9Q90 | pdb_00009q90

CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF

PDB DOI: https://doi.org/10.2210/pdb9Q90/pdb
EM Map EMD-14171: EMDB EMDataResource
NAKB: 9Q90

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

Deposited: 2025-02-26 Released: 2025-04-09
Deposition Author(s): Ye, F., Gao, F., Zhang, X.
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

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF

Ye, F.Z., Zhang, X.D.

To be published.

Macromolecule Content

Total Structure Weight: 656.53 kDa
Atom Count: 41,495
Modelled Residue Count: 5,317
Deposited Residue Count: 5,717
Unique protein chains: 6
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Psp operon transcriptional activator	A [auth 1] B [auth 2] C [auth 3] D [auth 4] E [auth 5] A [auth 1], B [auth 2], C [auth 3], D [auth 4], E [auth 5], F [auth 6]	275	Escherichia coli K-12	Mutation(s): 0 Gene Names: pspF, ycjB, b1303, JW1296
UniProt
Find proteins for P37344 (Escherichia coli (strain K12)) Explore P37344 Go to UniProtKB: P37344
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37344
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	G [auth A], H [auth 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A7Z4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	I [auth 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A8V2
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	J [auth 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A8T7
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	K [auth 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A800
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma-54 factor	L [auth M]	497	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: rpoN, KPN_03612
UniProt
Find proteins for A6TEM1 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TEM1 Go to UniProtKB: A6TEM1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6TEM1
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (36-MER)	M [auth N]	36	Escherichia coli K-12
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (36-MER)	N [auth T]	36	Escherichia coli K-12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain AA [auth 6] SDF format, chain O [auth 1] SDF format, chain R [auth 2] SDF format, chain U [auth 3] SDF format, chain X [auth 4] MOL2 format, chain AA [auth 6] MOL2 format, chain O [auth 1] MOL2 format, chain R [auth 2] MOL2 format, chain U [auth 3] MOL2 format, chain X [auth 4] mmCIF format, chain AA [auth 6] mmCIF format, chain O [auth 1] mmCIF format, chain R [auth 2] mmCIF format, chain U [auth 3] mmCIF format, chain X [auth 4]	AA [auth 6], O [auth 1], R [auth 2], U [auth 3], X [auth 4]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth 6] Focus chain O [auth 1] Focus chain R [auth 2] Focus chain U [auth 3] Focus chain X [auth 4] Interactions & Density Focus chain AA [auth 6] Focus chain O [auth 1] Focus chain R [auth 2] Focus chain U [auth 3] Focus chain X [auth 4]
AF3 Query on AF3 Download Ideal Coordinates CCD File SDF format, chain P [auth 1] SDF format, chain S [auth 2] SDF format, chain V [auth 3] SDF format, chain Y [auth 4] MOL2 format, chain P [auth 1] MOL2 format, chain S [auth 2] MOL2 format, chain V [auth 3] MOL2 format, chain Y [auth 4] mmCIF format, chain P [auth 1] mmCIF format, chain S [auth 2] mmCIF format, chain V [auth 3] mmCIF format, chain Y [auth 4]	P [auth 1], S [auth 2], V [auth 3], Y [auth 4]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain P [auth 1] Focus chain S [auth 2] Focus chain V [auth 3] Focus chain Y [auth 4] Interactions & Density Focus chain P [auth 1] Focus chain S [auth 2] Focus chain V [auth 3] Focus chain Y [auth 4]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Q [auth 1] SDF format, chain T [auth 2] SDF format, chain W [auth 3] SDF format, chain Z [auth 4] MOL2 format, chain Q [auth 1] MOL2 format, chain T [auth 2] MOL2 format, chain W [auth 3] MOL2 format, chain Z [auth 4] mmCIF format, chain Q [auth 1] mmCIF format, chain T [auth 2] mmCIF format, chain W [auth 3] mmCIF format, chain Z [auth 4]	Q [auth 1], T [auth 2], W [auth 3], Z [auth 4]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth 1] Focus chain T [auth 2] Focus chain W [auth 3] Focus chain Z [auth 4] Interactions & Density Focus chain Q [auth 1] Focus chain T [auth 2] Focus chain W [auth 3] Focus chain Z [auth 4]