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PDBsum entry 4a3e

Go to PDB code: 
protein dna_rna ligands metals Protein-protein interface(s) links
Transcription PDB id
4a3e
Jmol
Contents
Protein chains
1423 a.a.
1115 a.a.
266 a.a.
178 a.a.
214 a.a.
84 a.a.
171 a.a.
133 a.a.
119 a.a.
65 a.a.
115 a.a.
46 a.a.
DNA/RNA
Ligands
APC
Metals
_MG
_ZN ×8
PDB id:
4a3e
Name: Transcription
Title: RNA polymerase ii initial transcribing complex with a 5nt dn hybrid and soaked with ampcpp
Structure: DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Fragment: residues 1-1732. Synonym: rpb1, RNA polymerase ii subunit 1, RNA polymerase subunit b1, DNA-directed RNA polymerase iii largest subuni polymerase ii subunit b220. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: rpb2, RNA polymerase ii subunit 2, b150, DNA-direc
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Synthetic: yes. Organism_taxid: 4932
Resolution:
3.40Å     R-factor:   0.160     R-free:   0.187
Authors: A.C.M.Cheung,S.Sainsbury,P.Cramer
Key ref: A.C.Cheung et al. (2011). Structural basis of initial RNA polymerase II transcription. EMBO J, 30, 4755-4763. PubMed id: 22056778 DOI: 10.1038/emboj.2011.396
Date:
30-Sep-11     Release date:   07-Dec-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1733 a.a.
1423 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1224 a.a.
1115 a.a.
Protein chain
Pfam   ArchSchema ?
P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3
Seq:
Struc:
318 a.a.
266 a.a.
Protein chain
Pfam   ArchSchema ?
P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4
Seq:
Struc:
221 a.a.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1
Seq:
Struc:
215 a.a.
214 a.a.
Protein chain
Pfam   ArchSchema ?
P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2
Seq:
Struc:
155 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7
Seq:
Struc:
171 a.a.
171 a.a.
Protein chain
Pfam   ArchSchema ?
P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3
Seq:
Struc:
146 a.a.
133 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9
Seq:
Struc:
122 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5
Seq:
Struc:
70 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11
Seq:
Struc:
120 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P40422  (RPAB4_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4
Seq:
Struc:
70 a.a.
46 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   8 terms 
  Biological process     transcription, RNA-dependent   22 terms 
  Biochemical function     RNA polymerase II activity     20 terms  

 

 
    reference    
 
 
DOI no: 10.1038/emboj.2011.396 EMBO J 30:4755-4763 (2011)
PubMed id: 22056778  
 
 
Structural basis of initial RNA polymerase II transcription.
A.C.Cheung, S.Sainsbury, P.Cramer.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23151482 S.Sainsbury, J.Niesser, and P.Cramer (2013).
Structure and function of the initially transcribing RNA polymerase II-TFIIB complex.
  Nature, 493, 437-440.
PDB codes: 4bbr 4bbs
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