4OIP | pdb_00004oip

Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077, ATP, and CMPcPP

PDB DOI: https://doi.org/10.2210/pdb4OIP/pdb
NAKB: 4OIP

Classification: TRANSCRIPTION, TRANSFERASE/ANTIBIOTIC
Organism(s): Thermus thermophilus HB8, Actinomadura sp.
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-01-20 Released: 2014-05-07
Deposition Author(s): Zhang, Y., Ebright, R.H., Arnold, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.246 (Depositor), 0.238 (DCC)
R-Value Work:
0.208 (Depositor)
R-Value Observed:
0.209 (Depositor)

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

GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.

Zhang, Y., Degen, D., Ho, M.X., Sineva, E., Ebright, K.Y., Ebright, Y.W., Mekler, V., Vahedian-Movahed, H., Feng, Y., Yin, R., Tuske, S., Irschik, H., Jansen, R., Maffioli, S., Donadio, S., Arnold, E., Ebright, R.H.

(2014) Elife 3: e02450-e02450

PubMed: 24755292 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.02450
Primary Citation Related Structures:
4MQ9, 4OIN, 4OIO, 4OIP, 4OIQ, 4OIR

PubMed Abstract:
Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center 'i' and 'i+1' nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance. DOI: http://dx.doi.org/10.7554/eLife.02450.001.

Organizational Affiliation

Waksman Institute, Rutgers University, Piscataway, United States.

Macromolecule Content

Total Structure Weight: 445.37 kDa
Atom Count: 28,603
Modeled Residue Count: 3,543
Deposited Residue Count: 3,870
Unique protein chains: 6
Unique nucleic acid chains: 2

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	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

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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 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

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	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

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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 thermophilus HB8	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RQE7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA directed RNA polymerase sigma factor A	F	443	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: rpoD, TTHA0532
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

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
GE23077	I	7	Actinomadura sp.	Mutation(s): 0

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 6
5'-D(CPCPTPGPCPAPTPCPCPGPTPGPAPGPTPCPGPAPGPGP*G)-3'	G	21	N/A
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 7
5'-D(TPAPTPAPAPTPGPGPGPAPGPCPTPGPTPCPAPCPGPGPAPTPGPCPAPGP*G)-3'	H	27	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
MB8 Query on MB8 Download:Ideal Coordinates CCD File SDF format, chain S [auth I] MOL2 format, chain S [auth I] mmCIF format, chain S [auth I]	S [auth I]	(2Z)-2-methylbut-2-enoic acid C₅ H₈ O₂ UIERETOOQGIECD-ARJAWSKDSA-N		Interactions Focus chain S [auth I] Interactions & Density Focus chain S [auth I]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D]	K [auth D], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain K [auth D] Focus chain L [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain R [auth F] SDF format, chain P [auth D] SDF format, chain M [auth D] SDF format, chain J [auth B] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain R [auth F] MOL2 format, chain P [auth D] MOL2 format, chain M [auth D] MOL2 format, chain J [auth B] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain R [auth F] mmCIF format, chain P [auth D] mmCIF format, chain M [auth D] mmCIF format, chain J [auth B]	J [auth B] M [auth D] N [auth D] O [auth D] P [auth D] J [auth B], M [auth D], N [auth D], O [auth D], P [auth D], R [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth F] Interactions & Density Focus chain J [auth B] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth F]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0QZ Query on 0QZ	I	D-PEPTIDE LINKING	C₃ H₇ N O₃		--
2RA Query on 2RA	I	D-PEPTIDE LINKING	C₃ H₈ N₂ O₂		ALA
2TL Query on 2TL	I	D-PEPTIDE LINKING	C₄ H₉ N O₃		--
DSN Query on DSN	I	D-PEPTIDE LINKING	C₃ H₇ N O₃		--
DVA Query on DVA	I	D-PEPTIDE LINKING	C₅ H₁₁ N O₂		--
FGL Query on FGL	I	L-PEPTIDE LINKING	C₃ H₅ N O₄		GLY
R2T Query on R2T	I	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₅		--

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 8
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001181 Query on PRD_001181	I	GE23077	Cyclic peptide / Antibiotic, Antimicrobial		Interactions Focus chain I Interactions & Density Focus chain I

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.246 (Depositor), 0.238 (DCC)
R-Value Work: 0.208 (Depositor)
R-Value Observed: 0.209 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.92	α = 90
b = 104.391	β = 98.97
c = 294.211	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-05-07

Deposition Author(s):

Zhang, Y.

Ebright, R.H.

Arnold, E.

Revision History (Full details and data files)

Version 1.0: 2014-05-07
Type: Initial release
Version 1.1: 2014-05-14
Changes: Non-polymer description
Version 1.2: 2023-09-20
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2025-08-13
Changes: Structure summary

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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.

4OIP | pdb_00004oip

Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077, ATP, and CMPcPP

Literature

GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 8

Entity ID: 6

Sequence Annotations

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Entity ID: 7

Sequence Annotations

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Small Molecules

Biologically Interesting Molecules (External Reference)

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)