3DXJ | pdb_00003dxj

Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin

PDB DOI: https://doi.org/10.2210/pdb3DXJ/pdb

Classification: TRANSCRIPTION,TRANSFERASE
Organism(s): Thermus thermophilus HB8
Mutation(s): Yes

Deposited: 2008-07-24 Released: 2008-10-14
Deposition Author(s): Das, K., Arnold, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.289 (Depositor), 0.276 (DCC)
R-Value Work:
0.235 (Depositor), 0.221 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5TMF

Literature

The RNA polymerase "switch region" is a target for inhibitors.

Mukhopadhyay, J., Das, K., Ismail, S., Koppstein, D., Jang, M., Hudson, B., Sarafianos, S., Tuske, S., Patel, J., Jansen, R., Irschik, H., Arnold, E., Ebright, R.H.

(2008) Cell 135: 295-307

PubMed: 18957204 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2008.09.033
Primary Citation Related Structures:
3DXJ

PubMed Abstract:
The alpha-pyrone antibiotic myxopyronin (Myx) inhibits bacterial RNA polymerase (RNAP). Here, through a combination of genetic, biochemical, and structural approaches, we show that Myx interacts with the RNAP "switch region"--the hinge that mediates opening and closing of the RNAP active center cleft--to prevent interaction of RNAP with promoter DNA. We define the contacts between Myx and RNAP and the effects of Myx on RNAP conformation and propose that Myx functions by interfering with opening of the RNAP active-center cleft during transcription initiation. We further show that the structurally related alpha-pyrone antibiotic corallopyronin (Cor) and the structurally unrelated macrocyclic-lactone antibiotic ripostatin (Rip) function analogously to Myx. The RNAP switch region is distant from targets of previously characterized RNAP inhibitors, and, correspondingly, Myx, Cor, and Rip do not exhibit crossresistance with previously characterized RNAP inhibitors. The RNAP switch region is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents.

Organizational Affiliation

Howard Hughes Medical Institute, Rutgers University, Piscataway, NJ 08854, USA.

Macromolecule Content

Total Structure Weight: 855.05 kDa
Atom Count: 56,149
Modeled Residue Count: 7,082
Deposited Residue Count: 7,590
Unique protein chains: 5

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L	A, B, G [auth K], H [auth L]	315	Thermus thermophilus HB8	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q5SHR6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHR6 Go to UniProtKB: Q5SHR6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHR6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BACTERIAL RNA POLYMERASE BETA SUBUNIT; CHAIN C, M	C, I [auth M]	1,119	Thermus thermophilus HB8	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE9 Go to UniProtKB: Q8RQE9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RQE9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BACTERIAL RNA POLYMERASE BETA-PRIME SUBUNIT; CHAIN D, N	D, J [auth N]	1,524	Thermus thermophilus HB8	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE8 Go to UniProtKB: Q8RQE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RQE8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BACTERIAL RNA POLYMERASE OMEGA SUBUNIT; CHAIN E, O	E, K [auth O]	99	Thermus thermophilus HB8	Mutation(s): 3 EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE7 Go to UniProtKB: Q8RQE7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RQE7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase pricipal sigma factor (RpoD); CHAIN F, P	F, L [auth P]	423	Thermus thermophilus HB8	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q5SKW1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKW1 Go to UniProtKB: Q5SKW1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SKW1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NE6 Query on NE6 Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain Z [auth N] MOL2 format, chain U [auth D] MOL2 format, chain Z [auth N] mmCIF format, chain U [auth D] mmCIF format, chain Z [auth N]	U [auth D], Z [auth N]	methyl [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-dimethylocta-2,4-dienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate C₂₃ H₃₁ N O₆ LTDLIPXLSBMTFP-FSAISGGASA-N		Interactions Focus chain U [auth D] Focus chain Z [auth N] Interactions & Density Focus chain U [auth D] Focus chain Z [auth N]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain V [auth M] SDF format, chain P [auth C] SDF format, chain O [auth C] MOL2 format, chain V [auth M] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] mmCIF format, chain V [auth M] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C]	O [auth C], P [auth C], V [auth M]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain O [auth C] Focus chain P [auth C] Focus chain V [auth M] Interactions & Density Focus chain O [auth C] Focus chain P [auth C] Focus chain V [auth M]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain M [auth A] MOL2 format, chain T [auth D] MOL2 format, chain M [auth A] mmCIF format, chain T [auth D] mmCIF format, chain M [auth A]	M [auth A], T [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth A] Focus chain T [auth D] Interactions & Density Focus chain M [auth A] Focus chain T [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain W [auth N] SDF format, chain X [auth N] SDF format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain W [auth N] MOL2 format, chain X [auth N] MOL2 format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain W [auth N] mmCIF format, chain X [auth N] mmCIF format, chain R [auth D]	Q [auth D], R [auth D], W [auth N], X [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Focus chain R [auth D] Focus chain W [auth N] Focus chain X [auth N] Interactions & Density Focus chain Q [auth D] Focus chain R [auth D] Focus chain W [auth N] Focus chain X [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth N] SDF format, chain S [auth D] SDF format, chain N [auth B] MOL2 format, chain Y [auth N] MOL2 format, chain S [auth D] MOL2 format, chain N [auth B] mmCIF format, chain Y [auth N] mmCIF format, chain S [auth D] mmCIF format, chain N [auth B]	N [auth B], S [auth D], Y [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain S [auth D] Focus chain Y [auth N] Interactions & Density Focus chain N [auth B] Focus chain S [auth D] Focus chain Y [auth N]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.289 (Depositor), 0.276 (DCC)
R-Value Work: 0.235 (Depositor), 0.221 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 235.09	α = 90
b = 235.09	β = 90
c = 250.88	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-10-14

Deposition Author(s):

Das, K.

Arnold, E.

Revision History (Full details and data files)

Version 1.0: 2008-10-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

3DXJ | pdb_00003dxj

Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin

Re-refinement Note

Literature

The RNA polymerase "switch region" is a target for inhibitors.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Expand

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)