9Q94 | pdb_00009q94

CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 3

PDB DOI: https://doi.org/10.2210/pdb9Q94/pdb
EM Map EMD-52917: EMDB EMDataResource
NAKB: 9Q94

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): Gao, F., Zhang, X.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 5.80 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

Subunit specialisation in AAA+ proteins and substrate unfolding during transcription complex remodelling

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

To be published.

Macromolecule Content

Total Structure Weight: 650.28 kDa
Atom Count: 26,953
Modelled Residue Count: 5,221
Deposited Residue Count: 5,662
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 6] B [auth 1] C [auth 2] D [auth 3] E [auth 4] A [auth 6], B [auth 1], C [auth 2], D [auth 3], E [auth 4], F [auth 5]	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
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma-54 factor	I [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 A0A0N9UTC1 (Klebsiella pneumoniae) Explore A0A0N9UTC1 Go to UniProtKB: A0A0N9UTC1
Entity Groups
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UniProt Group	A0A0N9UTC1
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	J [auth A], K [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
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UniProt Group	P0A7Z4
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	L [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
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UniProt Group	P0A8V2
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	M [auth D]	1,376	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
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UniProt Group	P0A8T7
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	N [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
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UniProt Group	P0A800
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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (34-MER)	G [auth N]	34	Escherichia coli K-12
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Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (34-MER)	H [auth T]	34	Escherichia coli K-12
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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 5] 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 5] 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 5] 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 5], 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 5] 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 5] 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 BA [auth 5] SDF format, chain P [auth 1] SDF format, chain S [auth 2] SDF format, chain V [auth 3] SDF format, chain Z [auth 5] MOL2 format, chain BA [auth 5] MOL2 format, chain P [auth 1] MOL2 format, chain S [auth 2] MOL2 format, chain V [auth 3] MOL2 format, chain Z [auth 5] mmCIF format, chain BA [auth 5] mmCIF format, chain P [auth 1] mmCIF format, chain S [auth 2] mmCIF format, chain V [auth 3] mmCIF format, chain Z [auth 5]	BA [auth 5], P [auth 1], S [auth 2], V [auth 3], Z [auth 5]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain BA [auth 5] Focus chain P [auth 1] Focus chain S [auth 2] Focus chain V [auth 3] Focus chain Z [auth 5] Interactions & Density Focus chain BA [auth 5] Focus chain P [auth 1] Focus chain S [auth 2] Focus chain V [auth 3] Focus chain Z [auth 5]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth 5] SDF format, chain Q [auth 2] SDF format, chain T [auth 2] SDF format, chain W [auth 3] SDF format, chain Y [auth 4] MOL2 format, chain CA [auth 5] MOL2 format, chain Q [auth 2] MOL2 format, chain T [auth 2] MOL2 format, chain W [auth 3] MOL2 format, chain Y [auth 4] mmCIF format, chain CA [auth 5] mmCIF format, chain Q [auth 2] mmCIF format, chain T [auth 2] mmCIF format, chain W [auth 3] mmCIF format, chain Y [auth 4]	CA [auth 5], Q [auth 2], T [auth 2], W [auth 3], Y [auth 4]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth 5] Focus chain Q [auth 2] Focus chain T [auth 2] Focus chain W [auth 3] Focus chain Y [auth 4] Interactions & Density Focus chain CA [auth 5] Focus chain Q [auth 2] Focus chain T [auth 2] Focus chain W [auth 3] Focus chain Y [auth 4]