Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 347.94 kDa 
• Atom Count: 21254 
• Modelled Residue Count: 2838 
• Deposited Residue Count: 3109 
• Unique protein chains: 4

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

• DOI: 10.2210/pdb1HQM/pdb
• Entry: 1HQM supersedes: 1DDQ

• Classification: TRANSFERASE
• Organism(s): Thermus aquaticus
• Mutation(s): No 


• Deposited: 2000-12-18 Released: 2001-02-07 
• Deposition Author(s): Minakhin, L., Bhagat, S., Brunning, A., Campbell, E.A., Darst, S.A., Ebright, R.H., Severinov, K.

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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 

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

• PubMed: 11158566 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	313	Thermus aquaticus	Mutation(s): 0  Gene Names: rpoA EC: 2.7.7.6
Find proteins for Q9KWU8 (Thermus aquaticus) Explore Q9KWU8  Go to UniProtKB:  Q9KWU8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C	1119	Thermus aquaticus	Mutation(s): 0  Gene Names: rpoB EC: 2.7.7.6
Find proteins for Q9KWU7 (Thermus aquaticus) Explore Q9KWU7  Go to UniProtKB:  Q9KWU7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	1265	Thermus aquaticus	Mutation(s): 0  Gene Names: rpoC EC: 2.7.7.6
Find proteins for Q9KWU6 (Thermus aquaticus) Explore Q9KWU6  Go to UniProtKB:  Q9KWU6

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E	99	Thermus aquaticus	Mutation(s): 0  Gene Names: rpoZ EC: 2.7.7.6
Find proteins for Q9EVV4 (Thermus aquaticus) Explore Q9EVV4  Go to UniProtKB:  Q9EVV4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	F [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 200.76	α = 90
b = 200.76	β = 90
c = 292.938	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-12-18 
• Released Date: 2001-02-07 
Deposition Author(s): Minakhin, L., Bhagat, S., Brunning, A., Campbell, E.A., Darst, S.A., Ebright, R.H., Severinov, K.
• This entry supersedes: 1DDQ

Revision History  

• 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