1HQM

CRYSTAL STRUCTURE OF THERMUS AQUATICUS CORE RNA POLYMERASE-INCLUDES COMPLETE STRUCTURE WITH SIDE-CHAINS (EXCEPT FOR DISORDERED REGIONS)-FURTHER REFINED FROM ORIGINAL DEPOSITION-CONTAINS ADDITIONAL SEQUENCE INFORMATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.360 
  • R-Value Work: 0.300 
  • R-Value Observed: 0.300 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly.

Minakhin, L.Bhagat, S.Brunning, A.Campbell, E.A.Darst, S.A.Ebright, R.H.Severinov, K.

(2001) Proc Natl Acad Sci U S A 98: 892-897

  • DOI: 10.1073/pnas.98.3.892
  • Primary Citation of Related Structures:  
    1HQM

  • PubMed Abstract: 
  • Bacterial DNA-dependent RNA polymerase (RNAP) has subunit composition beta'betaalpha(I)alpha(II)omega. The role of omega has been unclear. We show that omega is homologous in sequence and structure to RPB6, an essential subunit shared in eukaryotic RNAP I, II, and III ...

    Bacterial DNA-dependent RNA polymerase (RNAP) has subunit composition beta'betaalpha(I)alpha(II)omega. The role of omega has been unclear. We show that omega is homologous in sequence and structure to RPB6, an essential subunit shared in eukaryotic RNAP I, II, and III. In Escherichia coli, overproduction of omega suppresses the assembly defect caused by substitution of residue 1362 of the largest subunit of RNAP, beta'. In yeast, overproduction of RPB6 suppresses the assembly defect caused by the equivalent substitution in the largest subunit of RNAP II, RPB1. High-resolution structural analysis of the omega-beta' interface in bacterial RNAP, and comparison with the RPB6-RPB1 interface in yeast RNAP II, confirms the structural relationship and suggests a "latching" mechanism for the role of omega and RPB6 in promoting RNAP assembly.


    Organizational Affiliation

    Waksman Institute, Department of Genetics, Department of Chemistry and Howard Hughes Medical Institute, Rutgers, The State University, Piscataway, NJ 08854, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B313Thermus aquaticusMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for Q9KWU8 (Thermus aquaticus)
Explore Q9KWU8 
Go to UniProtKB:  Q9KWU8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1119Thermus aquaticusMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for Q9KWU7 (Thermus aquaticus)
Explore Q9KWU7 
Go to UniProtKB:  Q9KWU7
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1265Thermus aquaticusMutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for Q9KWU6 (Thermus aquaticus)
Explore Q9KWU6 
Go to UniProtKB:  Q9KWU6
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE99Thermus aquaticusMutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q9EVV4 (Thermus aquaticus)
Explore Q9EVV4 
Go to UniProtKB:  Q9EVV4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.360 
  • R-Value Work: 0.300 
  • R-Value Observed: 0.300 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.76α = 90
b = 200.76β = 90
c = 292.938γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Database references, Source and taxonomy, Structure summary