6QCA | pdb_00006qca

Ovine respiratory complex I FRC open class 5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 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: https://doi.org/10.1016/j.molcel.2019.07.022
  • Primary Citation 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 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; Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.

Macromolecule Content 

  • Total Structure Weight: 974.5 kDa 
  • Atom Count: 40,144 
  • Modeled Residue Count: 8,086 
  • Deposited Residue Count: 8,509 
  • Unique protein chains: 44

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialA [auth V1]445Ovis ariesMutation(s): 0 
EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (PDB Primary Data)
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFV2B [auth V2]217Ovis ariesMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S1C [auth S1]704Ovis ariesMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFS2D [auth S2]430Ovis ariesMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S3E [auth S3]228Ovis ariesMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFS7F [auth S7]179Ovis ariesMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFS8G [auth S8]176Ovis ariesMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFV3H [auth V3]75Ovis ariesMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFS6I [auth S6]96Ovis ariesMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit S4J [auth S4]133Ovis ariesMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A9K [auth A9]338Ovis ariesMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2L [auth A2]98Ovis ariesMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFA5M [auth A5]115Ovis ariesMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A6N [auth A6]127Ovis ariesMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFA7O [auth A7]112Ovis ariesMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12P [auth AL]145Ovis ariesMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Acyl carrier proteinAA [auth AB],
Q [auth AA]
88Ovis ariesMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3R [auth D3]115Ovis ariesMutation(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
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UniProt GroupO78753
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1S [auth D1]318Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O78747 (Ovis aries)
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Go to UniProtKB:  O78747
Entity Groups
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UniProt GroupO78747
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6T [auth D6]175Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O78757 (Ovis aries)
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Entity Groups
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UniProt GroupO78757
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LU [auth 4L]98Ovis ariesMutation(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
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UniProt GroupO78754
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5V [auth D5]606Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O78756 (Ovis aries)
Explore O78756 
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Entity Groups
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UniProt GroupO78756
Sequence Annotations
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Reference Sequence
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4W [auth D4]459Ovis ariesMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO78755
Sequence Annotations
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Reference Sequence
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2X [auth D2]347Ovis ariesMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO78748
Sequence Annotations
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Reference Sequence
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFA11Y [auth AK]140Ovis ariesMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B5Z [auth B5]143Ovis ariesMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8BA [auth A8]171Ovis ariesMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB10CA [auth BJ]175Ovis ariesMutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialDA [auth AJ]320Ovis ariesMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit S5EA [auth S5]105Ovis ariesMutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A3FA [auth A3]83Ovis ariesMutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B3GA [auth B3]97Ovis ariesMutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2HA [auth C2]120Ovis ariesMutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B4IA [auth B4]128Ovis ariesMutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFA13JA [auth AM]143Ovis ariesMutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB6KA [auth B6]127Ovis ariesMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B7LA [auth B7]136Ovis ariesMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B9MA [auth B9]178Ovis ariesMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B2NA [auth B2]72Ovis ariesMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialOA [auth B8]158Ovis ariesMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB11PA [auth BK]125Ovis ariesMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFC1QA [auth C1]49Ovis ariesMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB1RA [auth B1]57Ovis ariesMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFA1SA [auth A1]70Ovis ariesMutation(s): 0 

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP

Query on NDP



Download:Ideal Coordinates CCD File
DB [auth A9]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
ZMP

Query on ZMP



Download:Ideal Coordinates CCD File
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
FMN

Query on FMN



Download:Ideal Coordinates CCD File
UA [auth V1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
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-UHFFFAOYSA-N
FES

Query on FES



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

Query on ZN



Download:Ideal Coordinates CCD File
CB [auth S6]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13-2998
RECONSTRUCTIONRELION2

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
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references, Refinement description