7ZME | pdb_00007zme

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 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7ZME

This is version 1.2 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
  • Primary Citation 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 2.4-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.

Macromolecule Content 

  • Total Structure Weight: 729.6 kDa 
  • Atom Count: 36,964 
  • Modeled Residue Count: 4,396 
  • Deposited Residue Count: 6,253 
  • Unique protein chains: 26

Macromolecules

Find similar proteins by:|  3D Structure
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))
Explore G1DJA6 
Go to UniProtKB:  G1DJA6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1DJA6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 2B [auth 2]571Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for G1DJ98 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G1DJ98 
Go to UniProtKB:  G1DJ98
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1DJ98
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Find proteins for G1DJ99 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G1DJ99 
Go to UniProtKB:  G1DJ99
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1DJ99
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Find proteins for G1DJA7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G1DJA7 
Go to UniProtKB:  G1DJA7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1DJA7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Find proteins for G1DJA3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G1DJA3 
Go to UniProtKB:  G1DJA3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1DJA3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Find proteins for G1DJ96 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G1DJ96 
Go to UniProtKB:  G1DJ96
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1DJ96
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 
UniProt
Find proteins for G0SAE9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SAE9 
Go to UniProtKB:  G0SAE9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SAE9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 
UniProt
Find proteins for G0SG48 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SG48 
Go to UniProtKB:  G0SG48
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SG48
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I)I [auth D]86Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Find similar proteins by:|  3D Structure
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))
Explore G0S2B3 
Go to UniProtKB:  G0S2B3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S2B3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Find proteins for G1DJA2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G1DJA2 
Go to UniProtKB:  G1DJA2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1DJA2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Acyl carrier proteinL [auth Q]141Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SBG9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SBG9 
Go to UniProtKB:  G0SBG9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SBG9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Complex I-B22M [auth R]99Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G0SAY0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SAY0 
Go to UniProtKB:  G0SAY0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SAY0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 
UniProt
Find proteins for G0SAN0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SAN0 
Go to UniProtKB:  G0SAN0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SAN0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductaseO [auth U]186Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G0S0R3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S0R3 
Go to UniProtKB:  G0S0R3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S0R3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 
UniProt
Find proteins for G0SB83 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SB83 
Go to UniProtKB:  G0SB83
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SB83
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase-like proteinQ [auth X]191Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G0S0S8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S0S8 
Go to UniProtKB:  G0S0S8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S0S8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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))
Explore G0RXU4 
Go to UniProtKB:  G0RXU4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0RXU4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Find proteins for G0S812 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S812 
Go to UniProtKB:  G0S812
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S812
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Find proteins for G0S681 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S681 
Go to UniProtKB:  G0S681
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S681
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Find proteins for G0SEZ1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SEZ1 
Go to UniProtKB:  G0SEZ1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SEZ1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NDUFB2 of NADH-ubiquinone oxidoreductase (Complex I)V [auth e]46Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NDUFA3 of NADH-ubiquinone oxidoreductase (Complex I)W [auth g]82Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0RZZ2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0RZZ2 
Go to UniProtKB:  G0RZZ2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0RZZ2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 
UniProt
Find proteins for G0S569 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S569 
Go to UniProtKB:  G0S569
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S569
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 
UniProt
Find proteins for G0S5C8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S5C8 
Go to UniProtKB:  G0S5C8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S5C8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Subunit NDUFB5 of NADH-ubiquinone oxidoreductase (Complex I)Z [auth n]184Thermochaetoides thermophila DSM 1495Mutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for G0S086 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S086 
Go to UniProtKB:  G0S086
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S086
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
AB [auth g],
DA [auth 2],
HA [auth 4],
UA [auth D],
ZA [auth X]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
LMN

Query on LMN



Download:Ideal Coordinates CCD File
EA [auth 2],
KA [auth 4],
WA [auth J]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
PC1

Query on PC1



Download:Ideal Coordinates CCD File
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
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
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
ZMP

Query on ZMP



Download:Ideal Coordinates CCD File
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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
MODEL REFINEMENTCoot0.9.2
RECONSTRUCTIONcryoSPARC3.0.1

Structure Validation

View Full Validation Report



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
  • Version 1.2: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary