2Y0S | pdb_00002y0s

Crystal structure of Sulfolobus shibatae RNA polymerase in P21 space group

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 
    0.354 (Depositor), 0.344 (DCC) 
  • R-Value Work: 
    0.300 (Depositor), 0.288 (DCC) 
  • R-Value Observed: 
    0.302 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history. 

Literature

Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit.

Wojtas, M., Peralta, B., Ondiviela, M., Mogni, M., Bell, S.D., Abrescia, N.G.

(2011) Biochem Soc Trans 39: 25-30

  • DOI: https://doi.org/10.1042/BST0390025
  • Primary Citation Related Structures: 
    2Y0S

  • PubMed Abstract: 

    We review recent results on the complete structure of the archaeal RNAP (RNA polymerase) enzyme of Sulfolobus shibatae. We compare the three crystal forms in which this RNAP packs (space groups P2₁2₁2₁, P2₁2₁2 and P2₁) and provide a preliminary biophysical characterization of the newly identified 13-subunit Rpo13. The availability of different crystal forms for this RNAP allows the analysis of the packing degeneracy and the intermolecular interactions that determine this degeneracy. We observe the pivotal role played by the protruding stalk composed of subunits Rpo4 and Rpo7 in the lattice contacts. Aided by MALLS (multi-angle laser light scattering), we have initiated the biophysical characterization of the recombinantly expressed and purified subunit Rpo13, a necessary step towards the understanding of Rpo13's role in archaeal transcription.

    • Organizational Affiliation: 
    • Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain.

Macromolecule Content 

  • Total Structure Weight: 812.82 kDa 
  • Atom Count: 52,472 
  • Modeled Residue Count: 6,610 
  • Deposited Residue Count: 7,170 
  • Unique protein chains: 13

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE
A, W
880Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB53 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE
B, R
1,131Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB55 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
C, Y
395Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB54 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE SUBUNIT D
D, S
265Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB56 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA POLYMERASE SUBUNIT 4
E, T
180Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB57 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA POLYMERASE SUBUNIT 7
F, U
113Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB58 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA POLYMERASE SUBUNIT 8
G, V
132Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB59 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE SUBUNIT H
H, Z
84Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB60 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE SUBUNIT K
I, K
95Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB61 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA POLYMERASE SUBUNIT 13
J, Q
104Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB65 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE SUBUNIT L
L, M
92Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB62 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE SUBUNIT N
N, O
66Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
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Find proteins for B8YB63 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA POLYMERASE SUBUNIT 12
P, X
48Saccharolobus shibataeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for B8YB64 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12))
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F3S

Query on F3S


Download:Ideal Coordinates CCD File
GA [auth D],
NA [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]
EA [auth B]
FA [auth B]
AA [auth A],
BA [auth A],
DA [auth B],
EA [auth B],
FA [auth B],
HA [auth N],
IA [auth O],
JA [auth P],
KA [auth R],
LA [auth R],
MA [auth R],
OA [auth W],
PA [auth W],
RA [auth X]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
CA [auth A],
QA [auth W]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free:  0.354 (Depositor), 0.344 (DCC) 
  • R-Value Work:  0.300 (Depositor), 0.288 (DCC) 
  • R-Value Observed: 0.302 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.33α = 90
b = 195.909β = 105.73
c = 212.451γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-30
    Changes: Data collection, Derived calculations, Other
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary