7ZDJ

Complex I from Ovis aries at pH5.5, Open state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 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

A universal coupling mechanism of respiratory complex I

Kravchuk, V.Petrova, O.Kampjut, D.Wojciechowska-Bason, A.Breese, Z.Sazanov, L.

(2022) Nature 


Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-49kDA [auth 4]463Ovis ariesMutation(s): 0 
Gene Names: NDUFS2
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3B [auth A]115Ovis ariesMutation(s): 0 
Gene Names: MT-ND3MTND3NADH3ND3
EC: 7.1.1.2
UniProt
Find proteins for O78753 (Ovis aries)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1C [auth H]318Ovis ariesMutation(s): 0 
Gene Names: MT-ND1MTND1NADH1ND1
EC: 7.1.1.2
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6D [auth J]175Ovis ariesMutation(s): 0 
Gene Names: MT-ND6MTND6NADH6ND6
EC: 7.1.1.2
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LE [auth K]98Ovis ariesMutation(s): 0 
Gene Names: MT-ND4LMTND4LNADH4LND4L
EC: 7.1.1.2
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5F [auth L]606Ovis ariesMutation(s): 0 
Gene Names: MT-ND5MTND5NADH5ND5
EC: 7.1.1.2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4G [auth M]459Ovis ariesMutation(s): 0 
Gene Names: MT-ND4MTND4NADH4ND4
EC: 7.1.1.2
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2H [auth N]347Ovis ariesMutation(s): 0 
Gene Names: MT-ND2MTND2NADH2ND2
EC: 7.1.1.2
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B14.7I [auth V]140Ovis ariesMutation(s): 0 
Gene Names: NDUFA11
UniProt
Find proteins for A0A6P3E4K7 (Ovis aries)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-SGDHJ [auth W]139Ovis ariesMutation(s): 0 
Gene Names: NDUFB5
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier proteinK [auth X],
SA [auth j]
157Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8L [auth Y]171Ovis ariesMutation(s): 0 
Gene Names: NDUFA8
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-PDSWM [auth Z]171Ovis ariesMutation(s): 0 
Gene Names: NDUFB10JEQ12_012218
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialN [auth k]320Ovis ariesMutation(s): 0 
Gene Names: NDUFA10
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5O [auth l]105Ovis ariesMutation(s): 0 
Gene Names: JEQ12_000171
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B9P [auth m]80Ovis ariesMutation(s): 0 
Gene Names: NDUFA3
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B12Q [auth n]79Ovis ariesMutation(s): 0 
Gene Names: LOC101106662LOC114108659
UniProt
Find proteins for A0A6P3E8V0 (Ovis aries)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2R [auth o]120Ovis ariesMutation(s): 0 
Gene Names: NDUFC2
UniProt
Find proteins for W5P9Q8 (Ovis aries)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B4S [auth p]128Ovis ariesMutation(s): 0 
Gene Names: NDUFB4
UniProt
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13T [auth q]144Ovis ariesMutation(s): 0 
Gene Names: NDUFA13
UniProt
Find proteins for A0A6P3E975 (Ovis aries)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B17 subunitU [auth r]128Ovis ariesMutation(s): 0 
Gene Names: NDUFB6
UniProt
Find proteins for W5PZE3 (Ovis aries)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B18V [auth s]122Ovis ariesMutation(s): 0 
Gene Names: NDUFB7
UniProt
Find proteins for W5P5V3 (Ovis aries)
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UniProt GroupW5P5V3
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B22W [auth t]177Ovis ariesMutation(s): 0 
Gene Names: NDUFB9
UniProt
Find proteins for W5PGA3 (Ovis aries)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-AGGGX [auth u]65Ovis ariesMutation(s): 0 
Gene Names: NDUFB2
UniProt
Find proteins for A0A6P3EC72 (Ovis aries)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialY [auth v]155Ovis ariesMutation(s): 0 
Gene Names: NDUFB8
UniProt
Find proteins for W5Q1B0 (Ovis aries)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-ESSSZ [auth w]101Ovis ariesMutation(s): 0 
Gene Names: JEQ12_020035
UniProt
Find proteins for A0A836CQA7 (Ovis aries)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-KFYIAA [auth x]49Ovis ariesMutation(s): 0 
Gene Names: LOC114112897
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-MNLLBA [auth y]50Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-MWFECA [auth z]70Ovis ariesMutation(s): 0 
Gene Names: NDUFA1
UniProt
Find proteins for A0A6P9FRJ5 (Ovis aries)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialDA [auth 1]430Ovis ariesMutation(s): 0 
Gene Names: JEQ12_011320
EC: 7.1.1.2
UniProt
Find proteins for A0A835ZPN7 (Ovis aries)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialEA [auth 2]213Ovis ariesMutation(s): 0 
Gene Names: NDUFV2
UniProt
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialFA [auth 3]688Ovis ariesMutation(s): 0 
Gene Names: NDUFS1
UniProt
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-30kDGA [auth 5]208Ovis ariesMutation(s): 0 
Gene Names: NDUFS3JEQ12_006524
UniProt
Find proteins for A0A6P3EKX5 (Ovis aries)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-20kDHA [auth 6]156Ovis ariesMutation(s): 0 
Gene Names: NDUFS7
UniProt
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-23kDIA [auth 9]176Ovis ariesMutation(s): 0 
Gene Names: NDUFS8
UniProt
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-9kDJA [auth a]44Ovis ariesMutation(s): 0 
Gene Names: JEQ12_001857
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialKA [auth b]95Ovis ariesMutation(s): 0 
Gene Names: NDUFS6JEQ12_007015
UniProt
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialLA [auth c]126Ovis ariesMutation(s): 0 
Gene Names: NDUFS4
UniProt
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A9MA [auth d]380Ovis ariesMutation(s): 0 
Gene Names: NDUFA9
UniProt
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2NA [auth e]86Ovis ariesMutation(s): 0 
Gene Names: NDUFA2
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I subunit B13OA [auth f]113Ovis ariesMutation(s): 0 
Gene Names: NDUFA5LOC101114379
UniProt
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B14PA [auth g]114Ovis ariesMutation(s): 0 
Gene Names: NDUFA6
UniProt
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B14.5a subunitQA [auth h]114Ovis ariesMutation(s): 0 
Gene Names: NDUFA7
UniProt
Find proteins for W5P0I2 (Ovis aries)
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Go to UniProtKB:  W5P0I2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW5P0I2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12RA [auth i]145Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0A6P3CXE3 (Ovis aries)
Explore A0A6P3CXE3 
Go to UniProtKB:  A0A6P3CXE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6P3CXE3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

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HB [auth d]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
NAI
Query on NAI

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XA [auth 1]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
ZMP
Query on ZMP

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IB [auth j],
TA [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
 Ligand Interaction
FMN
Query on FMN

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WA [auth 1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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AB [auth 3],
DB [auth 6],
EB [auth 9],
FB [auth 9],
VA [auth 1],
AB [auth 3],
DB [auth 6],
EB [auth 9],
FB [auth 9],
VA [auth 1],
ZA [auth 3]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MYR
Query on MYR

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UA [auth s]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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BB [auth 3],
YA [auth 2]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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GB [auth b]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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CB [auth 3]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
2MR
Query on 2MR
A [auth 4]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
FME
Query on FME
E [auth K]L-PEPTIDE LINKINGC6 H11 N O3 SMET
AYA
Query on AYA
I [auth V]L-PEPTIDE LINKINGC5 H9 N O3ALA
SEP
Query on SEP
N [auth k]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101020697

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release