6ZKA | pdb_00006zka

Membrane domain of open complex I during turnover

PDB DOI: https://doi.org/10.2210/pdb6ZKA/pdb
EM Map EMD-11242: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Ovis aries
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2020-06-30 Released: 2020-10-07
Deposition Author(s): Kampjut, D., Sazanov, L.A.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The coupling mechanism of mammalian respiratory complex I.

Kampjut, D., Sazanov, L.A.

(2020) Science 370

PubMed: 32972993 Search on PubMed
DOI: https://doi.org/10.1126/science.abc4209
Primary Citation Related Structures:
6ZK9, 6ZKA, 6ZKB, 6ZKC, 6ZKD, 6ZKE, 6ZKF, 6ZKG, 6ZKH, 6ZKI, 6ZKJ, 6ZKK, 6ZKL, 6ZKM, 6ZKN, 6ZKO, 6ZKP, 6ZKQ, 6ZKR, 6ZKS, 6ZKT, 6ZKU, 6ZKV

PubMed Abstract:
Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.

Organizational Affiliation

IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria.

Macromolecule Content

Total Structure Weight: 660.27 kDa
Atom Count: 40,800
Modeled Residue Count: 4,694
Deposited Residue Count: 5,550
Unique protein chains: 29

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 3	A	115	Ovis aries	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O78753 (Ovis aries) Explore O78753 Go to UniProtKB: O78753
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O78753
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 1	B [auth H]	318	Ovis aries	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O78747 (Ovis aries) Explore O78747 Go to UniProtKB: O78747
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O78747
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 6	C [auth J]	175	Ovis aries	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O78757 (Ovis aries) Explore O78757 Go to UniProtKB: O78757
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O78757
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4L	D [auth K]	98	Ovis aries	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O78754 (Ovis aries) Explore O78754 Go to UniProtKB: O78754
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O78754
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 5	E [auth L]	606	Ovis aries	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O78756 (Ovis aries) Explore O78756 Go to UniProtKB: O78756
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O78756
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4	F [auth M]	459	Ovis aries	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O78755 (Ovis aries) Explore O78755 Go to UniProtKB: O78755
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O78755
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 2	G [auth N]	347	Ovis aries	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O78748 (Ovis aries) Explore O78748 Go to UniProtKB: O78748
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O78748
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, B14.7 subunit	H [auth V]	141	Ovis aries	Mutation(s): 0

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B5	I [auth W]	189	Ovis aries	Mutation(s): 0

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	J [auth X]	157	Ovis aries	Mutation(s): 0

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8	K [auth Y]	172	Ovis aries	Mutation(s): 0

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, PDSW subunit	L [auth Z]	175	Ovis aries	Mutation(s): 0

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial	M [auth k]	355	Ovis aries	Mutation(s): 0

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit S5	N [auth l]	106	Ovis aries	Mutation(s): 0

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit A3	O [auth m]	84	Ovis aries	Mutation(s): 0

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B3	P [auth n]	98	Ovis aries	Mutation(s): 0

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 subunit C2	Q [auth o]	122	Ovis aries	Mutation(s): 0

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B4	R [auth p]	130	Ovis aries	Mutation(s): 0

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, B16.6 subunit	S [auth q]	144	Ovis aries	Mutation(s): 0

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, B17 subunit	T [auth r]	128	Ovis aries	Mutation(s): 0

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B7	U [auth s]	137	Ovis aries	Mutation(s): 0

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B9	V [auth t]	179	Ovis aries	Mutation(s): 0

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B2	W [auth u]	108	Ovis aries	Mutation(s): 0

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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial	X [auth v]	186	Ovis aries	Mutation(s): 0

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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, ESSS subunit	Y [auth w]	154	Ovis aries	Mutation(s): 0

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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, KFYI subunit	Z [auth x]	76	Ovis aries	Mutation(s): 0

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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, MNLL subunit	AA [auth y]	58	Ovis aries	Mutation(s): 0

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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, MWFE subunit	BA [auth z]	70	Ovis aries	Mutation(s): 0

