7ZMH

CryoEM structure of mitochondrial complex I from Chaetomium thermophilum (state 1) - membrane arm


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Conformational changes in mitochondrial complex I of the thermophilic eukaryote Chaetomium thermophilum.

Laube, E.Meier-Credo, J.Langer, J.D.Kuhlbrandt, W.

(2022) Sci Adv 8: eadc9952-eadc9952

  • DOI: https://doi.org/10.1126/sciadv.adc9952

  • PubMed Abstract: 

    Mitochondrial complex I is a redox-driven proton pump that generates proton-motive force across the inner mitochondrial membrane, powering oxidative phosphorylation and ATP synthesis in eukaryotes. We report the structure of complex I from the thermophilic fungus Chaetomium thermophilum , determined by cryoEM up to 2.4-Å resolution. We show that the complex undergoes a transition between two conformations, which we refer to as state 1 and state 2. The conformational switch is manifest in a twisting movement of the peripheral arm relative to the membrane arm, but most notably in substantial rearrangements of the Q-binding cavity and the E-channel, resulting in a continuous aqueous passage from the E-channel to subunit ND5 at the far end of the membrane arm. The conformational changes in the complex interior resemble those reported for mammalian complex I, suggesting a highly conserved, universal mechanism of coupling electron transport to proton pumping.


  • Organizational Affiliation

    Max-Planck-Institute of Biophysics, Frankfurt 60438, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1A [auth 1]378Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for G1DJA6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 2B [auth 2]571Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3C [auth 3]146Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4D [auth 4]542Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5E [auth 5]679Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6F [auth 6]224Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7G [auth 8]86Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NDUFS5 of NADH-ubiquinone oxidoreductase (Complex I)H [auth 9]785Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I)I [auth D]86Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase-like protein199Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G0S2B3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LK [auth L]89Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinL [auth Q]141Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B22M [auth R]99Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-ESSSN [auth S]143Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 3.6.4.12
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductaseO [auth U]186Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13P [auth W]121Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase-like proteinQ [auth X]191Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase (Ubiquinone)-like proteinR [auth a]815Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0RXU4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NDUFC2 of NADH-ubiquinone oxidoreductase (Complex I)S [auth b]94Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NDUFB3 of NADH-ubiquinone oxidoreductase (Complex I)T [auth c]93Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NDUFB10 of NADH-ubiquinone oxidoreductase (Complex I)U [auth d]105Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NDUFB2 of NADH-ubiquinone oxidoreductase (Complex I)V [auth e]46Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NDUFA3 of NADH-ubiquinone oxidoreductase (Complex I)W [auth g]82Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NDUFB6 of NADH-ubiquinone oxidoreductase (Complex I)X [auth i]93Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NDUFB4 of NADH-ubiquinone oxidoreductase (Complex I)Y [auth j]75Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NDUFB5 of NADH-ubiquinone oxidoreductase (Complex I)Z [auth n]184Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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CA [auth 2],
RA [auth D],
UA [auth S],
YA [auth X],
ZA [auth X]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
LMN
Query on LMN

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DA [auth 2],
FB [auth j],
GA [auth 4]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
PC1
Query on PC1

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AB [auth X]
BA [auth 1]
BB [auth X]
EA [auth 3]
HA [auth 4]
AB [auth X],
BA [auth 1],
BB [auth X],
EA [auth 3],
HA [auth 4],
JA [auth 5],
OA [auth 5],
VA [auth S]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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AA [auth 1]
CB [auth g]
DB [auth g]
EB [auth i]
FA [auth 4]
AA [auth 1],
CB [auth g],
DB [auth g],
EB [auth i],
FA [auth 4],
GB [auth n],
HB [auth n],
IA [auth 4],
KA [auth 5],
LA [auth 5],
MA [auth 5],
NA [auth 5],
PA [auth 5],
QA [auth 6],
SA [auth J],
WA [auth W],
XA [auth W]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
ZMP
Query on ZMP

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TA [auth Q]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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
MODEL REFINEMENTCoot0.9.2
RECONSTRUCTIONcryoSPARC3.0.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references