7QV9 | pdb_00007qv9

CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF

PDB DOI: https://doi.org/10.2210/pdb7QV9/pdb
NAKB: 7QV9
EM Map EMD-14171: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Escherichia coli K-12, Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-20 Released: 2022-11-09
Deposition Author(s): Ye, F.Z., Zhang, X.D.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Mechanisms of DNA opening revealed in AAA+ transcription complex structures.

Ye, F., Gao, F., Liu, X., Buck, M., Zhang, X.

(2022) Sci Adv 8: eadd3479-eadd3479

PubMed: 36542713 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.add3479
Primary Citation Related Structures:
7QV9, 7QWP, 7QXI

PubMed Abstract:
Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter complex, where DNA is opened up. In bacteria, RNAP relies on σ factors for its promoter specificities. Using a special form of sigma factor (σ ⁵⁴), which forms a stable closed complex and requires its activator that belongs to the AAA+ ATPases (ATPases associated with diverse cellular activities), we obtained cryo-electron microscopy structures of transcription initiation complexes that reveal a previously unidentified process of DNA melting opening. The σ ⁵⁴ amino terminus threads through the locally opened up DNA and then becomes enclosed by the AAA+ hexameric ring in the activator-bound intermediate complex. Our structures suggest how ATP hydrolysis by the AAA+ activator could remove the σ ⁵⁴ inhibition while helping to open up DNA, using σ ⁵⁴ amino-terminal peptide as a pry bar.

Organizational Affiliation

Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, South Kensington SW7 2AZ, UK.

Macromolecule Content

Total Structure Weight: 683.98 kDa
Atom Count: 41,491
Modeled Residue Count: 5,317
Deposited Residue Count: 5,871
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	329	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpoA, pez, phs, sez, b3295, JW3257 EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4 Go to UniProtKB: P0A7Z4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7Z4
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	1,342	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12)) Explore P0A8V2 Go to UniProtKB: P0A8V2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8V2
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	1,407	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpoC, tabB, b3988, JW3951 EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12)) Explore P0A8T7 Go to UniProtKB: P0A8T7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8T7
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	91	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpoZ, b3649, JW3624 EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12)) Explore P0A800 Go to UniProtKB: P0A800
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A800
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription activator PspF	H [auth a] I [auth b] J [auth c] K [auth d] L [auth f] H [auth a], I [auth b], J [auth c], K [auth d], L [auth f], M [auth e]	295	Escherichia coli K-12	Mutation(s): 0 Gene Names: pspF
UniProt
Find proteins for P37344 (Escherichia coli (strain K12)) Explore P37344 Go to UniProtKB: P37344
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37344
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma-54 factor	N [auth M]	477	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: rpoN, A7B01_01570, B4U61_10775, B5L96_24890, BANRA_03272, BL124_00020515, BN49_0508, BS595_02095, C3F39_17700, DDJ63_09965... rpoN, A7B01_01570, B4U61_10775, B5L96_24890, BANRA_03272, BL124_00020515, BN49_0508, BS595_02095, C3F39_17700, DDJ63_09965, DRB11_15360, EAO17_11045, FXN67_08250, G5637_17550, G7Z27_02650, GJJ08_002620, GJJ12_002565, GNE24_14685, GNG14_08115, GPZ86_02700, HV479_13895, NCTC13465_03419, NCTC3279_03959, NCTC5047_03164, SAMEA3499874_03190, SAMEA3499901_03507, SAMEA3500057_00079, SAMEA3512100_03793, SAMEA3538828_04129, SAMEA3649733_03935, SAMEA3649758_00080, SAMEA3720909_03353, SAMEA3727630_04208, SAMEA3727643_03388, SAMEA3727679_00080, SAMEA3729663_03804, SAMEA4364603_00630, SAMEA4873632_04262
UniProt
Find proteins for A0A0H3H3L1 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3H3L1 Go to UniProtKB: A0A0H3H3L1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3H3L1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 5
Non-template promoter DNA	F [auth N]	63	Klebsiella pneumoniae
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 6
Template promoter DNA	G [auth T]	63	Klebsiella pneumoniae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain V [auth e] SDF format, chain T [auth f] SDF format, chain S [auth c] SDF format, chain Q [auth b] SDF format, chain O [auth a] MOL2 format, chain V [auth e] MOL2 format, chain T [auth f] MOL2 format, chain S [auth c] MOL2 format, chain Q [auth b] MOL2 format, chain O [auth a] mmCIF format, chain V [auth e] mmCIF format, chain T [auth f] mmCIF format, chain S [auth c] mmCIF format, chain Q [auth b] mmCIF format, chain O [auth a]	O [auth a], Q [auth b], S [auth c], T [auth f], V [auth e]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain O [auth a] Focus chain Q [auth b] Focus chain S [auth c] Focus chain T [auth f] Focus chain V [auth e] Interactions & Density Focus chain O [auth a] Focus chain Q [auth b] Focus chain S [auth c] Focus chain T [auth f] Focus chain V [auth e]
AF3 (Subject of Investigation/LOI) Query on AF3 Download:Ideal Coordinates CCD File SDF format, chain W [auth e] SDF format, chain U [auth f] SDF format, chain R [auth b] SDF format, chain P [auth a] MOL2 format, chain W [auth e] MOL2 format, chain U [auth f] MOL2 format, chain R [auth b] MOL2 format, chain P [auth a] mmCIF format, chain W [auth e] mmCIF format, chain U [auth f] mmCIF format, chain R [auth b] mmCIF format, chain P [auth a]	P [auth a], R [auth b], U [auth f], W [auth e]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain P [auth a] Focus chain R [auth b] Focus chain U [auth f] Focus chain W [auth e] Interactions & Density Focus chain P [auth a] Focus chain R [auth b] Focus chain U [auth f] Focus chain W [auth e]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	RELION 3.1
MODEL REFINEMENT	PHENIX	phenix/1.13-2998
MODEL REFINEMENT	REFMAC	ccp4/7.0 package

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-09

Deposition Author(s):

Ye, F.Z.

Zhang, X.D.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/N007816/1

Revision History (Full details and data files)

Version 1.0: 2022-11-09
Type: Initial release
Version 1.1: 2023-05-24
Changes: Database references, Refinement description
Version 1.2: 2024-07-17
Changes: Data collection, 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.

7QV9 | pdb_00007qv9

CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF

Literature

Mechanisms of DNA opening revealed in AAA+ transcription complex structures.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

Sequence Annotations

Entity ID: 6

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)