9TAJ | pdb_00009taj

E. coli Complex I WT purified in LMNG

PDB DOI: https://doi.org/10.2210/pdb9TAJ/pdb
EM Map EMD-55748: EMDB EMDataResource

Classification: PROTON TRANSPORT
Organism(s): Escherichia coli BW25113, Escherichia coli BL21(DE3)
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: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 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.

(2026) Nat Commun 17

PubMed: 42386739 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-026-74767-6
Primary Citation Related Structures:
9TAJ, 9TAK, 9TAL, 9TAM, 9TAN, 9TAO

PubMed Abstract:
Complex I is a highly intricate membrane-bound protein complex that powers the cellular energy metabolism by a long-range ( > 300 Å) proton-coupled electron transfer (PCET) reaction. Here, we investigate the highly debated coupling mechanism of Complex I by probing the charge transfer reaction along its functionally central carboxylate pathway (E-channel). By combining biophysical and site-directed mutagenesis experiments with high-resolution (2.6-2.8 Å) cryo-electron microscopy (cryo-EM) and multiscale simulations, we identify a conserved carboxylate switch point (D79 ^NuoA) that mediates proton transfer by establishing a kinetic gate and couples the redox chemistry to proton pumping. We find that mutation of the identified site, as found in patients suffering from severe neurodegenerative disorders, drastically perturbs the charge transfer mechanism, and results in a 20% PCET activity. Our combined findings illustrate mechanistic principles of molecular gates underlying long-range charge transfer reactions, and show how disease mutations perturb the function of conserved switch points in energy transduction.

Organizational Affiliation

Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

Macromolecule Content

Total Structure Weight: 562.96 kDa
Atom Count: 38,186
Modeled Residue Count: 4,698
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 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
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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
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Reference Sequence

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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
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Reference Sequence

