2WB1

The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 0.384 
  • R-Value Work: 0.333 
  • R-Value Observed: 0.335 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evolution of Complex RNA Polymerase: The Complete Archaeal RNA Polymerase Structure

Korkhin, Y.Unligil, U.M.Littlefield, O.Nelson, P.J.Stuart, D.I.Sigler, P.B.Bell, S.D.Abrescia, N.G.A.

(2009) PLoS Biol 7: E102

  • DOI: https://doi.org/10.1371/journal.pbio.1000102
  • Primary Citation of Related Structures:  
    2WAQ, 2WB1

  • PubMed Abstract: 

    The archaeal RNA polymerase (RNAP) shares structural similarities with eukaryotic RNAP II but requires a reduced subset of general transcription factors for promoter-dependent initiation. To deepen our knowledge of cellular transcription, we have determined the structure of the 13-subunit DNA-directed RNAP from Sulfolobus shibatae at 3.35 Å resolution. The structure contains the full complement of subunits, including RpoG/Rpb8 and the equivalent of the clamp-head and jaw domains of the eukaryotic Rpb1. Furthermore, we have identified subunit Rpo13, an RNAP component in the order Sulfolobales, which contains a helix-turn-helix motif that interacts with the RpoH/Rpb5 and RpoA'/Rpb1 subunits. Its location and topology suggest a role in the formation of the transcription bubble.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO1N SUBUNIT
A, W
880Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB53 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB53 
Go to UniProtKB:  B8YB53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB53
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT
B, R
1,131Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB55 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB55 
Go to UniProtKB:  B8YB55
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB55
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT
C, Y
395Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB54 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB54 
Go to UniProtKB:  B8YB54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB54
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASERPO3 SUBUNIT
D, S
265Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB56 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB56 
Go to UniProtKB:  B8YB56
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB56
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO7 SUBUNIT
E, T
180Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB57 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB57 
Go to UniProtKB:  B8YB57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB57
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO4 SUBUNIT
F, U
113Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB58 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB58 
Go to UniProtKB:  B8YB58
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB58
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO8 SUBUNIT
G, V
132Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB59 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB59 
Go to UniProtKB:  B8YB59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB59
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO5 SUBUNIT
H, Z
84Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB60 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB60 
Go to UniProtKB:  B8YB60
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB60
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO6 SUBUNIT
I, K
95Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB61 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB61 
Go to UniProtKB:  B8YB61
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB61
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO13 SUBUNIT
J, Q
104Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB65 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB65 
Go to UniProtKB:  B8YB65
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB65
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO11 SUBUNIT
L, M
92Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB62 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB62 
Go to UniProtKB:  B8YB62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB62
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO10 SUBUNIT
N, O
66Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB63 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB63 
Go to UniProtKB:  B8YB63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB63
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE RPO12 SUBUNIT
P, X
48Saccharolobus shibataeMutation(s): 0 
UniProt
Find proteins for B8YB64 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
Explore B8YB64 
Go to UniProtKB:  B8YB64
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YB64
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F3S
Query on F3S

Download Ideal Coordinates CCD File 
EA [auth D],
JA [auth S]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
DA [auth B]
FA [auth N]
GA [auth O]
AA [auth A],
BA [auth A],
DA [auth B],
FA [auth N],
GA [auth O],
HA [auth P],
IA [auth R],
KA [auth W],
LA [auth W],
NA [auth X]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth A],
MA [auth W]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 0.384 
  • R-Value Work: 0.333 
  • R-Value Observed: 0.335 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.095α = 90
b = 211.871β = 90
c = 238.905γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
GLRFphasing
MOLREPphasing
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Atomic model, Database references, Derived calculations, Other, Structure summary, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description