9CD6 | pdb_00009cd6

Cryo-EM structure of respiratory supercomplex I in open state

PDB DOI: https://doi.org/10.2210/pdb9CD6/pdb
EM Map EMD-45463: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Sus scrofa
Mutation(s): No

Deposited: 2024-06-24 Released: 2025-08-06
Deposition Author(s): Zhang, Z., Maharjan, R., Tringides, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 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

Cryo-EM structure of respiratory supercomplex I in open state

Zhang, Z., Maharjan, R., Tringides, M.

To be published.

Macromolecule Content

Total Structure Weight: 1,072.04 kDa
Atom Count: 65,688
Modeled Residue Count: 8,163
Deposited Residue Count: 9,449
Unique protein chains: 44

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial	A [auth B]	464	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for A0A4X1SZP7 (Sus scrofa) Explore A0A4X1SZP7 Go to UniProtKB: A0A4X1SZP7
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UniProt Group	A0A4X1SZP7
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial	B [auth C]	469	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for A0A480XQH6 (Sus scrofa) Explore A0A480XQH6 Go to UniProtKB: A0A480XQH6
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UniProt Group	A0A480XQH6
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial	C [auth D]	264	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A286ZNN4 (Sus scrofa) Explore A0A286ZNN4 Go to UniProtKB: A0A286ZNN4
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UniProt Group	A0A286ZNN4
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial	D [auth E]	249	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for A0A4X1VRV3 (Sus scrofa) Explore A0A4X1VRV3 Go to UniProtKB: A0A4X1VRV3
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UniProt Group	A0A4X1VRV3
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial	E [auth F]	123	Sus scrofa	Mutation(s): 0
UniProt
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UniProt Group	A0A4X1THU2
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial	F [auth H]	212	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for A0A286ZUN9 (Sus scrofa) Explore A0A286ZUN9 Go to UniProtKB: A0A286ZUN9
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UniProt Group	A0A286ZUN9
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial	G [auth I]	196	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VTL7 (Sus scrofa) Explore A0A4X1VTL7 Go to UniProtKB: A0A4X1VTL7
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UniProt Group	A0A4X1VTL7
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial	H [auth J]	175	Sus scrofa	Mutation(s): 0
UniProt
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UniProt Group	G8IFA6
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12	I [auth K]	145	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SQP4 (Sus scrofa) Explore F1SQP4 Go to UniProtKB: F1SQP4
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UniProt Group	F1SQP4
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial	J [auth L]	372	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SL07 (Sus scrofa) Explore F1SL07 Go to UniProtKB: F1SL07
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UniProt Group	F1SL07
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1	K [auth N]	116	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D0UWW0 (Sus scrofa) Explore A0A8D0UWW0 Go to UniProtKB: A0A8D0UWW0
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UniProt Group	A0A8D0UWW0
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	L [auth O], U [auth X]	156	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1WW27 (Sus scrofa) Explore A0A8D1WW27 Go to UniProtKB: A0A8D1WW27
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UniProt Group	A0A8D1WW27
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	M [auth P]	99	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1FN21 (Sus scrofa) Explore A0A8D1FN21 Go to UniProtKB: A0A8D1FN21
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UniProt Group	A0A8D1FN21
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6	N [auth Q]	154	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D0Z0K9 (Sus scrofa) Explore A0A8D0Z0K9 Go to UniProtKB: A0A8D0Z0K9
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UniProt Group	A0A8D0Z0K9
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial	O [auth R]	110	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A480TFA5 (Sus scrofa) Explore A0A480TFA5 Go to UniProtKB: A0A480TFA5
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UniProt Group	A0A480TFA5
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1	P [auth S]	70	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D0TJQ4 (Sus scrofa) Explore A0A8D0TJQ4 Go to UniProtKB: A0A8D0TJQ4
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UniProt Group	A0A8D0TJQ4
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3	Q [auth T]	169	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VPG4 (Sus scrofa) Explore A0A4X1VPG4 Go to UniProtKB: A0A4X1VPG4
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UniProt Group	A0A4X1VPG4
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial	R [auth U]	357	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SIS9 (Sus scrofa) Explore F1SIS9 Go to UniProtKB: F1SIS9
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UniProt Group	F1SIS9
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11	S [auth V]	141	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for I3LGM4 (Sus scrofa) Explore I3LGM4 Go to UniProtKB: I3LGM4
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UniProt Group	I3LGM4
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit A13	T [auth W]	144	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D0K655 (Sus scrofa) Explore A0A8D0K655 Go to UniProtKB: A0A8D0K655
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UniProt Group	A0A8D0K655
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B2	V [auth Y]	105	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1G9F4 (Sus scrofa) Explore A0A8D1G9F4 Go to UniProtKB: A0A8D1G9F4
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UniProt Group	A0A8D1G9F4
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3	W [auth Z]	114	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D0INK7 (Sus scrofa) Explore A0A8D0INK7 Go to UniProtKB: A0A8D0INK7
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UniProt Group	A0A8D0INK7
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial	X [auth a]	189	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SGC6 (Sus scrofa) Explore F1SGC6 Go to UniProtKB: F1SGC6
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UniProt Group	F1SGC6
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial	Y [auth c]	186	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1RWL7 (Sus scrofa) Explore F1RWL7 Go to UniProtKB: F1RWL7
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UniProt Group	F1RWL7
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10	Z [auth d]	176	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D0R7A9 (Sus scrofa) Explore A0A8D0R7A9 Go to UniProtKB: A0A8D0R7A9
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UniProt Group	A0A8D0R7A9
