3H0G | pdb_00003h0g

RNA Polymerase II from Schizosaccharomyces pombe

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 
    0.321 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.297 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 
    0.297 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 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
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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))
Explore P36594 
Go to UniProtKB:  P36594
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36594
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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))
Explore Q02061 
Go to UniProtKB:  Q02061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02061
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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))
Explore P37382 
Go to UniProtKB:  P37382
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37382
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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))
Explore O74825 
Go to UniProtKB:  O74825
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74825
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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))
Explore Q09191 
Go to UniProtKB:  Q09191
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09191
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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
Find proteins for P36595 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P36595 
Go to UniProtKB:  P36595
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36595
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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))
Explore O14459 
Go to UniProtKB:  O14459
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14459
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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))
Explore Q92399 
Go to UniProtKB:  Q92399
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92399
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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))
Explore O74635 
Go to UniProtKB:  O74635
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74635
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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))
Explore O13877 
Go to UniProtKB:  O13877
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13877
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11
K, W
123Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for P87123 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P87123 
Go to UniProtKB:  P87123
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP87123
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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
Find proteins for P48011 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P48011 
Go to UniProtKB:  P48011
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48011
Sequence Annotations
Expand
  • Reference Sequence
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 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.297 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 0.297 (Depositor) 
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

View Full Validation Report



View more in-depth experimental data
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
  • Version 1.4: 2024-11-06
    Changes: Structure summary