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 

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 U S A 106: 9185-9190

  • DOI: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit rpb1A, M1752Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpb1, SPBC28F2.12
EC: 2.7.7.6
Find proteins for P36594 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2B, N1210Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpb2, SPAC23G3.01, SPAC521.06
EC: 2.7.7.6
Find proteins for Q02061 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3C, O297Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpb3, SPCC1442.10c
Find proteins for P37382 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit rpb4D, P135Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpb4, SPBC337.14
Find proteins for O74825 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1E, Q210Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpb5, SPAC23C4.15
Find proteins for Q09191 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2F, R142Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpb6, rpo15, SPCC1020.04c
Find proteins for P36595 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit rpb7G, S172Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpb7, SPACUNK4.06c, SPAPYUK71.02
Find proteins for O14459 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H, T125Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpb8, SPBC14C8.12
Find proteins for Q92399 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9I, U113Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpb9, SPAPYUG7.04c
Find proteins for O74635 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5J, V71Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpb10, SPAC1B3.12c
Find proteins for O13877 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 11
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DNA-directed RNA polymerase II subunit RPB11K, W123Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpb11, SPAC3A12.07
Find proteins for P87123 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4L, X63Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: rpc10, rpb12, SPBC19C2.03
Find proteins for P48011 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
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BA [auth B] , CA [auth C] , DA [auth I] , EA [auth I] , FA [auth J] , GA [auth L] , HA [auth M] , IA [auth M] , 
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		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
 AA [auth A], JA [auth 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 
  • 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