8RGT

Open Complex I from murine brain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

SCAF1 drives the compositional diversity of mammalian respirasomes.

Vercellino, I.Sazanov, L.A.

(2024) Nat Struct Mol Biol 31: 1061-1071

  • DOI: https://doi.org/10.1038/s41594-024-01255-0
  • Primary Citation of Related Structures:  
    8PW5, 8PW6, 8PW7, 8RGP, 8RGQ, 8RGR, 8RGT

  • PubMed Abstract: 

    Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII 2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the 'canonical' respirasome (the C-respirasome, CICIII 2 CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the 'back' of CI, instead of the 'toe'. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.


  • Organizational Affiliation

    Institute of Science and Technology Austria, Klosterneuburg, Austria.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialA [auth 6]224Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:1922656
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialB [auth C]263Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:1915599
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialC [auth D]463Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:2385112
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialD [auth 2]248Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:1920150
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialE [auth 1]464Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:107851
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialF [auth 3]727Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:2443241
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialG [auth 9]212Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:2385079
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialH [auth P]377Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913358
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialI [auth Q]175Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialJ [auth 7]116Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:107932
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2K [auth S]99Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialL [auth T],
Z [auth U]
156Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5M [auth V]116Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6N [auth W]131Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1914380
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12O [auth q]145Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7P [auth r]113Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913666
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialQ [auth s]104Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1890894
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3R [auth A]115Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1S [auth H]318Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6T [auth J]172Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LU [auth K]98Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5V [auth L]607Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4W [auth M]459Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2X [auth N]345Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialY [auth O]355Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1914523
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8AA [auth X]172Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1915625
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11BA [auth Y]141Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1917125
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13CA [auth Z]144Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1DA [auth a]70Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3EA [auth b]84Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialFA [auth c]76Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2GA [auth d]120Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5HA [auth e]106Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1890889
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1IA [auth f]57Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialJA [auth g]151Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialKA [auth h]189Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913296
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6LA [auth i]128Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialMA [auth j]105Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3NA [auth k]104Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialOA [auth l]186Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1914514
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4PA [auth m]129Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CQC7 (Mus musculus)
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Go to UniProtKB:  Q9CQC7
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UniProt GroupQ9CQC7
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9QA [auth n]179Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQJ8 (Mus musculus)
Explore Q9CQJ8 
Go to UniProtKB:  Q9CQJ8
IMPC:  MGI:1913468
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UniProt GroupQ9CQJ8
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7RA [auth o]137Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CR61 (Mus musculus)
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UniProt GroupQ9CR61
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10SA [auth p]176Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9DCS9 (Mus musculus)
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UniProt GroupQ9DCS9
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  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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CC [auth d]
FC [auth h]
IC [auth m]
LB [auth r]
QB [auth L]
CC [auth d],
FC [auth h],
IC [auth m],
LB [auth r],
QB [auth L],
WB [auth N]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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FB [auth 9],
GB [auth 9],
TB [auth M],
VA [auth 6]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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BC [auth Y]
DC [auth d]
EC [auth d]
GC [auth h]
HC [auth i]
BC [auth Y],
DC [auth d],
EC [auth d],
GC [auth h],
HC [auth i],
JC [auth m],
KB [auth r],
MB [auth A],
NB [auth H],
OB [auth K],
PB [auth L],
RB [auth L],
SB [auth L],
UA [auth 6],
UB [auth M],
VB [auth M],
XB [auth N]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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

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AC [auth U],
JB [auth T]
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
DGT
Query on DGT

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YB [auth O]2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
FMN
Query on FMN

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

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AB [auth 3]
DB [auth 9]
EB [auth 9]
TA [auth 6]
YA [auth 1]
AB [auth 3],
DB [auth 9],
EB [auth 9],
TA [auth 6],
YA [auth 1],
ZA [auth 3]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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

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IB [auth 7]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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CB [auth 3]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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ZB [auth O]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
C [auth D]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
AYA
Query on AYA
P [auth r]L-PEPTIDE LINKINGC5 H9 N O3ALA
FME
Query on FME
R [auth A]L-PEPTIDE LINKINGC6 H11 N O3 SMET
SAC
Query on SAC
LA [auth i]L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19_4092:

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: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Data collection, Database references