6ZK9 | pdb_00006zk9

Peripheral domain of open complex I during turnover

PDB DOI: https://doi.org/10.2210/pdb6ZK9/pdb
EM Map EMD-11241: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Ovis aries
Mutation(s): No

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: 2.30 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: 491.95 kDa
Atom Count: 29,587
Modeled Residue Count: 3,480
Deposited Residue Count: 4,304
Unique protein chains: 18

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial	A [auth 1]	464	Ovis aries	Mutation(s): 0 EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (PDB Primary Data)

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, 24 kDa subunit	B [auth 2]	246	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase core subunit S1	C [auth 3]	727	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, 49 kDa subunit	D [auth 4]	463	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase core subunit S3	E [auth 5]	266	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, PSST subunit	F [auth 6]	223	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, TYKY subunit	G [auth 9]	217	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, 10 kDa subunit	H [auth a]	109	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, 13 kDa subunit	I [auth b]	124	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial	J [auth c]	170	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit A9	K [auth d]	380	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	L [auth e]	99	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, B13 subunit	M [auth f]	116	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit A6	N [auth g]	140	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, B14.5a subunit	O [auth h]	114	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12	P [auth i]	145	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	Q [auth j]	157	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, B16.6 subunit	R [auth q]	144	Ovis aries	Mutation(s): 0

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain JA [auth h] MOL2 format, chain JA [auth h] mmCIF format, chain JA [auth h]	JA [auth h]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain JA [auth h] Interactions & Density Focus chain JA [auth h]
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain DA [auth 9] SDF format, chain BA [auth 6] MOL2 format, chain DA [auth 9] MOL2 format, chain BA [auth 6] mmCIF format, chain DA [auth 9] mmCIF format, chain BA [auth 6]	BA [auth 6], DA [auth 9]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain BA [auth 6] Focus chain DA [auth 9] Interactions & Density Focus chain BA [auth 6] Focus chain DA [auth 9]
3PE Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain KA [auth i] SDF format, chain CA [auth 6] MOL2 format, chain KA [auth i] MOL2 format, chain CA [auth 6] mmCIF format, chain KA [auth i] mmCIF format, chain CA [auth 6]	CA [auth 6], KA [auth i]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain CA [auth 6] Focus chain KA [auth i] Interactions & Density Focus chain CA [auth 6] Focus chain KA [auth i]
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain HA [auth d] MOL2 format, chain HA [auth d] mmCIF format, chain HA [auth d]	HA [auth d]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain HA [auth d] Interactions & Density Focus chain HA [auth d]
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain U [auth 1] MOL2 format, chain U [auth 1] mmCIF format, chain U [auth 1]	U [auth 1]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain U [auth 1] Interactions & Density Focus chain U [auth 1]
ZMP Query on ZMP Download:Ideal Coordinates CCD File SDF format, chain IA [auth g] MOL2 format, chain IA [auth g] mmCIF format, chain IA [auth g]	IA [auth g]	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 IA [auth g] Interactions & Density Focus chain IA [auth g]
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain T [auth 1] MOL2 format, chain T [auth 1] mmCIF format, chain T [auth 1]	T [auth 1]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain T [auth 1] Interactions & Density Focus chain T [auth 1]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth 6] SDF format, chain EA [auth 9] SDF format, chain W [auth 3] SDF format, chain X [auth 3] SDF format, chain S [auth 1] SDF format, chain FA [auth 9] MOL2 format, chain AA [auth 6] MOL2 format, chain EA [auth 9] MOL2 format, chain W [auth 3] MOL2 format, chain X [auth 3] MOL2 format, chain S [auth 1] MOL2 format, chain FA [auth 9] mmCIF format, chain AA [auth 6] mmCIF format, chain EA [auth 9] mmCIF format, chain W [auth 3] mmCIF format, chain X [auth 3] mmCIF format, chain S [auth 1] mmCIF format, chain FA [auth 9]	AA [auth 6] EA [auth 9] FA [auth 9] S [auth 1] W [auth 3] AA [auth 6], EA [auth 9], FA [auth 9], S [auth 1], W [auth 3], X [auth 3]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth 6] Focus chain EA [auth 9] Focus chain FA [auth 9] Focus chain S [auth 1] Focus chain W [auth 3] Focus chain X [auth 3] Interactions & Density Focus chain AA [auth 6] Focus chain EA [auth 9] Focus chain FA [auth 9] Focus chain S [auth 1] Focus chain W [auth 3] Focus chain X [auth 3]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain V [auth 2] SDF format, chain Y [auth 3] MOL2 format, chain V [auth 2] MOL2 format, chain Y [auth 3] mmCIF format, chain V [auth 2] mmCIF format, chain Y [auth 3]	V [auth 2], Y [auth 3]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain V [auth 2] Focus chain Y [auth 3] Interactions & Density Focus chain V [auth 2] Focus chain Y [auth 3]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain GA [auth b] MOL2 format, chain GA [auth b] mmCIF format, chain GA [auth b]	GA [auth b]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain GA [auth b] Interactions & Density Focus chain GA [auth b]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain Z [auth 3] MOL2 format, chain Z [auth 3] mmCIF format, chain Z [auth 3]	Z [auth 3]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain Z [auth 3] Interactions & Density Focus chain Z [auth 3]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2MR Query on 2MR	D [auth 4]	L-PEPTIDE LINKING	C₈ H₁₈ N₄ O₂		ARG
AYA Query on AYA	O [auth h]	L-PEPTIDE LINKING	C₅ H₉ N O₃		ALA

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.30 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

View Full Validation Report

View more in-depth experimental data

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