6QC4

Ovine respiratory supercomplex I+III2 open class 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 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
UQCRC1A [auth a1],
K [auth a3]
446Ovis ariesMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase core protein 2B [auth a2],
L [auth a4]
439Ovis ariesMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bC [auth b1],
M [auth b2]
379Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1D [auth c1],
N [auth c2]
240Ovis ariesMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE [auth f1],
O [auth f2]
196Ovis ariesMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
UQCRBF [auth d1],
P [auth d2]
110Ovis ariesMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex III subunit VIIG [auth q1],
Q [auth q2]
81Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5PUP9 (Ovis aries)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6H [auth h1],
R [auth h2]
78Ovis ariesMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
UQCRFS1NI [auth x1],
S [auth x2]
78Ovis ariesMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase, complex III subunit XJ [auth i1],
T [auth i2]
63Ovis ariesMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3U [auth D3]115Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1V [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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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6W [auth D6]175Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LX [auth 4L]98Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5Y [auth D5]606Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4Z [auth D4]459Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2AA [auth D2]347Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA11BA [auth AK]140Ovis ariesMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B5CA [auth B5]143Ovis ariesMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinDA [auth AB],
MB [auth AA]
88Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8EA [auth A8]171Ovis ariesMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB10FA [auth BJ]175Ovis ariesMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialGA [auth AJ]320Ovis ariesMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit S5HA [auth S5]105Ovis ariesMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A3IA [auth A3]83Ovis ariesMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B3JA [auth B3]97Ovis ariesMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2KA [auth C2]120Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5P9Q8 (Ovis aries)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B4LA [auth B4]128Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA13MA [auth AM]143Ovis ariesMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB6NA [auth B6]127Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B7OA [auth B7]119Ovis ariesMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B9PA [auth B9]178Ovis ariesMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B2QA [auth B2]72Ovis ariesMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialRA [auth B8]158Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB11SA [auth BK]125Ovis ariesMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFC1TA [auth C1]49Ovis ariesMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB1UA [auth B1]57Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA1VA [auth A1]70Ovis ariesMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialWA [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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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFV2XA [auth V2]217Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S1YA [auth S1]704Ovis ariesMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS2ZA [auth S2]430Ovis ariesMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S3AB [auth S3]228Ovis ariesMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS7BB [auth S7]179Ovis ariesMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS8CB [auth S8]176Ovis ariesMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFV3DB [auth V3]75Ovis ariesMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS6EB [auth S6]96Ovis ariesMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit S4FB [auth S4]133Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A9GB [auth A9]338Ovis ariesMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2HB [auth A2]98Ovis ariesMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA5IB [auth A5]115Ovis ariesMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A6JB [auth A6]127Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA7KB [auth A7]112Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12LB [auth AL]145Ovis ariesMutation(s): 0 
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

Download Ideal Coordinates CCD File 
VB [auth D2]1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
NDP
Query on NDP

Download Ideal Coordinates CCD File 
HC [auth A9]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEC
Query on HEC

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PB [auth c1],
TB [auth c2]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
NB [auth b1],
OB [auth b1],
RB [auth b2],
SB [auth b2]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ZMP
Query on ZMP

Download Ideal Coordinates CCD File 
IC [auth AA],
WB [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

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

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AC [auth S1]
BC [auth S1]
DC [auth S7]
EC [auth S8]
FC [auth S8]
AC [auth S1],
BC [auth S1],
DC [auth S7],
EC [auth S8],
FC [auth S8],
XB [auth V1]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
CC [auth S1],
QB [auth f1],
UB [auth f2],
ZB [auth V2]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2
MODEL REFINEMENTPHENIX1.13-2998

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: 2019-12-18
    Changes: Other