1I3Q

RNA POLYMERASE II CRYSTAL FORM I AT 3.1 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.

Cramer, P.Bushnell, D.A.Kornberg, R.D.

(2001) Science 292: 1863-1876

  • DOI: 10.1126/science.1059493
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previ ...

    Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.


    Related Citations: 
    • Architecture of RNA Polymerase II and Implications for the Transcription Mechanism
      Cramer, P., Bushnell, D.A., Fu, J., Gnatt, A.L., Maier-Davis, B., Thompson, N.E., Burgess, R.R., Edwards, A.M., David, P.R., Kornberg, R.D.
      (2000) Science 288: 640

    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
A
1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04050

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE
B
1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08518

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE
C
318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16370

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 27KD POLYPEPTIDE
E
215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20434

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 23KD POLYPEPTIDE
F
155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20435

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 14.5KD POLYPEPTIDE
H
146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE
I
122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 8.3KD POLYPEPTIDE
J
70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22139

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE
K
120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38902

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 7.7KD POLYPEPTIDE
L
70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40422
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.7α = 90
b = 224.8β = 90
c = 369.4γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-25
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance