1I6V | pdb_00001i6v

THERMUS AQUATICUS CORE RNA POLYMERASE-RIFAMPICIN COMPLEX

PDB DOI: https://doi.org/10.2210/pdb1I6V/pdb

Classification: TRANSCRIPTION
Organism(s): Thermus aquaticus
Mutation(s): No

Deposited: 2001-03-05 Released: 2001-04-18
Deposition Author(s): Campbell, E.A., Korzheva, N., Mustaev, A., Murakami, K., Goldfarb, A., Darst, S.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.359 (Depositor)
R-Value Work:
0.276 (Depositor)
R-Value Observed:
0.280 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural mechanism for rifampicin inhibition of bacterial rna polymerase.

Campbell, E.A., Korzheva, N., Mustaev, A., Murakami, K., Nair, S., Goldfarb, A., Darst, S.A.

(2001) Cell 104: 901-912

PubMed: 11290327 Search on PubMed
DOI: https://doi.org/10.1016/s0092-8674(01)00286-0
Primary Citation Related Structures:
1I6V

PubMed Abstract:
Rifampicin (Rif) is one of the most potent and broad spectrum antibiotics against bacterial pathogens and is a key component of anti-tuberculosis therapy, stemming from its inhibition of the bacterial RNA polymerase (RNAP). We determined the crystal structure of Thermus aquaticus core RNAP complexed with Rif. The inhibitor binds in a pocket of the RNAP beta subunit deep within the DNA/RNA channel, but more than 12 A away from the active site. The structure, combined with biochemical results, explains the effects of Rif on RNAP function and indicates that the inhibitor acts by directly blocking the path of the elongating RNA when the transcript becomes 2 to 3 nt in length.

Organizational Affiliation

The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

Macromolecule Content

Total Structure Weight: 348.33 kDa
Atom Count: 21,292
Modeled Residue Count: 2,839
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	A, B	314	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	C	1,118	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	D	1,264	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	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RFP Query on RFP Download:Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	RIFAMPICIN C₄₃ H₅₈ N₄ O₁₂ JQXXHWHPUNPDRT-WLSIYKJHSA-N		Interactions Focus chain F [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D] mmCIF format, chain H [auth D]	H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth D]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.359 (Depositor)
R-Value Work: 0.276 (Depositor)
R-Value Observed: 0.280 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.45	α = 90
b = 199.45	β = 90
c = 289.13	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2001-04-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-04-18
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: 2023-08-09
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Structure summary