3H0G

RNA Polymerase II from Schizosaccharomyces pombe

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.297 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution.

Spahr, H., Calero, G., Bushnell, D.A., Kornberg, R.D.

(2009) Proc.Natl.Acad.Sci.USA 106: 9185-9190

  • DOI: 10.1073/pnas.0903361106

  • PubMed 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 ...

    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.

    Organizational Affiliation: 

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit rpb1
A, M
1752Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb1
EC: 2.7.7.6
Find proteins for P36594 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P36594
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB2
B, N
1210Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb2
EC: 2.7.7.6
Find proteins for Q02061 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q02061
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB3
C, O
297Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb3
Find proteins for P37382 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P37382
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit rpb4
D, P
135Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb4
Find proteins for O74825 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74825
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1
E, Q
210Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb5
Find proteins for Q09191 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q09191
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2
F, R
142Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb6 (rpo15)
Find proteins for P36595 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P36595
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit rpb7
G, S
172Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb7
Find proteins for O14459 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O14459
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3
H, T
125Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb8
Find proteins for Q92399 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q92399
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9
I, U
113Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb9
Find proteins for O74635 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74635
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5
J, V
71Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb10
Find proteins for O13877 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O13877
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB11
K, W
123Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb11
Find proteins for P87123 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P87123
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4
L, X
63Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpc10 (rpb12)
Find proteins for P48011 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P48011
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C, I, J, L, M, N, O, U, V, X
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, M
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.297 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 163.034α = 90.00
b = 202.684β = 90.00
c = 391.258γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-06-10
    Type: Derived calculations