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PDBsum entry 3h0g

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protein metals Protein-protein interface(s) links
Transcription PDB id
3h0g
Jmol
Contents
Protein chains
1496 a.a. *
1150 a.a. *
263 a.a. *
130 a.a. *
207 a.a. *
83 a.a. *
170 a.a. *
124 a.a. *
111 a.a. *
64 a.a. *
119 a.a. *
45 a.a. *
Metals
_MG ×2
_ZN ×16
* Residue conservation analysis
PDB id:
3h0g
Name: Transcription
Title: RNA polymerase ii from schizosaccharomyces pombe
Structure: DNA-directed RNA polymerase ii subunit rpb1. Chain: a, m. Synonym: RNA polymerase ii subunit b1, RNA polymerase ii subunit 1, DNA-directed RNA polymerase iii largest subunit. DNA-directed RNA polymerase ii subunit rpb2. Chain: b, n. Synonym: RNA polymerase ii subunit b2, RNA polymerase ii subunit 2, DNA-directed RNA polymerase ii 138 kda polypeptide.
Source: Schizosaccharomyces pombe. Organism_taxid: 284812. Strain: 972h-. Strain: 972h-
Resolution:
3.65Å     R-factor:   0.297     R-free:   0.321
Authors: H.Spahr,G.Calero,D.A.Bushnell,R.D.Kornberg
Key ref:
H.Spåhr et al. (2009). Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution. Proc Natl Acad Sci U S A, 106, 9185-9190. PubMed id: 19458260 DOI: 10.1073/pnas.0903361106
Date:
09-Apr-09     Release date:   25-Aug-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P36594  (RPB1_SCHPO) -  DNA-directed RNA polymerase II subunit rpb1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1752 a.a.
1496 a.a.
Protein chains
Pfam   ArchSchema ?
Q02061  (RPB2_SCHPO) -  DNA-directed RNA polymerase II subunit RPB2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1210 a.a.
1150 a.a.
Protein chains
Pfam   ArchSchema ?
P37382  (RPB3_SCHPO) -  DNA-directed RNA polymerase II subunit RPB3
Seq:
Struc:
297 a.a.
263 a.a.
Protein chains
Pfam   ArchSchema ?
O74825  (RPB4_SCHPO) -  DNA-directed RNA polymerase II subunit rpb4
Seq:
Struc:
135 a.a.
130 a.a.
Protein chains
Pfam   ArchSchema ?
Q09191  (RPAB1_SCHPO) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1
Seq:
Struc:
210 a.a.
207 a.a.
Protein chains
Pfam   ArchSchema ?
P36595  (RPAB2_SCHPO) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2
Seq:
Struc:
142 a.a.
83 a.a.
Protein chains
Pfam   ArchSchema ?
O14459  (RPB7_SCHPO) -  DNA-directed RNA polymerase II subunit rpb7
Seq:
Struc:
172 a.a.
170 a.a.
Protein chains
Pfam   ArchSchema ?
Q92399  (RPAB3_SCHPO) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3
Seq:
Struc:
125 a.a.
124 a.a.
Protein chains
Pfam   ArchSchema ?
O74635  (RPB9_SCHPO) -  DNA-directed RNA polymerase II subunit RPB9
Seq:
Struc:
113 a.a.
111 a.a.
Protein chains
Pfam   ArchSchema ?
O13877  (RPAB5_SCHPO) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5
Seq:
Struc:
71 a.a.
64 a.a.
Protein chains
Pfam   ArchSchema ?
P87123  (RPB11_SCHPO) -  DNA-directed RNA polymerase II subunit RPB11
Seq:
Struc:
123 a.a.
119 a.a.
Protein chains
Pfam   ArchSchema ?
P48011  (RPAB4_SCHPO) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4
Seq:
Struc:
63 a.a.
45 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, M, N: 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     nucleus   9 terms 
  Biological process     regulation of cytokinetic cell separation by regulation of transcription from RNA polymerase II promoter   12 terms 
  Biochemical function     catalytic activity     13 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0903361106 Proc Natl Acad Sci U S A 106:9185-9190 (2009)
PubMed id: 19458260  
 
 
Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution.
H.Spåhr, G.Calero, D.A.Bushnell, R.D.Kornberg.
 
  ABSTRACT  
 
The second structure of a eukaryotic RNA polymerase II so far determined, that of the enzyme from the fission yeast Schizosaccharomyces pombe, is reported here. Comparison with the previous structure of the enzyme from the budding yeast Saccharomyces cerevisiae reveals differences in regions implicated in start site selection and transcription factor interaction. These aspects of the transcription mechanism differ between S. pombe and S. cerevisiae, but are conserved between S. pombe and humans. Amino acid changes apparently responsible for the structural differences are also conserved between S. pombe and humans, suggesting that the S. pombe structure may be a good surrogate for that of the human enzyme.
 
  Selected figure(s)  
 
Figure 1.
Structures of pol II from S. pombe (Left) and S. cerevisiae (Right, PDB ID code 1WCM). Surface representation of front (Upper) and back (Lower) views shown. Individual subunits are colored as indicated (2).
Figure 5.
Rpb4/Rpb7 dimer. (A) Sequence alignments of Rpb4 and Rpb7 are as in Fig. 3. Mutations in human within the OB fold that decrease RNA binding are indicated by asterisks, and the temperature-sensitive G150D mutation is indicated by an arrow. (B) Structures of the Rpb4/Rpb7 dimer from human PDB ID code 2C35, S. pombe and S. cerevisiae PDB ID code 1WCM. The RNA-binding OB and RNP folds and the N and C termini of Rpb4 and Rpb7 are indicated.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265742 M.Wojtas, B.Peralta, M.Ondiviela, M.Mogni, S.D.Bell, and N.G.Abrescia (2011).
Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit.
  Biochem Soc Trans, 39, 25-30.
PDB code: 2y0s
20360047 G.Ruprich-Robert, and P.Thuriaux (2010).
Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases.
  Nucleic Acids Res, 38, 4559-4569.  
20094031 Z.A.Chen, A.Jawhari, L.Fischer, C.Buchen, S.Tahir, T.Kamenski, M.Rasmussen, L.Lariviere, J.C.Bukowski-Wills, M.Nilges, P.Cramer, and J.Rappsilber (2010).
Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry.
  EMBO J, 29, 717-726.  
19880312 A.Hirata, and K.S.Murakami (2009).
Archaeal RNA polymerase.
  Curr Opin Struct Biol, 19, 724-731.  
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 code is shown on the right.