9TAN | pdb_00009tan

Local refinement of E. coli Complex I D79N NuoA mutant hydrophilic domain in LMNG

PDB DOI: https://doi.org/10.2210/pdb9TAN/pdb
EM Map EMD-55752: 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): Beghiah, A., Kovalova, T., Kaila, V.R.I.
Funding Organization(s): Knut and Alice Wallenberg Foundation, Swedish Research Council

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.59 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

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, F., Kaila, V.R.I.

To be published.

Macromolecule Content

Total Structure Weight: 288.34 kDa
Atom Count: 19,678
Modeled Residue Count: 2,449
Deposited Residue Count: 2,537
Unique protein chains: 6

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit B	A [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

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit C/D	B [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

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit E	C [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

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit F	D [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

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit G	E [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

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit I	F [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

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 K [auth F] MOL2 format, chain K [auth F] mmCIF format, chain K [auth F]	K [auth F]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain K [auth F] Interactions & Density Focus chain K [auth F]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth F] SDF format, chain L [auth G] SDF format, chain M [auth G] SDF format, chain N [auth G] SDF format, chain R [auth I] SDF format, chain S [auth I] MOL2 format, chain G [auth B] MOL2 format, chain J [auth F] MOL2 format, chain L [auth G] MOL2 format, chain M [auth G] MOL2 format, chain N [auth G] MOL2 format, chain R [auth I] MOL2 format, chain S [auth I] mmCIF format, chain G [auth B] mmCIF format, chain J [auth F] mmCIF format, chain L [auth G] mmCIF format, chain M [auth G] mmCIF format, chain N [auth G] mmCIF format, chain R [auth I] mmCIF format, chain S [auth I]	G [auth B] J [auth F] L [auth G] M [auth G] N [auth G] G [auth B], J [auth F], L [auth G], M [auth G], N [auth G], R [auth I], S [auth I]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth F] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain R [auth I] Focus chain S [auth I] Interactions & Density Focus chain G [auth B] Focus chain J [auth F] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain R [auth I] Focus chain S [auth I]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain O [auth G] SDF format, chain H [auth E] MOL2 format, chain O [auth G] MOL2 format, chain H [auth E] mmCIF format, chain O [auth G] mmCIF format, chain H [auth E]	H [auth E], O [auth G]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain H [auth E] Focus chain O [auth G] Interactions & Density Focus chain H [auth E] Focus chain O [auth G]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth E] SDF format, chain P [auth G] SDF format, chain T [auth I] SDF format, chain Q [auth G] MOL2 format, chain I [auth E] MOL2 format, chain P [auth G] MOL2 format, chain T [auth I] MOL2 format, chain Q [auth G] mmCIF format, chain I [auth E] mmCIF format, chain P [auth G] mmCIF format, chain T [auth I] mmCIF format, chain Q [auth G]	I [auth E], P [auth G], Q [auth G], T [auth I]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth E] Focus chain P [auth G] Focus chain Q [auth G] Focus chain T [auth I] Interactions & Density Focus chain I [auth E] Focus chain P [auth G] Focus chain Q [auth G] Focus chain T [auth I]