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 

wwPDB Validation 3D Report Full Report


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: 10.1038/ncomms6132
  • Structures With Same Primary Citation

  • 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 e ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit DD, O259Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoDTK1503
EC: 2.7.7.6
Find proteins for Q5JJF4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JJF4 
Go to UniProtKB:  Q5JJF4
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase, subunit FF, R122Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK0901
Find proteins for Q5JI52 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JI52 
Go to UniProtKB:  Q5JI52
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit PP, W49Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoPTK0616
EC: 2.7.7.6
Find proteins for Q5JDM8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JDM8 
Go to UniProtKB:  Q5JDM8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymeraseA, I906Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK1082
EC: 2.7.7.6
Find proteins for Q5JE33 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JE33 
Go to UniProtKB:  Q5JE33
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit NN, V65Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoNTK1499
EC: 2.7.7.6
Find proteins for Q5JJC9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JJC9 
Go to UniProtKB:  Q5JJC9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymeraseB, J1123Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK1083
EC: 2.7.7.6
Find proteins for Q5JE32 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JE32 
Go to UniProtKB:  Q5JE32
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit A''C, M391Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoA2TK1081
EC: 2.7.7.6
Find proteins for Q5JE34 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JE34 
Go to UniProtKB:  Q5JE34
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase, subunit E'E, Q190Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK1699
Find proteins for Q5JIY4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JIY4 
Go to UniProtKB:  Q5JIY4
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit HH, S82Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoHTK1084
EC: 2.7.7.6
Find proteins for Q5JE31 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JE31 
Go to UniProtKB:  Q5JE31
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit KK, T57Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoKTK1498
EC: 2.7.7.6
Find proteins for Q5JJD0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JJD0 
Go to UniProtKB:  Q5JJD0
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit LL, U100Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpoLTK1167
EC: 2.7.7.6
Find proteins for Q5JE88 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JE88 
Go to UniProtKB:  Q5JE88
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download CCD File 
A, I
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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