8CA3

Cryo-EM structure NDUFS4 knockout complex I from Mus musculus heart (Class 2).


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Structural insights into respiratory complex I deficiency and assembly from the mitochondrial disease-related ndufs4 -/- mouse.

Yin, Z.Agip, A.A.Bridges, H.R.Hirst, J.

(2024) EMBO J 43: 225-249

  • DOI: https://doi.org/10.1038/s44318-023-00001-4
  • Primary Citation of Related Structures:  
    8C2S, 8CA1, 8CA3, 8CA4, 8CA5

  • PubMed Abstract: 

    Respiratory complex I (NADH:ubiquinone oxidoreductase) is essential for cellular energy production and NAD + homeostasis. Complex I mutations cause neuromuscular, mitochondrial diseases, such as Leigh Syndrome, but their molecular-level consequences remain poorly understood. Here, we use a popular complex I-linked mitochondrial disease model, the ndufs4 -/- mouse, to define the structural, biochemical, and functional consequences of the absence of subunit NDUFS4. Cryo-EM analyses of the complex I from ndufs4 -/- mouse hearts revealed a loose association of the NADH-dehydrogenase module, and discrete classes containing either assembly factor NDUFAF2 or subunit NDUFS6. Subunit NDUFA12, which replaces its paralogue NDUFAF2 in mature complex I, is absent from all classes, compounding the deletion of NDUFS4 and preventing maturation of an NDUFS4-free enzyme. We propose that NDUFAF2 recruits the NADH-dehydrogenase module during assembly of the complex. Taken together, the findings provide new molecular-level understanding of the ndufs4 -/- mouse model and complex I-linked mitochondrial disease.


  • Organizational Affiliation

    The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3115Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial224Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:1922656
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial263Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:1915599
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial463Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:2385112
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial245Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:1920150
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial464Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:107851
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial727Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:2443241
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1318Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial212Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:2385079
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6172Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4L98Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5607Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4459Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2345Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial355Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1914523
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial377Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913358
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialQ [auth R]116Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:107932
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2R [auth S]99Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CQ75 (Mus musculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialS [auth T],
T [auth U]
156Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CR21 (Mus musculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5U [auth V]116Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CPP6 (Mus musculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6V [auth W]131Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1914380
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8W [auth X]172Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1915625
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
MCG5603X [auth Y]143Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1917125
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13Y [auth Z]144Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1Z [auth a]70Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3AA [auth b]84Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9CQ91 (Mus musculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialBA [auth c]76Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2CA [auth d]120Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5DA [auth e]106Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1890889
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1EA [auth f]57Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialFA [auth g]151Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialGA [auth h]189Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913296
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6HA [auth i]127Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialIA [auth j]105Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3JA [auth k]104Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialKA [auth l]186Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1914514
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4LA [auth m]129Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9MA [auth n]179Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913468
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7NA [auth o]137Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10OA [auth p]176Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7PA [auth r]113Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913666
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z1P6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialQA [auth s]104Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8BK30 (Mus musculus)
Explore Q8BK30 
Go to UniProtKB:  Q8BK30
IMPC:  MGI:1890894
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BK30
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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GB [auth L]
KB [auth M]
LB [auth N]
MB [auth N]
UB [auth d]
GB [auth L],
KB [auth M],
LB [auth N],
MB [auth N],
UB [auth d],
VB [auth h]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
UQ9
Query on UQ9

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ZA [auth H]Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
PC1
Query on PC1

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AB [auth H],
SA [auth B]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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BB [auth H]
EB [auth J]
FB [auth L]
HB [auth L]
SB [auth Y]
BB [auth H],
EB [auth J],
FB [auth L],
HB [auth L],
SB [auth Y],
TB [auth Z],
WB [auth i]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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

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QB [auth T],
RB [auth U]
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
C25 H49 N2 O9 P S
JYSKQPQRUCZFIQ-REWPJTCUSA-N
GTP
Query on GTP

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NB [auth O]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
LMT
Query on LMT

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IB [auth L],
JB [auth L]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FMN
Query on FMN

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

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CB [auth I]
DB [auth I]
RA [auth B]
UA [auth F]
WA [auth G]
CB [auth I],
DB [auth I],
RA [auth B],
UA [auth F],
WA [auth G],
XA [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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TA [auth E],
YA [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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PB [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
2MR
Query on 2MR
D
L-PEPTIDE LINKINGC8 H18 N4 O2ARG
SAC
Query on SAC
HA [auth i]L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105663141
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00015/2
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00028/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data processing
  • Version 1.2: 2024-01-17
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Database references