4QIW

Crystal structure of euryarchaeal RNA polymerase from Thermococcus kodakarensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.279 

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This is version 1.1 of the entry. See complete history


Literature

The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration.

Jun, S.H.Hirata, A.Kanai, T.Santangelo, T.J.Imanaka, T.Murakami, K.S.

(2014) Nat Commun 5: 5132-5132

  • DOI: https://doi.org/10.1038/ncomms6132
  • Primary Citation of Related Structures:  
    4QIW, 4QJV

  • PubMed Abstract: 

    The archaeal transcription apparatus is closely related to the eukaryotic RNA polymerase II (Pol II) system. Archaeal RNA polymerase (RNAP) and Pol II evolved from a common ancestral structure and the euryarchaeal RNAP is the simplest member of the extant archaeal-eukaryotic RNAP family. Here we report the first crystal structure of euryarchaeal RNAP from Thermococcus kodakarensis (Tko). This structure reveals that the clamp domain is able to swing away from the main body of RNAP in the presence of the Rpo4/Rpo7 stalk by coordinated movements of these domains. More detailed structure-function analysis of yeast Pol II and Tko RNAP identifies structural additions to Pol II that correspond to the binding sites of Pol II-specific general transcription factors including TFIIF, TFIIH and Mediator. Such comparisons provide a framework for dissecting interactions between RNAP and these factors during formation of the pre-initiation complex.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymeraseA,
L [auth I]
906Thermococcus kodakarensis KOD1Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JE33 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymeraseB,
M [auth J]
1,123Thermococcus kodakarensis KOD1Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JE32 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit A''C,
N [auth M]
391Thermococcus kodakarensis KOD1Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JE34 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit D
D, O
259Thermococcus kodakarensis KOD1Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JJF4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase, subunit E'E,
P [auth Q]
190Thermococcus kodakarensis KOD1Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JIY4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase, subunit FF,
Q [auth R]
122Thermococcus kodakarensis KOD1Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JI52 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit HG [auth H],
R [auth S]
82Thermococcus kodakarensis KOD1Mutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit KH [auth K],
S [auth T]
57Thermococcus kodakarensis KOD1Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JJD0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit LI [auth L],
T [auth U]
100Thermococcus kodakarensis KOD1Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JE88 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit NJ [auth N],
U [auth V]
65Thermococcus kodakarensis KOD1Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JJC9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit PK [auth P],
V [auth W]
49Thermococcus kodakarensis KOD1Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JDM8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth N]
CA [auth P]
EA [auth I]
FA [auth I]
AA [auth B],
BA [auth N],
CA [auth P],
EA [auth I],
FA [auth I],
HA [auth J],
IA [auth V],
JA [auth W],
X [auth A],
Y [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth I],
GA [auth I],
W [auth A],
Z [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.279 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.975α = 90
b = 206.606β = 90
c = 365.157γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references