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

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit C/D	F [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
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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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit H	G [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: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit J	H [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
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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: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit K	I [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
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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: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit M	J [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
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit A	K [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
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFC3
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit L	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: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit N	M [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
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AFF0
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Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain OA [auth L] MOL2 format, chain OA [auth L] mmCIF format, chain OA [auth L]	OA [auth L]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain OA [auth L] Interactions & Density Focus chain OA [auth L]
3PE Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain ZA [auth N] SDF format, chain XA [auth N] SDF format, chain RA [auth L] SDF format, chain QA [auth L] SDF format, chain PA [auth L] SDF format, chain NA [auth L] SDF format, chain MA [auth L] SDF format, chain LA [auth A] SDF format, chain KA [auth A] SDF format, chain JA [auth M] SDF format, chain IA [auth M] SDF format, chain HA [auth M] SDF format, chain GA [auth J] SDF format, chain FA [auth J] SDF format, chain EA [auth H] SDF format, chain CA [auth H] MOL2 format, chain ZA [auth N] MOL2 format, chain XA [auth N] MOL2 format, chain RA [auth L] MOL2 format, chain QA [auth L] MOL2 format, chain PA [auth L] MOL2 format, chain NA [auth L] MOL2 format, chain MA [auth L] MOL2 format, chain LA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain JA [auth M] MOL2 format, chain IA [auth M] MOL2 format, chain HA [auth M] MOL2 format, chain GA [auth J] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth H] MOL2 format, chain CA [auth H] mmCIF format, chain ZA [auth N] mmCIF format, chain XA [auth N] mmCIF format, chain RA [auth L] mmCIF format, chain QA [auth L] mmCIF format, chain PA [auth L] mmCIF format, chain NA [auth L] mmCIF format, chain MA [auth L] mmCIF format, chain LA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain JA [auth M] mmCIF format, chain IA [auth M] mmCIF format, chain HA [auth M] mmCIF format, chain GA [auth J] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth H] mmCIF format, chain CA [auth H]	CA [auth H] EA [auth H] FA [auth J] GA [auth J] HA [auth M] CA [auth H], EA [auth H], FA [auth J], GA [auth J], HA [auth M], IA [auth M], JA [auth M], KA [auth A], LA [auth A], MA [auth L], NA [auth L], PA [auth L], QA [auth L], RA [auth L], XA [auth N], ZA [auth N]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain CA [auth H] Focus chain EA [auth H] Focus chain FA [auth J] Focus chain GA [auth J] Focus chain HA [auth M] Focus chain IA [auth M] Focus chain JA [auth M] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth L] Focus chain NA [auth L] Focus chain PA [auth L] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain XA [auth N] Focus chain ZA [auth N] Interactions & Density Focus chain CA [auth H] Focus chain EA [auth H] Focus chain FA [auth J] Focus chain GA [auth J] Focus chain HA [auth M] Focus chain IA [auth M] Focus chain JA [auth M] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth L] Focus chain NA [auth L] Focus chain PA [auth L] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain XA [auth N] Focus chain ZA [auth N]
UQ8 (Subject of Investigation/LOI) Query on UQ8 Download:Ideal Coordinates CCD File SDF format, chain WA [auth N] SDF format, chain VA [auth N] MOL2 format, chain WA [auth N] MOL2 format, chain VA [auth N] mmCIF format, chain WA [auth N] mmCIF format, chain VA [auth N]	VA [auth N], WA [auth N]	Ubiquinone-8 C₄₉ H₇₄ O₄ ICFIZJQGJAJRSU-SGHXUWJISA-N		Interactions Focus chain VA [auth N] Focus chain WA [auth N] Interactions & Density Focus chain VA [auth N] Focus chain WA [auth N]
FMN (Subject of Investigation/LOI) 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 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth I] SDF format, chain X [auth G] SDF format, chain S [auth G] SDF format, chain R [auth G] SDF format, chain Q [auth F] SDF format, chain BA [auth B] SDF format, chain AA [auth I] MOL2 format, chain Z [auth I] MOL2 format, chain X [auth G] MOL2 format, chain S [auth G] MOL2 format, chain R [auth G] MOL2 format, chain Q [auth F] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth I] mmCIF format, chain Z [auth I] mmCIF format, chain X [auth G] mmCIF format, chain S [auth G] mmCIF format, chain R [auth G] mmCIF format, chain Q [auth F] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth I]	AA [auth I] BA [auth B] Q [auth F] R [auth G] S [auth G] AA [auth I], BA [auth B], Q [auth F], R [auth G], S [auth G], X [auth G], Z [auth I]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain BA [auth B] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth G] Focus chain X [auth G] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth B] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth G] Focus chain X [auth G] Focus chain Z [auth I]
LFA Query on LFA Download:Ideal Coordinates CCD File SDF format, chain YA [auth N] SDF format, chain DA [auth H] MOL2 format, chain YA [auth N] MOL2 format, chain DA [auth H] mmCIF format, chain YA [auth N] mmCIF format, chain DA [auth H]	DA [auth H], YA [auth N]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain DA [auth H] Focus chain YA [auth N] Interactions & Density Focus chain DA [auth H] Focus chain YA [auth N]
TRD Query on TRD Download:Ideal Coordinates CCD File SDF format, chain UA [auth N] SDF format, chain TA [auth L] SDF format, chain SA [auth L] MOL2 format, chain UA [auth N] MOL2 format, chain TA [auth L] MOL2 format, chain SA [auth L] mmCIF format, chain UA [auth N] mmCIF format, chain TA [auth L] mmCIF format, chain SA [auth L]	SA [auth L], TA [auth L], UA [auth N]	TRIDECANE C₁₃ H₂₈ IIYFAKIEWZDVMP-UHFFFAOYSA-N		Interactions Focus chain SA [auth L] Focus chain TA [auth L] Focus chain UA [auth N] Interactions & Density Focus chain SA [auth L] Focus chain TA [auth L] Focus chain UA [auth N]
FES (Subject of Investigation/LOI) 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 W [auth G] SDF format, chain V [auth G] SDF format, chain U [auth G] SDF format, chain O [auth E] MOL2 format, chain Y [auth I] MOL2 format, chain W [auth G] MOL2 format, chain V [auth G] MOL2 format, chain U [auth G] MOL2 format, chain O [auth E] mmCIF format, chain Y [auth I] mmCIF format, chain W [auth G] mmCIF format, chain V [auth G] mmCIF format, chain U [auth G] mmCIF format, chain O [auth E]	O [auth E], U [auth G], V [auth G], W [auth G], Y [auth I]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain O [auth E] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain Y [auth I] Interactions & Density Focus chain O [auth E] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain Y [auth I]