   
RNA_pol_Rpb8 Family P20436_7-146 3e-43 1 CL0021 T 7 146   
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: Multi-domain proteins (alpha and beta)
  Fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
    Superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
      Family: RNA-polymerase beta-prime
RBP1 A 2 1450 23 -
Class: Multi-domain proteins (alpha and beta)
  Fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
    Superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
      Family: RNA-polymerase beta
RBP2 B 20 1224 23 -
Class: Alpha and beta proteins (a+b)
  Fold: DCoH-like
    Superfamily: RBP11-like subunits of RNA polymerase
      Family: RNA polymerase alpha subunit dimerisation domain
RPB3 C 3 37 -
Class: Alpha and beta proteins (a+b)
  Fold: DCoH-like
    Superfamily: RBP11-like subunits of RNA polymerase
      Family: RNA polymerase alpha subunit dimerisation domain
RPB3 C 173 268 -
Class: Alpha and beta proteins (a+b)
  Fold: DCoH-like
    Superfamily: RBP11-like subunits of RNA polymerase
      Family: RNA polymerase alpha subunit dimerisation domain
RPB3 C 3 37 -
Class: Alpha and beta proteins (a+b)
  Fold: DCoH-like
    Superfamily: RBP11-like subunits of RNA polymerase
      Family: RNA polymerase alpha subunit dimerisation domain
RPB3 C 173 268 -
Class: Alpha and beta proteins (a+b)
  Fold: Insert subdomain of RNA polymerase alpha subunit
    Superfamily: Insert subdomain of RNA polymerase alpha subunit
      Family: Insert subdomain of RNA polymerase alpha subunit
RPB3 C 42 172 -
Class: Low resolution protein structures
  Fold: RNA polymerase
    Superfamily: RNA polymerase
      Family: RNA polymerase
Complete 12-subunit RNA polymerase II complex D 15 75 -
Class: Alpha and beta proteins (a/b)
  Fold: Restriction endonuclease-like
    Superfamily: Eukaryotic RPB5 N-terminal domain
      Family: Eukaryotic RPB5 N-terminal domain
Eukaryotic RPB5 N-terminal domain E 2 143 -
Class: Alpha and beta proteins (a+b)
  Fold: RPB5-like RNA polymerase subunit
    Superfamily: RPB5-like RNA polymerase subunit
      Family: RPB5
Eukaryotic RPB5 C-terminal domain E 144 215 -
Class: All alpha proteins
  Fold: RPB6/omega subunit-like
    Superfamily: RPB6/omega subunit-like
      Family: RPB6
RPB6 F 72 155 -
Class: All beta proteins
  Fold: OB-fold
    Superfamily: Nucleic acid-binding proteins
      Family: Cold shock DNA-binding domain-like
C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) G 81 171 -
Class: Alpha and beta proteins (a+b)
  Fold: Dodecin subunit-like
    Superfamily: N-terminal, heterodimerisation domain of RBP7 (RpoE)
      Family: N-terminal, heterodimerisation domain of RBP7 (RpoE)
N-terminal, heterodimerisation domain of RBP7 (RpoE) G 1 80 -
Class: All beta proteins
  Fold: OB-fold
    Superfamily: Nucleic acid-binding proteins
      Family: RNA polymerase subunit RBP8
RNA polymerase subunit RBP8 H 2 146 -
Class: Small proteins
  Fold: Rubredoxin-like
    Superfamily: Zinc beta-ribbon
      Family: Transcriptional factor domain
RBP9 subunit of RNA polymerase II I 2 49 -
Class: Small proteins
  Fold: Rubredoxin-like
    Superfamily: Zinc beta-ribbon
      Family: Transcriptional factor domain
RBP9 subunit of RNA polymerase II I 50 117 -
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: RNA polymerase subunit RPB10
      Family: RNA polymerase subunit RPB10
RNA polymerase subunit RPB10 J 1 65 -
Class: Alpha and beta proteins (a+b)
  Fold: DCoH-like
    Superfamily: RBP11-like subunits of RNA polymerase
      Family: RBP11/RpoL
RPB11 K 1 114 -
Class: Small proteins
  Fold: Rubredoxin-like
    Superfamily: RNA polymerase subunits
