4GZY | pdb_00004gzy

Crystal structures of bacterial RNA Polymerase paused elongation complexes

PDB DOI: https://doi.org/10.2210/pdb4GZY/pdb
NAKB: 4GZY

Classification: TRANSCRIPTION/DNA/RNA
Organism(s): Thermus thermophilus HB8, synthetic construct
Expression System: Thermus thermophilus
Mutation(s): No

Deposited: 2012-09-06 Released: 2013-02-13
Deposition Author(s): Weixlbaumer, A., Leon, K., Landick, R., Darst, S.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.51 Å
R-Value Free:
0.322 (Depositor), 0.325 (DCC)
R-Value Work:
0.263 (Depositor), 0.265 (DCC)
R-Value Observed:
0.266 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural basis of transcriptional pausing in bacteria.

Weixlbaumer, A., Leon, K., Landick, R., Darst, S.A.

(2013) Cell 152: 431-441

PubMed: 23374340 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2012.12.020
Primary Citation Related Structures:
4GZY, 4GZZ

PubMed Abstract:
Transcriptional pausing by multisubunit RNA polymerases (RNAPs) is a key mechanism for regulating gene expression in both prokaryotes and eukaryotes and is a prerequisite for transcription termination. Pausing and termination states are thought to arise through a common, elemental pause state that is inhibitory for nucleotide addition. We report three crystal structures of Thermus RNAP elemental paused elongation complexes (ePECs). The structures reveal the same relaxed, open-clamp RNAP conformation in the ePEC that may arise by failure to re-establish DNA contacts during translocation. A kinked bridge-helix sterically blocks the RNAP active site, explaining how this conformation inhibits RNAP catalytic activity. Our results provide a framework for understanding how RNA hairpin formation stabilizes the paused state and how the ePEC intermediate facilitates termination.

Organizational Affiliation

The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.

Macromolecule Content

Total Structure Weight: 399.53 kDa
Atom Count: 24,400
Modeled Residue Count: 3,022
Deposited Residue Count: 3,446
Unique protein chains: 4
Unique nucleic acid chains: 3

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 Gene Names: rpoA, TTHA1664 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 Gene Names: rpoB, TTHA1813 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	1,534	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: rpoC, TTHA1812 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 Gene Names: rpoZ, TTHA1561 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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Molecule	Chains	Length	Organism
Entity ID: 5
non-template DNA	F [auth N]	13	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 6
RNA transcript	G [auth R]	29	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
template DNA	H [auth T]	22	synthetic construct
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 J [auth D] SDF format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain I [auth D] mmCIF format, chain J [auth D] mmCIF format, chain I [auth D]	I [auth D], J [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain J [auth D] Interactions & Density Focus chain I [auth D] Focus chain J [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.51 Å
R-Value Free: 0.322 (Depositor), 0.325 (DCC)
R-Value Work: 0.263 (Depositor), 0.265 (DCC)
R-Value Observed: 0.266 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.21	α = 90
b = 207.21	β = 90
c = 203.223	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-13
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2019-07-17
Changes: Data collection, Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.

4GZY | pdb_00004gzy

Crystal structures of bacterial RNA Polymerase paused elongation complexes

Literature

Structural basis of transcriptional pausing in bacteria.

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

Sequence Annotations

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Entity ID: 6

Sequence Annotations

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Entity ID: 7

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)