9TAL | pdb_00009tal

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

PDB DOI: https://doi.org/10.2210/pdb9TAL/pdb
EM Map EMD-55750: 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: 2.66 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: 449.82 kDa
Atom Count: 20,425
Modeled Residue Count: 2,552
Deposited Residue Count: 3,984
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 E	A [auth E]	166	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoE, b2285, JW2280 EC: 7.1.1
UniProt
Find proteins for P0AFD1 (Escherichia coli (strain K12)) Explore P0AFD1 Go to UniProtKB: P0AFD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFD1
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 F	B [auth F]	461	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoF, b2284, JW2279 EC: 7.1.1
UniProt
Find proteins for P31979 (Escherichia coli (strain K12)) Explore P31979 Go to UniProtKB: P31979
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31979
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 G	C [auth G]	910	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoG, b2283, JW2278 EC: 7.1.1
UniProt
Find proteins for P33602 (Escherichia coli (strain K12)) Explore P33602 Go to UniProtKB: P33602
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33602
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 I	D [auth I]	180	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoI, b2281, JW2276 EC: 7.1.1
UniProt
Find proteins for P0AFD6 (Escherichia coli (strain K12)) Explore P0AFD6 Go to UniProtKB: P0AFD6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFD6
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 B	E [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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit C/D	F [auth C]	600	Escherichia coli BW25113	Mutation(s): 0 Gene Names: nuoC, nuoCD, nuoD, b2286, JW5375 EC: 7.1.1
UniProt
Find proteins for P33599 (Escherichia coli (strain K12)) Explore P33599 Go to UniProtKB: P33599
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33599
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 A	G [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: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit H	H, I [auth J], J [auth K], K [auth L]	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain N [auth F] MOL2 format, chain N [auth F] mmCIF format, chain N [auth F]	N [auth F]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain N [auth F] Interactions & Density Focus chain N [auth F]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain P [auth G] SDF format, chain Q [auth G] SDF format, chain V [auth G] SDF format, chain X [auth I] SDF format, chain Y [auth I] SDF format, chain Z [auth B] MOL2 format, chain O [auth F] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain V [auth G] MOL2 format, chain X [auth I] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth B] mmCIF format, chain O [auth F] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain V [auth G] mmCIF format, chain X [auth I] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth B]	O [auth F] P [auth G] Q [auth G] V [auth G] X [auth I] O [auth F], P [auth G], Q [auth G], V [auth G], X [auth I], Y [auth I], Z [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth G] Focus chain V [auth G] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth B] Interactions & Density Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth G] Focus chain V [auth G] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth B]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain R [auth G] MOL2 format, chain L [auth E] MOL2 format, chain R [auth G] mmCIF format, chain L [auth E] mmCIF format, chain R [auth G]	L [auth E], R [auth G]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain L [auth E] Focus chain R [auth G] Interactions & Density Focus chain L [auth E] Focus chain R [auth G]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain S [auth G] SDF format, chain T [auth G] SDF format, chain U [auth G] SDF format, chain W [auth I] MOL2 format, chain M [auth E] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G] MOL2 format, chain W [auth I] mmCIF format, chain M [auth E] mmCIF format, chain S [auth G] mmCIF format, chain T [auth G] mmCIF format, chain U [auth G] mmCIF format, chain W [auth I]	M [auth E], S [auth G], T [auth G], U [auth G], W [auth I]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain W [auth I] Interactions & Density Focus chain M [auth E] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain W [auth I]