Macromolecule Annotations for the Entities in PDB 2JA8

Domain Annotation: SCOP Classification SCOP Database (version: 1.75) Homepage

Chains Domain Info Class Fold Superfamily Family Domain Species
A2-1450 d2ja8a1 Multi-domain proteins (alpha and beta) beta and beta-prime subunits of DNA dependent RNA- polymerase beta and beta-prime subunits of DNA dependent RNA- polymerase RNA-polymerase beta-prime RBP1 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
B20-1224 d2ja8b1 Multi-domain proteins (alpha and beta) beta and beta-prime subunits of DNA dependent RNA- polymerase beta and beta-prime subunits of DNA dependent RNA- polymerase RNA-polymerase beta RBP2 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
C3-37,C173-268 d2ja8c1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RPB3 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
C42-172 d2ja8c2 Alpha and beta proteins (a+b) Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit RPB3 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
D15-75 d2ja8d1 Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
E2-143 d2ja8e1 Alpha and beta proteins (a/b) Restriction endonuclease-like Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
E144-215 d2ja8e2 Alpha and beta proteins (a+b) RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit RPB5 Eukaryotic RPB5 C-terminal domain Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
F72-155 d2ja8f1 All alpha proteins RPB6/omega subunit-like RPB6/omega subunit-like RPB6 RPB6 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
G81-171 d2ja8g1 All beta proteins OB-fold Nucleic acid-binding proteins Cold shock DNA-binding domain-like C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
G1-80 d2ja8g2 Alpha and beta proteins (a+b) Dodecin subunit-like N-terminal, heterodimerisation domain of RBP7 (RpoE) N-terminal, heterodimerisation domain of RBP7 (RpoE) N-terminal, heterodimerisation domain of RBP7 (RpoE) Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
H2-146 d2ja8h1 All beta proteins OB-fold Nucleic acid-binding proteins RNA polymerase subunit RBP8 RNA polymerase subunit RBP8 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
I2-49 d2ja8i1 Small proteins Rubredoxin-like Zinc beta-ribbon Transcriptional factor domain RBP9 subunit of RNA polymerase II Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
I50-117 d2ja8i2 Small proteins Rubredoxin-like Zinc beta-ribbon Transcriptional factor domain RBP9 subunit of RNA polymerase II Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
J1-65 d2ja8j1 All alpha proteins DNA/RNA-binding 3-helical bundle RNA polymerase subunit RPB10 RNA polymerase subunit RPB10 RNA polymerase subunit RPB10 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
K1-114 d2ja8k1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RBP11/RpoL RPB11 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
L25-70 d2ja8l1 Small proteins Rubredoxin-like RNA polymerase subunits RBP12 subunit of RNA polymerase II RBP12 subunit of RNA polymerase II Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Domain Annotation: CATH CATH Database (version 4.0.0) Homepage

Chains Domain Class Architecture Topology Homology
B4 2ja8B04 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
B6 2ja8B06 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
B7 2ja8B07 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P)
C1 2ja8C01 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
C2 2ja8C02 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 RNA Polymerase Alpha Subunit; Chain A, domain 2
E1 2ja8E01 Alpha Beta 3-Layer(aba) Sandwich Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
E2 2ja8E02 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit
F 2ja8F00 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit
G1 2ja8G01 Alpha Beta 2-Layer Sandwich Dna Ligase; domain 1 DNA-directed RNA polymerase ii subunit; domain 1
G2 2ja8G02 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
H 2ja8H00 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
I1 2ja8I01 Mainly Beta Single Sheet N-terminal domain of TfIIb
I2 2ja8I02 Mainly Beta Single Sheet N-terminal domain of TfIIb
J 2ja8J00 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Homeodomain-like
K 2ja8K00 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
L 2ja8L00 Mainly Beta Single Sheet Rubrerythrin, domain 2 RNA polymerase ii, chain L

Protein Family Annotation Pfam Database Homepage

Chains Pfam Accession Pfam Identifier Pfam Description Type Source

Gene Product Annotation Gene Ontology Consortium Homepage

Chains Polymer Molecular Function Biological Process Cellular Component
A DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT (2JA8:A)
B DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE (2JA8:B)
C DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE (2JA8:C)
D DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE (2JA8:D)
E DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE (2JA8:E)
F DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE (2JA8:F)
G DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE (2JA8:G)
H DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE (2JA8:H)
I DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 (2JA8:I)
J DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 (2JA8:J)
K DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE (2JA8:K)
L DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE (2JA8:L)
N 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)- 3' (2JA8:N)
  • none
  • none
  • none
P 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*AP*UP)-3' (2JA8:P)
  • none
  • none
  • none
T 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TP*TP*TTP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)- 3' (2JA8:T)
  • none
  • none
  • none

Protein Modification Annotation

Type PDB Residue Nr. Description