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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B313Thermus aquaticusMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU8 (Thermus aquaticus)
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Go to UniProtKB:  Q9KWU8
Entity Groups  
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UniProt GroupQ9KWU8
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1,119Thermus aquaticusMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU7 (Thermus aquaticus)
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UniProt GroupQ9KWU7
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1,265Thermus aquaticusMutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU6 (Thermus aquaticus)
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UniProt GroupQ9KWU6
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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
UniProt
Find proteins for Q9EVV4 (Thermus aquaticus)
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UniProt GroupQ9EVV4
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