7ZME

CryoEM structure of mitochondrial complex I from Chaetomium thermophilum (state 2) - membrane arm


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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: 10.1126/sciadv.adc9952
  • Primary Citation of Related Structures:  
    7ZM7, 7ZM8, 7ZMB, 7ZME, 7ZMG, 7ZMH

  • 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1A [auth 1]378Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_m000470
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
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 2B [auth 2]571Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_m000270
Membrane Entity: Yes 
UniProt
Find proteins for G1DJ98 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3C [auth 3]146Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_m000280
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4D [auth 4]542Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_m000480
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for G1DJA7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5E [auth 5]679Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_m000370
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6F [auth 6]224Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_m000070
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for G1DJ96 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7G [auth 8]86Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0042030
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NDUFS5 of NADH-ubiquinone oxidoreductase (Complex I)H [auth 9]785Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0065020
Membrane Entity: Yes 
UniProt
Find proteins for G0SG48 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I)I [auth D]86Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase-like proteinJ199Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0016630
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LK [auth L]89Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_m000360
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier proteinL [auth Q]141Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0050230
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B22M [auth R]99Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0048190
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-ESSSN [auth S]143Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0042860
EC: 3.6.4.12
Membrane Entity: Yes 
UniProt
Find proteins for G0SAN0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductaseO [auth U]186Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0010950
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13P [auth W]121Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0049240
Membrane Entity: Yes 
UniProt
Find proteins for G0SB83 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase-like proteinQ [auth X]191Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0011100
Membrane Entity: Yes 
UniProt
Find proteins for G0S0S8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase (Ubiquinone)-like proteinR [auth a]815Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0000410
UniProt
Find proteins for G0RXU4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NDUFC2 of NADH-ubiquinone oxidoreductase (Complex I)S [auth b]94Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0028990
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NDUFB3 of NADH-ubiquinone oxidoreductase (Complex I)T [auth c]93Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0025810
Membrane Entity: Yes 
UniProt
Find proteins for G0S681 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NDUFB10 of NADH-ubiquinone oxidoreductase (Complex I)U [auth d]105Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0060200
Membrane Entity: Yes 
UniProt
Find proteins for G0SEZ1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NDUFB2 of NADH-ubiquinone oxidoreductase (Complex I)V [auth e]46Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NDUFA3 of NADH-ubiquinone oxidoreductase (Complex I)W [auth g]82Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0008140
UniProt
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NDUFB6 of NADH-ubiquinone oxidoreductase (Complex I)X [auth i]93Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0032450
Membrane Entity: Yes 
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NDUFB4 of NADH-ubiquinone oxidoreductase (Complex I)Y [auth j]75Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0024350
Membrane Entity: Yes 
UniProt
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NDUFB5 of NADH-ubiquinone oxidoreductase (Complex I)Z [auth n]184Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 1 
Gene Names: CTHT_0009140
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AB [auth g],
DA [auth 2],
HA [auth 4],
UA [auth D],
ZA [auth X]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
LMN
Query on LMN

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EA [auth 2],
KA [auth 4],
WA [auth J]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
 Ligand Interaction
PC1
Query on PC1

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CA [auth 1],
EB [auth n],
FA [auth 2],
GA [auth 3],
LA [auth 4],
CA [auth 1],
EB [auth n],
FA [auth 2],
GA [auth 3],
LA [auth 4],
NA [auth 5],
RA [auth 5]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
3PE
Query on 3PE

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AA [auth 1],
BA [auth 1],
BB [auth g],
CB [auth g],
DB [auth n],
AA [auth 1],
BA [auth 1],
BB [auth g],
CB [auth g],
DB [auth n],
FB [auth n],
IA [auth 4],
JA [auth 4],
MA [auth 4],
OA [auth 5],
PA [auth 5],
QA [auth 5],
SA [auth 5],
TA [auth 8],
VA [auth J],
YA [auth W]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
ZMP
Query on ZMP

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XA [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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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