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PDBsum entry 4a3d
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protein dna_rna metals Protein-protein interface(s) links
Transcription PDB id
4a3d

 

 

 

 

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Contents
Protein chains
1422 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
Metals
_MG
_ZN ×8
PDB id:
4a3d
Name: Transcription
Title: RNA polymerase ii initial transcribing complex with a 6nt DNA-RNA hybrid
Structure: DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Fragment: residues 1-1732. Synonym: rpb1, RNA polymerase ii subunit 1, RNA polymerase ii subunit b1, DNA-directed RNA polymerase iii largest subunit, RNA polymerase ii subunit b220. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: rpb2, RNA polymerase ii subunit 2, b150, DNA-directed RNA
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Synthetic: yes. Organism_taxid: 4932
Resolution:
3.40Å     R-factor:   0.162     R-free:   0.186
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
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1733 a.a.
1422 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		318 a.a.
266 a.a.
Protein chain
Pfam   ArchSchema ?
P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		155 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		146 a.a.
133 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		70 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		70 a.a.
46 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  A-A-G-T-A-C-T-T-G-A 10 bases
  C-C-A-G-G-A 6 bases
  T-C-A-A-G-T-A-C-T-T-T-T-T-C-C-BRU-G-G-T-C 20 bases

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
RNA(n)
 + ribonucleoside 5'-triphosphate
 = RNA(n+1)
 + diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
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
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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