      Family: RBP12 subunit of RNA polymerase II
RBP12 subunit of RNA polymerase II L 25 70 -
Class: Multi-domain proteins (alpha and beta)
  Fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
    Superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
      Family: RNA-polymerase beta-prime
RBP1 M 2 1450 56 -
Class: Multi-domain proteins (alpha and beta)
  Fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
    Superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
      Family: RNA-polymerase beta
RBP2 N 20 1224 56 -
Class: Alpha and beta proteins (a+b)
  Fold: DCoH-like
    Superfamily: RBP11-like subunits of RNA polymerase
      Family: RNA polymerase alpha subunit dimerisation domain
RPB3 O 3 37 -
Class: Alpha and beta proteins (a+b)
  Fold: DCoH-like
    Superfamily: RBP11-like subunits of RNA polymerase
      Family: RNA polymerase alpha subunit dimerisation domain
RPB3 O 173 268 -
Class: Alpha and beta proteins (a+b)
  Fold: DCoH-like
    Superfamily: RBP11-like subunits of RNA polymerase
      Family: RNA polymerase alpha subunit dimerisation domain
RPB3 O 3 37 -
Class: Alpha and beta proteins (a+b)
  Fold: DCoH-like
    Superfamily: RBP11-like subunits of RNA polymerase
      Family: RNA polymerase alpha subunit dimerisation domain
RPB3 O 173 268 -
Class: Alpha and beta proteins (a+b)
  Fold: Insert subdomain of RNA polymerase alpha subunit
    Superfamily: Insert subdomain of RNA polymerase alpha subunit
      Family: Insert subdomain of RNA polymerase alpha subunit
RPB3 O 42 172 -
Class: Low resolution protein structures
  Fold: RNA polymerase
    Superfamily: RNA polymerase
      Family: RNA polymerase
Complete 12-subunit RNA polymerase II complex P 15 75 -
Class: Alpha and beta proteins (a/b)
  Fold: Restriction endonuclease-like
    Superfamily: Eukaryotic RPB5 N-terminal domain
      Family: Eukaryotic RPB5 N-terminal domain
Eukaryotic RPB5 N-terminal domain Q 2 143 -
Class: Alpha and beta proteins (a+b)
  Fold: RPB5-like RNA polymerase subunit
    Superfamily: RPB5-like RNA polymerase subunit
      Family: RPB5
Eukaryotic RPB5 C-terminal domain Q 144 215 -
Class: All alpha proteins
  Fold: RPB6/omega subunit-like
    Superfamily: RPB6/omega subunit-like
      Family: RPB6
RPB6 R 72 155 -
Class: All beta proteins
  Fold: OB-fold
    Superfamily: Nucleic acid-binding proteins
      Family: Cold shock DNA-binding domain-like
C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) S 81 171 -
Class: Alpha and beta proteins (a+b)
  Fold: Dodecin subunit-like
    Superfamily: N-terminal, heterodimerisation domain of RBP7 (RpoE)
      Family: N-terminal, heterodimerisation domain of RBP7 (RpoE)
N-terminal, heterodimerisation domain of RBP7 (RpoE) S 1 80 -
Class: All beta proteins
  Fold: OB-fold
    Superfamily: Nucleic acid-binding proteins
      Family: RNA polymerase subunit RBP8
RNA polymerase subunit RBP8 T 2 146 -
Class: Small proteins
  Fold: Rubredoxin-like
    Superfamily: Zinc beta-ribbon
      Family: Transcriptional factor domain
RBP9 subunit of RNA polymerase II U 2 49 -
Class: Small proteins
  Fold: Rubredoxin-like
    Superfamily: Zinc beta-ribbon
      Family: Transcriptional factor domain
RBP9 subunit of RNA polymerase II U 50 117 -
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: RNA polymerase subunit RPB10
      Family: RNA polymerase subunit RPB10
RNA polymerase subunit RPB10 V 1 65 -
Class: Alpha and beta proteins (a+b)
  Fold: DCoH-like
    Superfamily: RBP11-like subunits of RNA polymerase
      Family: RBP11/RpoL
RPB11 W 1 114 -
Class: Small proteins
  Fold: Rubredoxin-like
    Superfamily: RNA polymerase subunits
      Family: RBP12 subunit of RNA polymerase II
