9TAK | pdb_00009tak

Local refinement of E. coli Complex I WT membrane domain in LMNG

PDB DOI: https://doi.org/10.2210/pdb9TAK/pdb
EM Map EMD-55749: EMDB EMDataResource

Classification: PROTON TRANSPORT
Organism(s): Escherichia coli BW25113
Expression System: Escherichia coli BW25113
Mutation(s): No

Deposited: 2025-11-18 Released: 2026-05-06
Deposition Author(s): Kovalova, T., Beghiah, A., Kaila, V.R.I.
Funding Organization(s): Knut and Alice Wallenberg Foundation, Swedish Research Council

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 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

A Carboxylate Switch Point Controls Long-Range Energy Transduction in Respiratory Complex I

Beghiah, A., Saura, P., Kovalova, T., Hoeser, F., Friedrich, T., Kaila, V.R.I.

To be published.

Macromolecule Content

Total Structure Weight: 299.66 kDa
Atom Count: 19,437
Modeled Residue Count: 2,358
Deposited Residue Count: 2,583
Unique protein chains: 8

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit H	A [auth H]	325	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoH, b2282, JW2277 EC: 7.1.1
UniProt
Find proteins for P0AFD4 (Escherichia coli (strain K12)) Explore P0AFD4 Go to UniProtKB: P0AFD4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFD4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit J	B [auth J]	184	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoJ, b2280, JW2275 EC: 7.1.1
UniProt
Find proteins for P0AFE0 (Escherichia coli (strain K12)) Explore P0AFE0 Go to UniProtKB: P0AFE0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFE0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit K	C [auth K]	100	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoK, b2279, JW2274 EC: 7.1.1
UniProt
Find proteins for P0AFE4 (Escherichia coli (strain K12)) Explore P0AFE4 Go to UniProtKB: P0AFE4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFE4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit M	D [auth M]	509	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoM, b2277, JW2272 EC: 7.1.1
UniProt
Find proteins for P0AFE8 (Escherichia coli (strain K12)) Explore P0AFE8 Go to UniProtKB: P0AFE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFE8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit A	E [auth A]	147	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoA, b2288, JW2283 EC: 7.1.1
UniProt
Find proteins for P0AFC3 (Escherichia coli (strain K12)) Explore P0AFC3 Go to UniProtKB: P0AFC3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFC3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit B	F [auth B]	220	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoB, b2287, JW5875 EC: 7.1.1
UniProt
Find proteins for P0AFC7 (Escherichia coli (strain K12)) Explore P0AFC7 Go to UniProtKB: P0AFC7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFC7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit L	G [auth L]	613	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoL, b2278, JW2273 EC: 7.1.1
UniProt
Find proteins for P33607 (Escherichia coli (strain K12)) Explore P33607 Go to UniProtKB: P33607
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33607
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit N	H [auth N]	485	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoN, b2276, JW2271 EC: 7.1.1
UniProt
Find proteins for P0AFF0 (Escherichia coli (strain K12)) Explore P0AFF0 Go to UniProtKB: P0AFF0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFF0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain U [auth L] MOL2 format, chain U [auth L] mmCIF format, chain U [auth L]	U [auth L]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain U [auth L] Interactions & Density Focus chain U [auth L]
3PE Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain X [auth L] SDF format, chain W [auth L] SDF format, chain V [auth L] SDF format, chain T [auth L] SDF format, chain S [auth L] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth M] SDF format, chain O [auth M] SDF format, chain N [auth M] SDF format, chain M [auth J] SDF format, chain L [auth J] SDF format, chain K [auth H] SDF format, chain I [auth H] SDF format, chain EA [auth N] SDF format, chain CA [auth N] MOL2 format, chain X [auth L] MOL2 format, chain W [auth L] MOL2 format, chain V [auth L] MOL2 format, chain T [auth L] MOL2 format, chain S [auth L] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth M] MOL2 format, chain O [auth M] MOL2 format, chain N [auth M] MOL2 format, chain M [auth J] MOL2 format, chain L [auth J] MOL2 format, chain K [auth H] MOL2 format, chain I [auth H] MOL2 format, chain EA [auth N] MOL2 format, chain CA [auth N] mmCIF format, chain X [auth L] mmCIF format, chain W [auth L] mmCIF format, chain V [auth L] mmCIF format, chain T [auth L] mmCIF format, chain S [auth L] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth M] mmCIF format, chain O [auth M] mmCIF format, chain N [auth M] mmCIF format, chain M [auth J] mmCIF format, chain L [auth J] mmCIF format, chain K [auth H] mmCIF format, chain I [auth H] mmCIF format, chain EA [auth N] mmCIF format, chain CA [auth N]	CA [auth N] EA [auth N] I [auth H] K [auth H] L [auth J] CA [auth N], EA [auth N], I [auth H], K [auth H], L [auth J], M [auth J], N [auth M], O [auth M], P [auth M], Q [auth A], R [auth A], S [auth L], T [auth L], V [auth L], W [auth L], X [auth L]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain CA [auth N] Focus chain EA [auth N] Focus chain I [auth H] Focus chain K [auth H] Focus chain L [auth J] Focus chain M [auth J] Focus chain N [auth M] Focus chain O [auth M] Focus chain P [auth M] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth L] Focus chain T [auth L] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L] Interactions & Density Focus chain CA [auth N] Focus chain EA [auth N] Focus chain I [auth H] Focus chain K [auth H] Focus chain L [auth J] Focus chain M [auth J] Focus chain N [auth M] Focus chain O [auth M] Focus chain P [auth M] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth L] Focus chain T [auth L] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L]
UQ8 (Subject of Investigation/LOI) Query on UQ8 Download:Ideal Coordinates CCD File SDF format, chain FA [auth N] SDF format, chain BA [auth N] MOL2 format, chain FA [auth N] MOL2 format, chain BA [auth N] mmCIF format, chain FA [auth N] mmCIF format, chain BA [auth N]	BA [auth N], FA [auth N]	Ubiquinone-8 C₄₉ H₇₄ O₄ ICFIZJQGJAJRSU-SGHXUWJISA-N		Interactions Focus chain BA [auth N] Focus chain FA [auth N] Interactions & Density Focus chain BA [auth N] Focus chain FA [auth N]
LFA Query on LFA Download:Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain DA [auth N] MOL2 format, chain J [auth H] MOL2 format, chain DA [auth N] mmCIF format, chain J [auth H] mmCIF format, chain DA [auth N]	DA [auth N], J [auth H]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain DA [auth N] Focus chain J [auth H] Interactions & Density Focus chain DA [auth N] Focus chain J [auth H]
TRD Query on TRD Download:Ideal Coordinates CCD File SDF format, chain Z [auth L] SDF format, chain Y [auth L] SDF format, chain AA [auth N] MOL2 format, chain Z [auth L] MOL2 format, chain Y [auth L] MOL2 format, chain AA [auth N] mmCIF format, chain Z [auth L] mmCIF format, chain Y [auth L] mmCIF format, chain AA [auth N]	AA [auth N], Y [auth L], Z [auth L]	TRIDECANE C₁₃ H₂₈ IIYFAKIEWZDVMP-UHFFFAOYSA-N		Interactions Focus chain AA [auth N] Focus chain Y [auth L] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth N] Focus chain Y [auth L] Focus chain Z [auth L]