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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, ND4L subunit	CA [auth 4]	463	Ovis aries	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain BB [auth o] SDF format, chain LA [auth L] SDF format, chain PA [auth M] SDF format, chain TA [auth V] SDF format, chain UA [auth V] SDF format, chain VA [auth W] SDF format, chain XA [auth Y] MOL2 format, chain BB [auth o] MOL2 format, chain LA [auth L] MOL2 format, chain PA [auth M] MOL2 format, chain TA [auth V] MOL2 format, chain UA [auth V] MOL2 format, chain VA [auth W] MOL2 format, chain XA [auth Y] mmCIF format, chain BB [auth o] mmCIF format, chain LA [auth L] mmCIF format, chain PA [auth M] mmCIF format, chain TA [auth V] mmCIF format, chain UA [auth V] mmCIF format, chain VA [auth W] mmCIF format, chain XA [auth Y]	BB [auth o] LA [auth L] PA [auth M] TA [auth V] UA [auth V] BB [auth o], LA [auth L], PA [auth M], TA [auth V], UA [auth V], VA [auth W], XA [auth Y]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BB [auth o] Focus chain LA [auth L] Focus chain PA [auth M] Focus chain TA [auth V] Focus chain UA [auth V] Focus chain VA [auth W] Focus chain XA [auth Y] Interactions & Density Focus chain BB [auth o] Focus chain LA [auth L] Focus chain PA [auth M] Focus chain TA [auth V] Focus chain UA [auth V] Focus chain VA [auth W] Focus chain XA [auth Y]
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain EB [auth w] SDF format, chain GA [auth H] SDF format, chain KA [auth L] SDF format, chain OA [auth M] MOL2 format, chain DA [auth A] MOL2 format, chain EB [auth w] MOL2 format, chain GA [auth H] MOL2 format, chain KA [auth L] MOL2 format, chain OA [auth M] mmCIF format, chain DA [auth A] mmCIF format, chain EB [auth w] mmCIF format, chain GA [auth H] mmCIF format, chain KA [auth L] mmCIF format, chain OA [auth M]	DA [auth A], EB [auth w], GA [auth H], KA [auth L], OA [auth M]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain DA [auth A] Focus chain EB [auth w] Focus chain GA [auth H] Focus chain KA [auth L] Focus chain OA [auth M] Interactions & Density Focus chain DA [auth A] Focus chain EB [auth w] Focus chain GA [auth H] Focus chain KA [auth L] Focus chain OA [auth M]
3PE Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain AB [auth o] SDF format, chain CB [auth p] SDF format, chain FA [auth H] SDF format, chain HA [auth K] SDF format, chain IA [auth L] SDF format, chain JA [auth L] SDF format, chain MA [auth L] SDF format, chain NA [auth M] SDF format, chain QA [auth N] SDF format, chain RA [auth V] SDF format, chain SA [auth V] SDF format, chain ZA [auth m] MOL2 format, chain AB [auth o] MOL2 format, chain CB [auth p] MOL2 format, chain FA [auth H] MOL2 format, chain HA [auth K] MOL2 format, chain IA [auth L] MOL2 format, chain JA [auth L] MOL2 format, chain MA [auth L] MOL2 format, chain NA [auth M] MOL2 format, chain QA [auth N] MOL2 format, chain RA [auth V] MOL2 format, chain SA [auth V] MOL2 format, chain ZA [auth m] mmCIF format, chain AB [auth o] mmCIF format, chain CB [auth p] mmCIF format, chain FA [auth H] mmCIF format, chain HA [auth K] mmCIF format, chain IA [auth L] mmCIF format, chain JA [auth L] mmCIF format, chain MA [auth L] mmCIF format, chain NA [auth M] mmCIF format, chain QA [auth N] mmCIF format, chain RA [auth V] mmCIF format, chain SA [auth V] mmCIF format, chain ZA [auth m]	AB [auth o] CB [auth p] FA [auth H] HA [auth K] IA [auth L] AB [auth o], CB [auth p], FA [auth H], HA [auth K], IA [auth L], JA [auth L], MA [auth L], NA [auth M], QA [auth N], RA [auth V], SA [auth V], ZA [auth m]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain AB [auth o] Focus chain CB [auth p] Focus chain FA [auth H] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain MA [auth L] Focus chain NA [auth M] Focus chain QA [auth N] Focus chain RA [auth V] Focus chain SA [auth V] Focus chain ZA [auth m] Interactions & Density Focus chain AB [auth o] Focus chain CB [auth p] Focus chain FA [auth H] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain MA [auth L] Focus chain NA [auth M] Focus chain QA [auth N] Focus chain RA [auth V] Focus chain SA [auth V] Focus chain ZA [auth m]
ZMP Query on ZMP Download:Ideal Coordinates CCD File SDF format, chain WA [auth X] MOL2 format, chain WA [auth X] mmCIF format, chain WA [auth X]	WA [auth X]	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 WA [auth X] Interactions & Density Focus chain WA [auth X]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain YA [auth k] MOL2 format, chain YA [auth k] mmCIF format, chain YA [auth k]	YA [auth k]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain YA [auth k] Interactions & Density Focus chain YA [auth k]
DCQ Query on DCQ Download:Ideal Coordinates CCD File SDF format, chain EA [auth H] MOL2 format, chain EA [auth H] mmCIF format, chain EA [auth H]	EA [auth H]	2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione C₁₉ H₃₀ O₄ VMEGFMNVSYVVOM-UHFFFAOYSA-N		Interactions Focus chain EA [auth H] Interactions & Density Focus chain EA [auth H]
MYR Query on MYR Download:Ideal Coordinates CCD File SDF format, chain DB [auth s] MOL2 format, chain DB [auth s] mmCIF format, chain DB [auth s]	DB [auth s]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain DB [auth s] Interactions & Density Focus chain DB [auth s]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	D [auth K]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET
AYA Query on AYA	H [auth V]	L-PEPTIDE LINKING	C₅ H₉ N O₃		ALA
SEP Query on SEP	M [auth k]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.12
RECONSTRUCTION	RELION	3.0

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-07

Deposition Author(s):

Kampjut, D.

Sazanov, L.A.

Funding Organization	Location	Grant Number
European Commission	European Union	665385
European Commission	European Union	653706

Revision History (Full details and data files)

Version 1.0: 2020-10-07
Type: Initial release
Version 1.1: 2020-10-14
Changes: Database references
Version 1.2: 2020-11-11
Changes: Database references
Version 1.3: 2025-04-09
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

6ZKA | pdb_00006zka

Membrane domain of open complex I during turnover

Literature

The coupling mechanism of mammalian respiratory complex I.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

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Entity ID: 3

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Entity ID: 4

UniProt

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Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 8

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Entity ID: 13

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)