6ZKP | pdb_00006zkp

Native complex I, open1

PDB DOI: https://doi.org/10.2210/pdb6ZKP/pdb
EM Map EMD-11257: 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: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

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: 1,081.04 kDa
Atom Count: 67,353
Modeled Residue Count: 8,157
Deposited Residue Count: 9,247
Unique protein chains: 44

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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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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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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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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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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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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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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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 3	H [auth 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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 1	I [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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 6	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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4L	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: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 5	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: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4	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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 2	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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, B14.7 subunit	O [auth V]	141	Ovis aries	Mutation(s): 0

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B5	P [auth W]	189	Ovis aries	Mutation(s): 0

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

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8	R [auth Y]	172	Ovis aries	Mutation(s): 0

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, PDSW subunit	S [auth Z]	175	Ovis aries	Mutation(s): 0

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, 10 kDa subunit	T [auth a]	109	Ovis aries	Mutation(s): 0

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, 13 kDa subunit	U [auth b]	124	Ovis aries	Mutation(s): 0

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial	V [auth c]	170	Ovis aries	Mutation(s): 0

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit A9	W [auth d]	380	Ovis aries	Mutation(s): 0

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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	X [auth e]	99	Ovis aries	Mutation(s): 0

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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, B13 subunit	Y [auth f]	116	Ovis aries	Mutation(s): 0

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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit A6	Z [auth g]	140	Ovis aries	Mutation(s): 0

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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, B14.5a subunit	AA [auth h]	114	Ovis aries	Mutation(s): 0

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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12	BA [auth i]	145	Ovis aries	Mutation(s): 0

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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial	DA [auth k]	355	Ovis aries	Mutation(s): 0

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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit S5	EA [auth l]	106	Ovis aries	Mutation(s): 0

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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit A3	FA [auth m]	84	Ovis aries	Mutation(s): 0

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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B3	GA [auth n]	98	Ovis aries	Mutation(s): 0

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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 subunit C2	HA [auth o]	122	Ovis aries	Mutation(s): 0

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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B4	IA [auth p]	130	Ovis aries	Mutation(s): 0

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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, B16.6 subunit	JA [auth q]	144	Ovis aries	Mutation(s): 0

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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, B17 subunit	KA [auth r]	128	Ovis aries	Mutation(s): 0

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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B7	LA [auth s]	137	Ovis aries	Mutation(s): 0

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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B9	MA [auth t]	179	Ovis aries	Mutation(s): 0

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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:ubiquinone oxidoreductase subunit B2	NA [auth u]	108	Ovis aries	Mutation(s): 0

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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial	OA [auth v]	186	Ovis aries	Mutation(s): 0

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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, ESSS subunit	PA [auth w]	154	Ovis aries	Mutation(s): 0

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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, KFYI subunit	QA [auth x]	76	Ovis aries	Mutation(s): 0

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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, MNLL subunit	RA [auth y]	58	Ovis aries	Mutation(s): 0

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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial complex I, MWFE subunit	SA [auth z]	70	Ovis aries	Mutation(s): 0

