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 
  • R-Value Observed: 0.297 

Starting Model: experimental
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This is version 1.3 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 U S A 106: 9185-9190

  • DOI: https://doi.org/10.1073/pnas.0903361106
  • Primary Citation of Related Structures:  
    3H0G

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit rpb1
A, M
1,752Schizosaccharomyces pombe 972h-Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P36594 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupP36594
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2
B, N
1,210Schizosaccharomyces pombe 972h-Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q02061 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3
C, O
297Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for P37382 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit rpb4
D, P
135Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for O74825 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1
E, Q
210Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for Q09191 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2
F, R
142Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit rpb7
G, S
172Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for O14459 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3
H, T
125Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for Q92399 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9
I, U
113Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for O74635 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5
J, V
71Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for O13877 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11
K, W
123Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4
L, X
63Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth C]
DA [auth I]
EA [auth I]
FA [auth J]
BA [auth B],
CA [auth C],
DA [auth I],
EA [auth I],
FA [auth J],
GA [auth L],
HA [auth M],
IA [auth M],
KA [auth N],
LA [auth O],
MA [auth U],
NA [auth U],
OA [auth V],
PA [auth X],
Y [auth A],
Z [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A],
JA [auth M]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.297 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.034α = 90
b = 202.684β = 90
c = 391.258γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-06-10
    Changes: Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description