1HQM | pdb_00001hqm

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

PDB DOI: https://doi.org/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.

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.4 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

PubMed: 11158566 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.98.3.892
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 347.94 kDa
Atom Count: 21,254
Modeled Residue Count: 2,838
Deposited Residue Count: 3,109
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	313	Thermus aquaticus	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q9KWU8 (Thermus aquaticus) Explore Q9KWU8 Go to UniProtKB: Q9KWU8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KWU8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C	1,119	Thermus aquaticus	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q9KWU7 (Thermus aquaticus) Explore Q9KWU7 Go to UniProtKB: Q9KWU7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KWU7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	1,265	Thermus aquaticus	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q9KWU6 (Thermus aquaticus) Explore Q9KWU6 Go to UniProtKB: Q9KWU6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KWU6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E	99	Thermus aquaticus	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q9EVV4 (Thermus aquaticus) Explore Q9EVV4 Go to UniProtKB: Q9EVV4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9EVV4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D] mmCIF format, chain G [auth D]	G [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth D] MOL2 format, chain F [auth D] mmCIF format, chain F [auth D]	F [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

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

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2001-02-07

Deposition Author(s):

This entry supersedes: 1DDQ

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
Version 1.4: 2024-02-07
Changes: Advisory, Data collection, Database references, Derived calculations