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain ZB [auth W] SDF format, chain YB [auth V] SDF format, chain XB [auth V] SDF format, chain UB [auth N] SDF format, chain OB [auth L] SDF format, chain KC [auth y] SDF format, chain HC [auth o] SDF format, chain EC [auth h] MOL2 format, chain ZB [auth W] MOL2 format, chain YB [auth V] MOL2 format, chain XB [auth V] MOL2 format, chain UB [auth N] MOL2 format, chain OB [auth L] MOL2 format, chain KC [auth y] MOL2 format, chain HC [auth o] MOL2 format, chain EC [auth h] mmCIF format, chain ZB [auth W] mmCIF format, chain YB [auth V] mmCIF format, chain XB [auth V] mmCIF format, chain UB [auth N] mmCIF format, chain OB [auth L] mmCIF format, chain KC [auth y] mmCIF format, chain HC [auth o] mmCIF format, chain EC [auth h]	EC [auth h] HC [auth o] KC [auth y] OB [auth L] UB [auth N] EC [auth h], HC [auth o], KC [auth y], OB [auth L], UB [auth N], XB [auth V], YB [auth V], ZB [auth W]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain EC [auth h] Focus chain HC [auth o] Focus chain KC [auth y] Focus chain OB [auth L] Focus chain UB [auth N] Focus chain XB [auth V] Focus chain YB [auth V] Focus chain ZB [auth W] Interactions & Density Focus chain EC [auth h] Focus chain HC [auth o] Focus chain KC [auth y] Focus chain OB [auth L] Focus chain UB [auth N] Focus chain XB [auth V] Focus chain YB [auth V] Focus chain ZB [auth W]
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain RB [auth M] SDF format, chain NB [auth L] SDF format, chain MB [auth L] SDF format, chain HB [auth A] SDF format, chain EB [auth 9] SDF format, chain CB [auth 6] MOL2 format, chain RB [auth M] MOL2 format, chain NB [auth L] MOL2 format, chain MB [auth L] MOL2 format, chain HB [auth A] MOL2 format, chain EB [auth 9] MOL2 format, chain CB [auth 6] mmCIF format, chain RB [auth M] mmCIF format, chain NB [auth L] mmCIF format, chain MB [auth L] mmCIF format, chain HB [auth A] mmCIF format, chain EB [auth 9] mmCIF format, chain CB [auth 6]	CB [auth 6] EB [auth 9] HB [auth A] MB [auth L] NB [auth L] CB [auth 6], EB [auth 9], HB [auth A], MB [auth L], NB [auth L], RB [auth M]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain CB [auth 6] Focus chain EB [auth 9] Focus chain HB [auth A] Focus chain MB [auth L] Focus chain NB [auth L] Focus chain RB [auth M] Interactions & Density Focus chain CB [auth 6] Focus chain EB [auth 9] Focus chain HB [auth A] Focus chain MB [auth L] Focus chain NB [auth L] Focus chain RB [auth M]
3PE Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain WB [auth V] SDF format, chain VB [auth V] SDF format, chain TB [auth N] SDF format, chain SB [auth N] SDF format, chain QB [auth M] SDF format, chain PB [auth L] SDF format, chain LB [auth L] SDF format, chain KB [auth J] SDF format, chain JB [auth H] SDF format, chain IC [auth p] SDF format, chain IB [auth A] SDF format, chain FC [auth i] SDF format, chain DB [auth 6] SDF format, chain AB [auth 4] MOL2 format, chain WB [auth V] MOL2 format, chain VB [auth V] MOL2 format, chain TB [auth N] MOL2 format, chain SB [auth N] MOL2 format, chain QB [auth M] MOL2 format, chain PB [auth L] MOL2 format, chain LB [auth L] MOL2 format, chain KB [auth J] MOL2 format, chain JB [auth H] MOL2 format, chain IC [auth p] MOL2 format, chain IB [auth A] MOL2 format, chain FC [auth i] MOL2 format, chain DB [auth 6] MOL2 format, chain AB [auth 4] mmCIF format, chain WB [auth V] mmCIF format, chain VB [auth V] mmCIF format, chain TB [auth N] mmCIF format, chain SB [auth N] mmCIF format, chain QB [auth M] mmCIF format, chain PB [auth L] mmCIF format, chain LB [auth L] mmCIF format, chain KB [auth J] mmCIF format, chain JB [auth H] mmCIF format, chain IC [auth p] mmCIF format, chain IB [auth A] mmCIF format, chain FC [auth i] mmCIF format, chain DB [auth 6] mmCIF format, chain AB [auth 4]	AB [auth 4] DB [auth 6] FC [auth i] IB [auth A] IC [auth p] AB [auth 4], DB [auth 6], FC [auth i], IB [auth A], IC [auth p], JB [auth H], KB [auth J], LB [auth L], PB [auth L], QB [auth M], SB [auth N], TB [auth N], VB [auth V], WB [auth V]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain AB [auth 4] Focus chain DB [auth 6] Focus chain FC [auth i] Focus chain IB [auth A] Focus chain IC [auth p] Focus chain JB [auth H] Focus chain KB [auth J] Focus chain LB [auth L] Focus chain PB [auth L] Focus chain QB [auth M] Focus chain SB [auth N] Focus chain TB [auth N] Focus chain VB [auth V] Focus chain WB [auth V] Interactions & Density Focus chain AB [auth 4] Focus chain DB [auth 6] Focus chain FC [auth i] Focus chain IB [auth A] Focus chain IC [auth p] Focus chain JB [auth H] Focus chain KB [auth J] Focus chain LB [auth L] Focus chain PB [auth L] Focus chain QB [auth M] Focus chain SB [auth N] Focus chain TB [auth N] Focus chain VB [auth V] Focus chain WB [auth V]