RBP12 subunit of RNA polymerase II X 25 70 -
GO terms
Protein chains: GO type: GO description:
A/M=1-1733 C cytoplasmic stress granule
A/M=1-1733 C mitochondrion
A/M=1-1733 C nucleus
A/M=1-1733 C RNA polymerase II, core complex
A/M=1-1733 F DNA binding
A/M=1-1733 F DNA-directed 5'-3' RNA polymerase activity
A/M=1-1733 F metal ion binding
A/M=1-1733 P transcription by RNA polymerase II
A/M=1-1733 P transcription, RNA-templated
A/M=1-1733 P translesion synthesis
B/N=1-1224 C cytoplasmic stress granule
B/N=1-1224 C mitochondrion
B/N=1-1224 C nucleus
B/N=1-1224 C RNA polymerase II, core complex
B/N=1-1224 F DNA binding
B/N=1-1224 F DNA-directed 5'-3' RNA polymerase activity
B/N=1-1224 F metal ion binding
B/N=1-1224 F mRNA binding
B/N=1-1224 F ribonucleoside binding
B/N=1-1224 P transcription by RNA polymerase II
B/N=1-1224 P transcription, RNA-templated
C/O=1-318 C nucleoplasm
C/O=1-318 C RNA polymerase II, core complex
C/O=1-318 F DNA binding
C/O=1-318 F DNA-directed 5'-3' RNA polymerase activity
C/O=1-318 F metal ion binding
C/O=1-318 F protein dimerization activity
C/O=1-318 P termination of RNA polymerase II transcription
C/O=1-318 P transcription by RNA polymerase II
C/O=1-318 P transcription, RNA-templated
D/P=1-221 C cytoplasm
D/P=1-221 C nucleus
D/P=1-221 C P-body
D/P=1-221 C RNA polymerase II, core complex
D/P=1-221 F DNA-directed 5'-3' RNA polymerase activity
D/P=1-221 F nucleotide binding
D/P=1-221 F translation initiation factor binding
D/P=1-221 P mRNA export from nucleus in response to heat stress
D/P=1-221 P nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
D/P=1-221 P positive regulation of translational initiation
D/P=1-221 P recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
D/P=1-221 P transcription by RNA polymerase II
D/P=1-221 P transcription initiation from RNA polymerase II promoter
D/P=1-221 P transcription, RNA-templated
E/Q=1-215 C host cell nucleus
E/Q=1-215 C nucleoplasm
E/Q=1-215 C RNA polymerase I complex
E/Q=1-215 C RNA polymerase II, core complex
E/Q=1-215 C RNA polymerase III complex
E/Q=1-215 F DNA binding
E/Q=1-215 F RNA polymerase I activity
E/Q=1-215 P ribosome biogenesis
E/Q=1-215 P termination of RNA polymerase III transcription
E/Q=1-215 P transcription by RNA polymerase I
E/Q=1-215 P transcription by RNA polymerase II
E/Q=1-215 P transcription by RNA polymerase III
E/Q=1-215 P transcription, RNA-templated
E/Q=1-215 P tRNA transcription by RNA polymerase III
F/R=1-155 C cytoplasm
F/R=1-155 C nucleoplasm
F/R=1-155 C RNA polymerase I complex
F/R=1-155 C RNA polymerase II, core complex
F/R=1-155 C RNA polymerase III complex
F/R=1-155 F DNA binding
F/R=1-155 F RNA polymerase I activity
F/R=1-155 P ribosome biogenesis
F/R=1-155 P termination of RNA polymerase III transcription
F/R=1-155 P transcription by RNA polymerase I
F/R=1-155 P transcription by RNA polymerase II
F/R=1-155 P transcription by RNA polymerase III
F/R=1-155 P transcription, RNA-templated
F/R=1-155 P tRNA transcription by RNA polymerase III
G/S=1-171 C cytoplasm
G/S=1-171 C nucleus
G/S=1-171 C P-body
G/S=1-171 C RNA polymerase II, core complex
G/S=1-171 F DNA-directed 5'-3' RNA polymerase activity
G/S=1-171 F single-stranded DNA binding
G/S=1-171 F single-stranded RNA binding
G/S=1-171 F translation initiation factor binding
G/S=1-171 P nuclear-transcribed mRNA catabolic process, exonucleolytic
G/S=1-171 P positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
G/S=1-171 P positive regulation of translational initiation
G/S=1-171 P transcription by RNA polymerase II
G/S=1-171 P transcription initiation from RNA polymerase II promoter
G/S=1-171 P transcription, RNA-templated