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial	AA [auth e]	154	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1EYI7 (Sus scrofa) Explore A0A8D1EYI7 Go to UniProtKB: A0A8D1EYI7
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UniProt Group	A0A8D1EYI7
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial	BA [auth f]	76	Sus scrofa	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 subunit C2	CA [auth g]	122	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A480JRW3 (Sus scrofa) Explore A0A480JRW3 Go to UniProtKB: A0A480JRW3
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UniProt Group	A0A480JRW3
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5	DA [auth h]	106	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VX77 (Sus scrofa) Explore A0A4X1VX77 Go to UniProtKB: A0A4X1VX77
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UniProt Group	A0A4X1VX77
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 2	EA [auth i]	347	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for O79875 (Sus scrofa) Explore O79875 Go to UniProtKB: O79875
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UniProt Group	O79875
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 3	FA [auth j]	115	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for O79880 (Sus scrofa) Explore O79880 Go to UniProtKB: O79880
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UniProt Group	O79880
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4L	GA [auth k]	98	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for P56632 (Sus scrofa) Explore P56632 Go to UniProtKB: P56632
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UniProt Group	P56632
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 5	HA [auth l]	606	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for Q9TDR1 (Sus scrofa) Explore Q9TDR1 Go to UniProtKB: Q9TDR1
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UniProt Group	Q9TDR1
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 6	IA [auth m]	175	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for O79882 (Sus scrofa) Explore O79882 Go to UniProtKB: O79882
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UniProt Group	O79882
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1	JA [auth n]	58	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1SNY5 (Sus scrofa) Explore A0A4X1SNY5 Go to UniProtKB: A0A4X1SNY5
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UniProt Group	A0A4X1SNY5
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4	KA [auth o]	129	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1T6M0 (Sus scrofa) Explore A0A4X1T6M0 Go to UniProtKB: A0A4X1T6M0
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UniProt Group	A0A4X1T6M0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9	LA [auth p]	221	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for K7GSE5 (Sus scrofa) Explore K7GSE5 Go to UniProtKB: K7GSE5
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UniProt Group	K7GSE5
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4	MA [auth q]	459	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for O79881 (Sus scrofa) Explore O79881 Go to UniProtKB: O79881
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UniProt Group	O79881
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 1	NA [auth r]	318	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for O79874 (Sus scrofa) Explore O79874 Go to UniProtKB: O79874
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UniProt Group	O79874
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8	OA [auth s]	249	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SLR1 (Sus scrofa) Explore F1SLR1 Go to UniProtKB: F1SLR1
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UniProt Group	F1SLR1
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7	PA [auth t]	137	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SCH1 (Sus scrofa) Explore F1SCH1 Go to UniProtKB: F1SCH1
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UniProt Group	F1SCH1
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial	QA [auth G]	727	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2
UniProt
Find proteins for A0A287ARY3 (Sus scrofa) Explore A0A287ARY3 Go to UniProtKB: A0A287ARY3
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UniProt Group	A0A287ARY3
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7	RA [auth M]	113	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8W4F7N8 (Sus scrofa) Explore A0A8W4F7N8 Go to UniProtKB: A0A8W4F7N8
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UniProt Group	A0A8W4F7N8
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6	SA [auth b]	128	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1UIV8 (Sus scrofa) Explore A0A4X1UIV8 Go to UniProtKB: A0A4X1UIV8
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UniProt Group	A0A4X1UIV8
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Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain ZA [auth L] MOL2 format, chain ZA [auth L] mmCIF format, chain ZA [auth L]	ZA [auth L]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain ZA [auth L] Interactions & Density Focus chain ZA [auth L]
ZMP Query on ZMP Download Ideal Coordinates CCD File SDF format, chain AB [auth Q] MOL2 format, chain AB [auth Q] mmCIF format, chain AB [auth Q]	AB [auth Q]	S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate C₂₅ H₄₉ N₂ O₈ P S HDTINWYIVVMRIN-HSZRJFAPSA-N		Interactions Focus chain AB [auth Q] Interactions & Density Focus chain AB [auth Q]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain TA [auth B] MOL2 format, chain TA [auth B] mmCIF format, chain TA [auth B]	TA [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain TA [auth B] Interactions & Density Focus chain TA [auth B]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain BB [auth G] SDF format, chain CB [auth G] SDF format, chain UA [auth B] SDF format, chain WA [auth H] SDF format, chain XA [auth H] SDF format, chain YA [auth I] MOL2 format, chain BB [auth G] MOL2 format, chain CB [auth G] MOL2 format, chain UA [auth B] MOL2 format, chain WA [auth H] MOL2 format, chain XA [auth H] MOL2 format, chain YA [auth I] mmCIF format, chain BB [auth G] mmCIF format, chain CB [auth G] mmCIF format, chain UA [auth B] mmCIF format, chain WA [auth H] mmCIF format, chain XA [auth H] mmCIF format, chain YA [auth I]	BB [auth G] CB [auth G] UA [auth B] WA [auth H] XA [auth H] BB [auth G], CB [auth G], UA [auth B], WA [auth H], XA [auth H], YA [auth I]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain BB [auth G] Focus chain CB [auth G] Focus chain UA [auth B] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain YA [auth I] Interactions & Density Focus chain BB [auth G] Focus chain CB [auth G] Focus chain UA [auth B] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain YA [auth I]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain DB [auth G] SDF format, chain VA [auth E] MOL2 format, chain DB [auth G] MOL2 format, chain VA [auth E] mmCIF format, chain DB [auth G] mmCIF format, chain VA [auth E]	DB [auth G], VA [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain DB [auth G] Focus chain VA [auth E] Interactions & Density Focus chain DB [auth G] Focus chain VA [auth E]