6Q9D

CI Peripheral Arm focused refinement from Ovine respiratory SC I+III2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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 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 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.


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)
Membrane Entity: Yes 
UniProt
Find proteins for W5PUX0 (Ovis aries)
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UniProt GroupW5PUX0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialB [auth V2]217Ovis ariesMutation(s): 0 
UniProt
Find proteins for W5NRY1 (Ovis aries)
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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
NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2D [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 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S7F [auth S7]179Ovis ariesMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S8G [auth S8]176Ovis ariesMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit V3H [auth V3]75Ovis ariesMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialI [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 
Membrane Entity: Yes 
UniProt
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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
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5M [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 
Membrane Entity: Yes 
UniProt
Find proteins for W5QC06 (Ovis aries)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7O [auth A7]112Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5P0I2 (Ovis aries)
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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 proteinQ [auth AA]88Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13R [auth AM]143Ovis ariesMutation(s): 0 
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

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

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DA [auth AA]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

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T [auth V1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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AA [auth S8]
S [auth V1]
V [auth S1]
W [auth S1]
Y [auth S7]
AA [auth S8],
S [auth V1],
V [auth S1],
W [auth S1],
Y [auth S7],
Z [auth S8]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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U [auth V2],
X [auth S1]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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BA [auth S6]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13-2998
RECONSTRUCTIONRELION2

Structure Validation

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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: 2019-12-18
    Changes: Other