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain CC [auth d] MOL2 format, chain CC [auth d] mmCIF format, chain CC [auth d]	CC [auth d]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain CC [auth d] Interactions & Density Focus chain CC [auth d]
ZMP Query on ZMP Download:Ideal Coordinates CCD File SDF format, chain DC [auth g] SDF format, chain AC [auth X] MOL2 format, chain DC [auth g] MOL2 format, chain AC [auth X] mmCIF format, chain DC [auth g] mmCIF format, chain AC [auth X]	AC [auth X], DC [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 AC [auth X] Focus chain DC [auth g] Interactions & Density Focus chain AC [auth X] Focus chain DC [auth g]
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain UA [auth 1] MOL2 format, chain UA [auth 1] mmCIF format, chain UA [auth 1]	UA [auth 1]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain UA [auth 1] Interactions & Density Focus chain UA [auth 1]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain XA [auth 3] SDF format, chain WA [auth 3] SDF format, chain TA [auth 1] SDF format, chain GB [auth 9] SDF format, chain FB [auth 9] SDF format, chain BB [auth 6] MOL2 format, chain XA [auth 3] MOL2 format, chain WA [auth 3] MOL2 format, chain TA [auth 1] MOL2 format, chain GB [auth 9] MOL2 format, chain FB [auth 9] MOL2 format, chain BB [auth 6] mmCIF format, chain XA [auth 3] mmCIF format, chain WA [auth 3] mmCIF format, chain TA [auth 1] mmCIF format, chain GB [auth 9] mmCIF format, chain FB [auth 9] mmCIF format, chain BB [auth 6]	BB [auth 6] FB [auth 9] GB [auth 9] TA [auth 1] WA [auth 3] BB [auth 6], FB [auth 9], GB [auth 9], TA [auth 1], WA [auth 3], XA [auth 3]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain BB [auth 6] Focus chain FB [auth 9] Focus chain GB [auth 9] Focus chain TA [auth 1] Focus chain WA [auth 3] Focus chain XA [auth 3] Interactions & Density Focus chain BB [auth 6] Focus chain FB [auth 9] Focus chain GB [auth 9] Focus chain TA [auth 1] Focus chain WA [auth 3] Focus chain XA [auth 3]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain GC [auth k] MOL2 format, chain GC [auth k] mmCIF format, chain GC [auth k]	GC [auth k]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain GC [auth k] Interactions & Density Focus chain GC [auth k]
MYR Query on MYR Download:Ideal Coordinates CCD File SDF format, chain JC [auth s] MOL2 format, chain JC [auth s] mmCIF format, chain JC [auth s]	JC [auth s]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain JC [auth s] Interactions & Density Focus chain JC [auth s]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain YA [auth 3] SDF format, chain VA [auth 2] MOL2 format, chain YA [auth 3] MOL2 format, chain VA [auth 2] mmCIF format, chain YA [auth 3] mmCIF format, chain VA [auth 2]	VA [auth 2], YA [auth 3]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain VA [auth 2] Focus chain YA [auth 3] Interactions & Density Focus chain VA [auth 2] Focus chain YA [auth 3]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain BC [auth b] MOL2 format, chain BC [auth b] mmCIF format, chain BC [auth b]	BC [auth b]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BC [auth b] Interactions & Density Focus chain BC [auth b]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain ZA [auth 3] MOL2 format, chain ZA [auth 3] mmCIF format, chain ZA [auth 3]	ZA [auth 3]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain ZA [auth 3] Interactions & Density Focus chain ZA [auth 3]

Modified Residues 4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2MR Query on 2MR	D [auth 4]	L-PEPTIDE LINKING	C₈ H₁₈ N₄ O₂		ARG
FME Query on FME	K	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET
AYA Query on AYA	O [auth V]	L-PEPTIDE LINKING	C₅ H₉ N O₃		ALA
SEP Query on SEP	DA [auth k]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 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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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

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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.

6ZKP | pdb_00006zkp

Native complex I, open1

Literature

The coupling mechanism of mammalian respiratory complex I.

Biological Assembly 1

Macromolecules

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Small Molecules

Experimental Data & Validation