H/T=1-146 C nucleoplasm
H/T=1-146 C RNA polymerase I complex
H/T=1-146 C RNA polymerase II, core complex
H/T=1-146 C RNA polymerase III complex
H/T=1-146 F DNA binding
H/T=1-146 F RNA polymerase I activity
H/T=1-146 P ribosome biogenesis
H/T=1-146 P termination of RNA polymerase III transcription
H/T=1-146 P transcription by RNA polymerase I
H/T=1-146 P transcription by RNA polymerase II
H/T=1-146 P transcription by RNA polymerase III
H/T=1-146 P transcription, RNA-templated
H/T=1-146 P tRNA transcription by RNA polymerase III
I/U=1-122 C nucleolus
I/U=1-122 C RNA polymerase II, core complex
I/U=1-122 F DNA-directed 5'-3' RNA polymerase activity
I/U=1-122 F nucleic acid binding
I/U=1-122 F zinc ion binding
I/U=1-122 P maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter
I/U=1-122 P mRNA cleavage
I/U=1-122 P transcription by RNA polymerase II
I/U=1-122 P transcription initiation from RNA polymerase II promoter
I/U=1-122 P transcription, RNA-templated
I/U=1-122 P transcription-coupled nucleotide-excision repair
J/V=1-70 C nucleoplasm
J/V=1-70 C RNA polymerase I complex
J/V=1-70 C RNA polymerase II, core complex
J/V=1-70 C RNA polymerase III complex
J/V=1-70 F DNA binding
J/V=1-70 F RNA polymerase I activity
J/V=1-70 F zinc ion binding
J/V=1-70 P ribosome biogenesis
J/V=1-70 P termination of RNA polymerase III transcription
J/V=1-70 P transcription by RNA polymerase I
J/V=1-70 P transcription by RNA polymerase II
J/V=1-70 P transcription by RNA polymerase III
J/V=1-70 P transcription, RNA-templated
J/V=1-70 P tRNA transcription by RNA polymerase III
K/W=1-120 C RNA polymerase II, core complex
K/W=1-120 F DNA binding
K/W=1-120 F protein dimerization activity
K/W=1-120 F RNA polymerase II activity
K/W=1-120 P termination of RNA polymerase II transcription
K/W=1-120 P transcription by RNA polymerase II
K/W=1-120 P transcription, RNA-templated
L/X=1-70 C cytoplasm
L/X=1-70 C nucleolus
L/X=1-70 C nucleoplasm
L/X=1-70 C nucleus
L/X=1-70 C RNA polymerase I complex
L/X=1-70 C RNA polymerase II, core complex
L/X=1-70 C RNA polymerase III complex
L/X=1-70 F DNA binding
L/X=1-70 F RNA polymerase I activity
L/X=1-70 F zinc ion binding
L/X=1-70 P ribosome biogenesis
L/X=1-70 P termination of RNA polymerase III transcription
L/X=1-70 P transcription by RNA polymerase I
L/X=1-70 P transcription by RNA polymerase II
L/X=1-70 P transcription by RNA polymerase III
L/X=1-70 P transcription, RNA-templated
L/X=1-70 P tRNA transcription by RNA polymerase III
Sequences
Download file with secondary structure created by Stride  
2ja7.pdb1.pdb:   [ download sequences in FASTA format ]
1 (dna): 
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2 (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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3 (rna): 
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2ja7.pdb2.pdb:   [ download sequences in FASTA format ]
4 (dna): 
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5 (dna): 
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M (protein): 
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N (protein): 
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O (protein): 
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P (protein): 
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Q (protein): 
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R (protein): 
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S (protein): 
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T (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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6 (rna): 
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