6QC9

Ovine respiratory complex I FRC open class 4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of Respiratory Supercomplex I+III2Reveal Functional and Conformational Crosstalk.

Letts, J.A.Fiedorczuk, K.Degliesposti, G.Skehel, M.Sazanov, L.A.

(2019) Mol Cell 75: 1131-1146.e6

  • DOI: 10.1016/j.molcel.2019.07.022
  • Primary Citation of Related Structures:  
    6Q9B, 6Q9D, 6Q9E, 6QA9, 6QBX, 6QC2, 6QC3, 6QC4, 6QC5, 6QC6, 6QC7, 6QC8, 6QC9, 6QCA, 6QCF

  • PubMed Abstract: 
  • The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III 2 limits complex (C)I turnover, arguing against channeling ...

    The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III 2 limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII 2 . CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII 2 , demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII 2 , suggesting that interaction with CI disrupts CIII 2 symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.


    Organizational Affiliation

    Institute of Science and Technology Austria, Klosterneuberg 3400, Austria. Electronic address: sazanov@ist.ac.at.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialA [auth V1]445Ovis ariesMutation(s): 0 
Gene Names: NDUFV1
EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NDUFV2B [auth V2]217Ovis ariesMutation(s): 0 
Gene Names: NDUFV2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S1C [auth S1]704Ovis ariesMutation(s): 0 
Gene Names: NDUFS1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NDUFS2D [auth S2]430Ovis ariesMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S3E [auth S3]228Ovis ariesMutation(s): 0 
Gene Names: NDUFS3
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NDUFS7F [auth S7]179Ovis ariesMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NDUFS8G [auth S8]176Ovis ariesMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NDUFV3H [auth V3]75Ovis ariesMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NDUFS6I [auth S6]96Ovis ariesMutation(s): 0 
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Entity ID: 10
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NADH:ubiquinone oxidoreductase subunit S4J [auth S4]133Ovis ariesMutation(s): 0 
Gene Names: NDUFS4
Membrane Entity: Yes 
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Entity ID: 11
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NADH:ubiquinone oxidoreductase subunit A9K [auth A9]338Ovis ariesMutation(s): 0 
Gene Names: NDUFA9
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Entity ID: 12
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2L [auth A2]98Ovis ariesMutation(s): 0 
Gene Names: NDUFA2
Membrane Entity: Yes 
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Entity ID: 13
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NDUFA5M [auth A5]115Ovis ariesMutation(s): 0 
Gene Names: NDUFA5
Membrane Entity: Yes 
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Entity ID: 14
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NADH:ubiquinone oxidoreductase subunit A6N [auth A6]127Ovis ariesMutation(s): 0 
Gene Names: NDUFA6
Membrane Entity: Yes 
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Entity ID: 15
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NDUFA7O [auth A7]112Ovis ariesMutation(s): 0 
Gene Names: NDUFA7
Membrane Entity: Yes 
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Entity ID: 16
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12P [auth AL]145Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier proteinQ [auth AA],
AA [auth AB]
88Ovis ariesMutation(s): 0 
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Entity ID: 18
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NADH-ubiquinone oxidoreductase chain 3R [auth D3]115Ovis ariesMutation(s): 0 
Gene Names: MT-ND3MTND3NADH3ND3
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1S [auth D1]318Ovis ariesMutation(s): 0 
Gene Names: MT-ND1MTND1NADH1ND1
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 20
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NADH-ubiquinone oxidoreductase chain 6T [auth D6]175Ovis ariesMutation(s): 0 
Gene Names: MT-ND6MTND6NADH6ND6
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LU [auth 4L]98Ovis ariesMutation(s): 0 
Gene Names: MT-ND4LMTND4LNADH4LND4L
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5V [auth D5]606Ovis ariesMutation(s): 0 
Gene Names: MT-ND5MTND5NADH5ND5
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4W [auth D4]459Ovis ariesMutation(s): 0 
Gene Names: MT-ND4MTND4NADH4ND4
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2X [auth D2]347Ovis ariesMutation(s): 0 
Gene Names: MT-ND2MTND2NADH2ND2
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
NDUFA11Y [auth AK]140Ovis ariesMutation(s): 0 
Gene Names: NDUFA11
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B5Z [auth B5]143Ovis ariesMutation(s): 0 
Gene Names: NDUFB5
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8BA [auth A8]171Ovis ariesMutation(s): 0 
Gene Names: NDUFA8
Membrane Entity: Yes 
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Entity ID: 28
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NDUFB10CA [auth BJ]175Ovis ariesMutation(s): 0 
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Entity ID: 29
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialDA [auth AJ]320Ovis ariesMutation(s): 0 
Gene Names: NDUFA10
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Entity ID: 30
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NADH:ubiquinone oxidoreductase subunit S5EA [auth S5]105Ovis ariesMutation(s): 0 
Gene Names: NDUFS5
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A3FA [auth A3]83Ovis ariesMutation(s): 0 
Gene Names: NDUFA3
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B3GA [auth B3]97Ovis ariesMutation(s): 0 
Gene Names: LOC114108659
Membrane Entity: Yes 
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Entity ID: 33
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NADH dehydrogenase [ubiquinone] 1 subunit C2HA [auth C2]120Ovis ariesMutation(s): 0 
Gene Names: NDUFC2
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B4IA [auth B4]128Ovis ariesMutation(s): 0 
Gene Names: NDUFB4
Membrane Entity: Yes 
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Entity ID: 35
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NDUFA13JA [auth AM]143Ovis ariesMutation(s): 0 
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Entity ID: 36
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NDUFB6KA [auth B6]127Ovis ariesMutation(s): 0 
Gene Names: NDUFB6
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B7LA [auth B7]136Ovis ariesMutation(s): 0 
Gene Names: NDUFB7
Membrane Entity: Yes 
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Entity ID: 38
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NADH:ubiquinone oxidoreductase subunit B9MA [auth B9]178Ovis ariesMutation(s): 0 
Gene Names: NDUFB9
Membrane Entity: Yes 
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Entity ID: 39
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NADH:ubiquinone oxidoreductase subunit B2NA [auth B2]72Ovis ariesMutation(s): 0 
Gene Names: NDUFB2
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialOA [auth B8]158Ovis ariesMutation(s): 0 
Gene Names: NDUFB8
Membrane Entity: Yes 
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Entity ID: 41
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NDUFB11PA [auth BK]125Ovis ariesMutation(s): 0 
Gene Names: NDUFB11
Membrane Entity: Yes 
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Entity ID: 42
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NDUFC1QA [auth C1]49Ovis ariesMutation(s): 0 
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Entity ID: 43
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NDUFB1RA [auth B1]57Ovis ariesMutation(s): 0 
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Entity ID: 44
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NDUFA1SA [auth A1]70Ovis ariesMutation(s): 0 
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Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

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DB [auth A9]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
ZMP
Query on ZMP

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EB [auth A6],
FB [auth AB]
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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UA [auth V1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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AB [auth S8],
BB [auth S8],
TA [auth V1],
WA [auth S1],
XA [auth S1],
AB [auth S8],
BB [auth S8],
TA [auth V1],
WA [auth S1],
XA [auth S1],
ZA [auth S7]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
VA [auth V2],
YA [auth S1]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CB [auth S6]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 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 CouncilAustria701309

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-02
    Changes: Data collection, Database references