9TAM | pdb_00009tam

E. coli Complex I D79N NuoA mutant purified in LMNG

PDB DOI: https://doi.org/10.2210/pdb9TAM/pdb
EM Map EMD-55751: EMDB EMDataResource

Classification: PROTON TRANSPORT
Organism(s): Escherichia coli BL21(DE3), Escherichia coli BW25113
Expression System: Escherichia coli BL21(DE3), Escherichia coli BW25113
Mutation(s): No

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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.96 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.

To be published.

Macromolecule Content

Total Structure Weight: 560.13 kDa
Atom Count: 38,164
Modeled Residue Count: 4,717
Deposited Residue Count: 4,900
Unique protein chains: 13

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit C/D	A [auth C]	600	Escherichia coli BL21(DE3)	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
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit E	B [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
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Reference Sequence

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| 3D Structure

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

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

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit I	E [auth I]	180	Escherichia coli BL21(DE3)	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
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Reference Sequence

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

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit K	G [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
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit L	H [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
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33607
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit M	I [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
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFE8
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit N	J [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
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit B	K [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
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit H	L [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
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit A	M [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
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Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PE Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain EA [auth L] SDF format, chain FA [auth M] SDF format, chain Z [auth J] SDF format, chain SA [auth A] SDF format, chain QA [auth H] SDF format, chain PA [auth H] SDF format, chain LA [auth N] SDF format, chain KA [auth N] SDF format, chain JA [auth N] SDF format, chain IA [auth N] SDF format, chain DA [auth L] SDF format, chain CA [auth L] MOL2 format, chain EA [auth L] MOL2 format, chain FA [auth M] MOL2 format, chain Z [auth J] MOL2 format, chain SA [auth A] MOL2 format, chain QA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain LA [auth N] MOL2 format, chain KA [auth N] MOL2 format, chain JA [auth N] MOL2 format, chain IA [auth N] MOL2 format, chain DA [auth L] MOL2 format, chain CA [auth L] mmCIF format, chain EA [auth L] mmCIF format, chain FA [auth M] mmCIF format, chain Z [auth J] mmCIF format, chain SA [auth A] mmCIF format, chain QA [auth H] mmCIF format, chain PA [auth H] mmCIF format, chain LA [auth N] mmCIF format, chain KA [auth N] mmCIF format, chain JA [auth N] mmCIF format, chain IA [auth N] mmCIF format, chain DA [auth L] mmCIF format, chain CA [auth L]	CA [auth L] DA [auth L] EA [auth L] FA [auth M] IA [auth N] CA [auth L], DA [auth L], EA [auth L], FA [auth M], IA [auth N], JA [auth N], KA [auth N], LA [auth N], PA [auth H], QA [auth H], SA [auth A], Z [auth J]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain CA [auth L] Focus chain DA [auth L] Focus chain EA [auth L] Focus chain FA [auth M] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain LA [auth N] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain SA [auth A] Focus chain Z [auth J] Interactions & Density Focus chain CA [auth L] Focus chain DA [auth L] Focus chain EA [auth L] Focus chain FA [auth M] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain LA [auth N] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain SA [auth A] Focus chain Z [auth J]
UQ8 (Subject of Investigation/LOI) Query on UQ8 Download:Ideal Coordinates CCD File SDF format, chain MA [auth N] SDF format, chain NA [auth N] MOL2 format, chain MA [auth N] MOL2 format, chain NA [auth N] mmCIF format, chain MA [auth N] mmCIF format, chain NA [auth N]	MA [auth N], NA [auth N]	Ubiquinone-8 C₄₉ H₇₄ O₄ ICFIZJQGJAJRSU-SGHXUWJISA-N		Interactions Focus chain MA [auth N] Focus chain NA [auth N] Interactions & Density Focus chain MA [auth N] Focus chain NA [auth N]
7PH Query on 7PH Download:Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain BA [auth J] SDF format, chain RA [auth H] SDF format, chain HA [auth M] SDF format, chain GA [auth M] MOL2 format, chain AA [auth J] MOL2 format, chain BA [auth J] MOL2 format, chain RA [auth H] MOL2 format, chain HA [auth M] MOL2 format, chain GA [auth M] mmCIF format, chain AA [auth J] mmCIF format, chain BA [auth J] mmCIF format, chain RA [auth H] mmCIF format, chain HA [auth M] mmCIF format, chain GA [auth M]	AA [auth J], BA [auth J], GA [auth M], HA [auth M], RA [auth H]	(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate C₂₉ H₅₇ O₈ P UYOIGTVMJVHOSC-HHHXNRCGSA-N		Interactions Focus chain AA [auth J] Focus chain BA [auth J] Focus chain GA [auth M] Focus chain HA [auth M] Focus chain RA [auth H] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth J] Focus chain GA [auth M] Focus chain HA [auth M] Focus chain RA [auth H]
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain P [auth F] MOL2 format, chain P [auth F] mmCIF format, chain P [auth F]	P [auth F]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain P [auth F] Interactions & Density Focus chain P [auth F]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain X [auth I] SDF format, chain W [auth I] SDF format, chain S [auth G] SDF format, chain R [auth G] SDF format, chain Q [auth G] SDF format, chain OA [auth B] SDF format, chain O [auth F] MOL2 format, chain X [auth I] MOL2 format, chain W [auth I] MOL2 format, chain S [auth G] MOL2 format, chain R [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth F] mmCIF format, chain X [auth I] mmCIF format, chain W [auth I] mmCIF format, chain S [auth G] mmCIF format, chain R [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth F]	O [auth F] OA [auth B] Q [auth G] R [auth G] S [auth G] O [auth F], OA [auth B], Q [auth G], R [auth G], S [auth G], W [auth I], X [auth I]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain O [auth F] Focus chain OA [auth B] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain W [auth I] Focus chain X [auth I] Interactions & Density Focus chain O [auth F] Focus chain OA [auth B] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain W [auth I] Focus chain X [auth I]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain T [auth G] SDF format, chain N [auth E] MOL2 format, chain T [auth G] MOL2 format, chain N [auth E] mmCIF format, chain T [auth G] mmCIF format, chain N [auth E]	N [auth E], T [auth G]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain N [auth E] Focus chain T [auth G] Interactions & Density Focus chain N [auth E] Focus chain T [auth G]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Y [auth I] SDF format, chain V [auth G] SDF format, chain U [auth G] MOL2 format, chain Y [auth I] MOL2 format, chain V [auth G] MOL2 format, chain U [auth G] mmCIF format, chain Y [auth I] mmCIF format, chain V [auth G] mmCIF format, chain U [auth G]	U [auth G], V [auth G], Y [auth I]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain U [auth G] Focus chain V [auth G] Focus chain Y [auth I] Interactions & Density Focus chain U [auth G] Focus chain V [auth G] Focus chain Y [auth I]