1ZYR

Structure of Thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic streptolydigin

PDB DOI: https://doi.org/10.2210/pdb1ZYR/pdb

Classification: TRANSCRIPTION,TRANSFERASE
Organism(s): Thermus thermophilus
Mutation(s): No

Deposited: 2005-06-10 Released: 2005-09-13
Deposition Author(s): Tuske, S., Sarafianos, S.G., Wang, X., Hudson, B., Sineva, E., Mukhopadhyay, J., Birktoft, J.J., Leroy, O., Ismail, S., Clark, A.D., Dharia, C., Napoli, A., Laptenko, O., Lee, J., Borukhov, S., Ebright, R.H., Arnold, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.281
R-Value Work: 0.261

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.

Tuske, S., Sarafianos, S.G., Wang, X., Hudson, B., Sineva, E., Mukhopadhyay, J., Birktoft, J.J., Leroy, O., Ismail, S., Clark, A.D., Dharia, C., Napoli, A., Laptenko, O., Lee, J., Borukhov, S., Ebright, R.H., Arnold, E.

(2005) Cell 122: 541-552

PubMed: 16122422 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2005.07.017
Primary Citation of Related Structures:
1ZYR, 2CW0

PubMed Abstract:
We define the target, mechanism, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the tetramic acid antibiotic streptolydigin (Stl). Stl binds to a site adjacent to but not overlapping the RNAP active center and stabilizes an RNAP-active-center conformational state with a straight-bridge helix. The results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations exist and that cycling between straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations is required for RNAP function. The results set bounds on models for RNAP function and suggest strategies for design of novel antibacterial agents.

Organizational Affiliation

Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.

Macromolecule Content

Total Structure Weight: 854.78 kDa
Atom Count: 54,048
Modelled Residue Count: 6,818
Deposited Residue Count: 7,590
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase alpha chain	A, B, G [auth K], H [auth L]	315	Thermus thermophilus	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SHR6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase beta chain	C, I [auth M]	1,119	Thermus thermophilus	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RQE9
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta' chain	D, J [auth N]	1,524	Thermus thermophilus	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RQE8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase omega chain	E, K [auth O]	99	Thermus thermophilus	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RQE7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase sigma chain	F, L [auth P]	423	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SKW1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKW1 Go to UniProtKB: Q5SKW1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SKW1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STD Query on STD Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain Q [auth M] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth M] mmCIF format, chain M [auth D] mmCIF format, chain Q [auth M]	M [auth D], Q [auth M]	STREPTOLYDIGIN C₃₂ H₄₄ N₂ O₉ KVTPRMVXYZKLIG-NCAOFHFGSA-N		Interactions Focus chain M [auth D] Focus chain Q [auth M] Interactions & Density Focus chain M [auth D] Focus chain Q [auth M]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain R [auth N] SDF format, chain S [auth N] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain R [auth N] MOL2 format, chain S [auth N] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain R [auth N] mmCIF format, chain S [auth N]	N [auth D], O [auth D], R [auth N], S [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Focus chain O [auth D] Focus chain R [auth N] Focus chain S [auth N] Interactions & Density Focus chain N [auth D] Focus chain O [auth D] Focus chain R [auth N] Focus chain S [auth N]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain T [auth N] MOL2 format, chain P [auth D] MOL2 format, chain T [auth N] mmCIF format, chain P [auth D] mmCIF format, chain T [auth N]	P [auth D], T [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Focus chain T [auth N] Interactions & Density Focus chain P [auth D] Focus chain T [auth N]

Binding Affinity Annotations
ID	Source	Binding Affinity
STD	PDBBind: 1ZYR	Ki: 1800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.281
R-Value Work: 0.261
Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 237	α = 90
b = 237	β = 90
c = 250	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-09-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-09-13
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary