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- PDB-7zmb: CryoEM structure of mitochondrial complex I from Chaetomium therm... -

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Entry
Database: PDB / ID: 7zmb
TitleCryoEM structure of mitochondrial complex I from Chaetomium thermophilum (state 2)
Components
  • (NADH dehydrogenase (Ubiquinone)-like ...Respiratory complex I) x 2
  • (NADH dehydrogenase [ubiquinone] ...) x 5
  • (NADH-ubiquinone oxidoreductase ...) x 9
  • (NADH-ubiquinone oxidoreductase-like ...) x 7
  • (Oxidoreductase-like ...) x 2
  • Acyl carrier protein
  • Complex I-B22
  • Complex I-ESSS
  • NADH dehydrogenase subunit 2
  • NADH dehydrogenase-like protein
  • NADH-ubiquinone oxidoreductase
  • Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I)
  • Subunit NDUFA3 of NADH-ubiquinone oxidoreductase (Complex I)
  • Subunit NDUFB10 of NADH-ubiquinone oxidoreductase (Complex I)
  • Subunit NDUFB2 of NADH-ubiquinone oxidoreductase (Complex I)
  • Subunit NDUFB3 of NADH-ubiquinone oxidoreductase (Complex I)
  • Subunit NDUFB4 of NADH-ubiquinone oxidoreductase (Complex I)
  • Subunit NDUFB5 of NADH-ubiquinone oxidoreductase (Complex I)
  • Subunit NDUFB6 of NADH-ubiquinone oxidoreductase (Complex I)
  • Subunit NDUFC2 of NADH-ubiquinone oxidoreductase (Complex I)
  • Subunit NDUFS5 of NADH-ubiquinone oxidoreductase (Complex I)
  • Subunit NDUFV2 of NADH-ubiquinone oxidoreductase (Complex I)
KeywordsOXIDOREDUCTASE / Proton transporter / Mitochondrial membrane protein / Complex
Function / homology
Function and homology information


single-stranded DNA helicase activity / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding ...single-stranded DNA helicase activity / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / respiratory electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / DNA helicase / mitochondrial inner membrane / DNA replication / oxidoreductase activity / hydrolase activity / DNA repair / mitochondrion / DNA binding / ATP binding / membrane / metal ion binding / nucleus
Similarity search - Function
Oxidoreductase-like, N-terminal / Oxidoreductase-like domain-containing protein 1 / Oxidoreductase-like protein, N-terminal / NADH-ubiquinone oxidoreductase 17.8kDa subunit / : / Dna2 Rift barrel domain / DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / NADH dehydrogenase [ubiquinone] (complex I), 21kDa subunit, fungi ...Oxidoreductase-like, N-terminal / Oxidoreductase-like domain-containing protein 1 / Oxidoreductase-like protein, N-terminal / NADH-ubiquinone oxidoreductase 17.8kDa subunit / : / Dna2 Rift barrel domain / DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / NADH dehydrogenase [ubiquinone] (complex I), 21kDa subunit, fungi / Dna2/Cas4, domain of unknown function DUF83 / Domain of unknown function DUF83 / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / : / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / PD-(D/E)XK endonuclease-like domain superfamily / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Complex1_LYR-like / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / Soluble ligand binding domain / SLBB domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / GRIM-19 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NDUFA6, LYR domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / Complex 1 LYR protein domain / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / Complex 1 protein (LYR family) / 2Fe-2S iron-sulfur cluster binding domain / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / Chem-ZMP / NADH dehydrogenase (Ubiquinone)-like protein / NADH-ubiquinone oxidoreductase-like protein ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / Chem-ZMP / NADH dehydrogenase (Ubiquinone)-like protein / NADH-ubiquinone oxidoreductase-like protein / NADH-ubiquinone oxidoreductase 9.5 kDa subunit / NADH-ubiquinone oxidoreductase-like protein / NADH-ubiquinone oxidoreductase / NADH-ubiquinone oxidoreductase-like protein / NADH dehydrogenase-like protein / NADH-ubiquinone oxidoreductase-like protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH-ubiquinone oxidoreductase B14 subunit-like protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase B15 subunit / Uncharacterized protein / NADH-ubiquinone oxidoreductase-like protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit / Uncharacterized protein / NADH-ubiquinone oxidoreductase-like protein / NADH-ubiquinone oxidoreductase 30.4 kDa subunit-like protein / Oxidoreductase-like domain-containing protein / NADH-ubiquinone oxidoreductase-like protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / DNA replication ATP-dependent helicase/nuclease DNA2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase (Ubiquinone)-like protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Oxidoreductase-like protein / Acyl carrier protein / NADH-ubiquinone oxidoreductase 49 kDa subunit-like protein / NADH-ubiquinone oxidoreductase-like protein / NADH-ubiquinone oxidoreductase-like protein / NADH-ubiquinone oxidoreductase-like protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 4
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsLaube, E. / Kuehlbrandt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Sci Adv / Year: 2022
Title: Conformational changes in mitochondrial complex I of the thermophilic eukaryote .
Authors: Eike Laube / Jakob Meier-Credo / Julian D Langer / Werner Kühlbrandt /
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. ...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 , 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.
History
DepositionApr 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: NADH-ubiquinone oxidoreductase chain 1
2: NADH dehydrogenase subunit 2
3: NADH-ubiquinone oxidoreductase chain 3
4: NADH-ubiquinone oxidoreductase chain 4
5: NADH-ubiquinone oxidoreductase chain 5
6: NADH-ubiquinone oxidoreductase chain 6
8: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
9: Subunit NDUFS5 of NADH-ubiquinone oxidoreductase (Complex I)
A: NADH-ubiquinone oxidoreductase-like protein
B: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
C: NADH-ubiquinone oxidoreductase 49 kDa subunit-like protein
D: Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I)
E: NADH dehydrogenase (Ubiquinone)-like protein
F: NADH-ubiquinone oxidoreductase-like protein
G: NADH-ubiquinone oxidoreductase 30.4 kDa subunit-like protein
H: Subunit NDUFV2 of NADH-ubiquinone oxidoreductase (Complex I)
I: Oxidoreductase-like protein
J: NADH-ubiquinone oxidoreductase-like protein
K: NADH-ubiquinone oxidoreductase-like protein
L: NADH-ubiquinone oxidoreductase chain 4L
M: NADH-ubiquinone oxidoreductase-like protein
O: Acyl carrier protein
P: NADH-ubiquinone oxidoreductase B14 subunit-like protein
Q: Acyl carrier protein
R: Complex I-B22
S: Complex I-ESSS
U: NADH-ubiquinone oxidoreductase
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
X: NADH-ubiquinone oxidoreductase-like protein
Y: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
Z: NADH-ubiquinone oxidoreductase-like protein
a: NADH dehydrogenase (Ubiquinone)-like protein
b: Subunit NDUFC2 of NADH-ubiquinone oxidoreductase (Complex I)
c: Subunit NDUFB3 of NADH-ubiquinone oxidoreductase (Complex I)
d: Subunit NDUFB10 of NADH-ubiquinone oxidoreductase (Complex I)
e: Subunit NDUFB2 of NADH-ubiquinone oxidoreductase (Complex I)
f: NADH dehydrogenase-like protein
g: Subunit NDUFA3 of NADH-ubiquinone oxidoreductase (Complex I)
h: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
i: Subunit NDUFB6 of NADH-ubiquinone oxidoreductase (Complex I)
j: Subunit NDUFB4 of NADH-ubiquinone oxidoreductase (Complex I)
n: Subunit NDUFB5 of NADH-ubiquinone oxidoreductase (Complex I)
o: Oxidoreductase-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,217,49589
Polymers1,183,25543
Non-polymers34,24046
Water28,6981593
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, gel filtration, electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NADH-ubiquinone oxidoreductase ... , 9 types, 9 molecules 13456CGLP

#1: Protein NADH-ubiquinone oxidoreductase chain 1 / Subunit ND1 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 41716.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G1DJA6, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH-ubiquinone oxidoreductase chain 3 / Subunit ND3 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 16330.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G1DJ99, NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH-ubiquinone oxidoreductase chain 4 / Subunit ND4 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 60810.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G1DJA7, NADH:ubiquinone reductase (H+-translocating)
#5: Protein NADH-ubiquinone oxidoreductase chain 5 / Subunit ND5 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 75872.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids added according to map density, genome sequence and MS data.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G1DJA3, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH-ubiquinone oxidoreductase chain 6 / Subunit ND6 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 24819.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G1DJ96, NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH-ubiquinone oxidoreductase 49 kDa subunit-like protein / Subunit NDUFS2 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 55910.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids removed according to map density, genome sequence and MS data.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCG0
#15: Protein NADH-ubiquinone oxidoreductase 30.4 kDa subunit-like protein / Subunit NDUFS3 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 33377.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S8U1
#20: Protein NADH-ubiquinone oxidoreductase chain 4L / Subunit ND4L of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 9837.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G1DJA2, NADH:ubiquinone reductase (H+-translocating)
#23: Protein NADH-ubiquinone oxidoreductase B14 subunit-like protein / Subunit NDUFA6 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 14836.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S4Q3

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Protein , 16 types, 17 molecules 29DHOQRSUbcdfgijn

#2: Protein NADH dehydrogenase subunit 2 / / Subunit ND2 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 64129.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G1DJ98
#8: Protein Subunit NDUFS5 of NADH-ubiquinone oxidoreductase (Complex I) / Subunit NDUFS5 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 87142.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. One additional amino acid modelled according to map density and genome sequence.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SG48
#12: Protein Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I) / Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 9833.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: No entry (not annotated). Sequence modelled according to map density, genome sequence and MS data. Last five amino acids unknown and modelled as Poly-Ala
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#16: Protein Subunit NDUFV2 of NADH-ubiquinone oxidoreductase (Complex I) / Subunit NDUFV2 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 35005.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SDM6
#22: Protein Acyl carrier protein / / Subunit NDUFAB1 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 15593.649 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ZMP covalently linked to Ser98.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SBG9
#24: Protein Complex I-B22 / Subunit NDUFB9 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 11636.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAY0
#25: Protein Complex I-ESSS / Subunit NDUFB11 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 15847.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence renumbered (compared to entry sequence) according to map density and genome sequence.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAN0, DNA helicase
#26: Protein NADH-ubiquinone oxidoreductase / Subunit NDUFA8 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 21517.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0R3
#32: Protein Subunit NDUFC2 of NADH-ubiquinone oxidoreductase (Complex I) / Subunit NDUFC2 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 10823.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S812
#33: Protein Subunit NDUFB3 of NADH-ubiquinone oxidoreductase (Complex I) / Subunit NDUFB3 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 11153.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S681
#34: Protein Subunit NDUFB10 of NADH-ubiquinone oxidoreductase (Complex I) / Subunit NDUFB10 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 12514.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEZ1
#36: Protein NADH dehydrogenase-like protein / Subunit NDUFA2 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 10897.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acid removed according to map density, genome sequence and MS data.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1P3
#37: Protein Subunit NDUFA3 of NADH-ubiquinone oxidoreductase (Complex I) / Subunit NDUFA3 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 9076.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZZ2
#39: Protein Subunit NDUFB6 of NADH-ubiquinone oxidoreductase (Complex I) / Subunit NDUFB6 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 10857.294 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S569
#40: Protein Subunit NDUFB4 of NADH-ubiquinone oxidoreductase (Complex I) / Subunit NDUFB4 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 8760.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S5C8
#41: Protein Subunit NDUFB5 of NADH-ubiquinone oxidoreductase (Complex I) / Subunit NDUFB5 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 20824.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids added and removed according to map density and genome sequence.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S086

-
NADH dehydrogenase [ubiquinone] ... , 5 types, 5 molecules 8BWYh

#7: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Subunit NDUFB7 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 10312.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAE9
#10: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Subunit NDUFV1 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 55453.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G0SA46, NADH:ubiquinone reductase (H+-translocating)
#27: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Subunit NDUFA13 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 14039.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SB83
#29: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Subunit NDUFS4 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 23494.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S3Y7
#38: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit / Subunit NDUFA12 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 15967.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence renumbered (compared to entry sequence) according to map density, genome sequence and MS data.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S775

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NADH-ubiquinone oxidoreductase-like ... , 7 types, 7 molecules AFJKMXZ

#9: Protein NADH-ubiquinone oxidoreductase-like protein / Subunit NDUFS1 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 82096.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids removed and added to sequence according to map density, genome sequence and MS data.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYA1
#14: Protein NADH-ubiquinone oxidoreductase-like protein / Subunit NDUFA5 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 29244.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S8H4
#18: Protein NADH-ubiquinone oxidoreductase-like protein / Subunit NDUFA11 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 21612.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S2B3
#19: Protein NADH-ubiquinone oxidoreductase-like protein / Subunit NDUFS7 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 25549.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9I6
#21: Protein NADH-ubiquinone oxidoreductase-like protein / Subunit NDUFS6 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 18613.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids added and removed according to map density, genome sequence and MS data.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S6J1
#28: Protein NADH-ubiquinone oxidoreductase-like protein / Subunit NUXM of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 21645.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0S8
#30: Protein NADH-ubiquinone oxidoreductase-like protein / Subunit NDUFA7 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 21164.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids removed and added according to map density and genome sequence.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEF0

-
NADH dehydrogenase (Ubiquinone)-like ... , 2 types, 2 molecules Ea

#13: Protein NADH dehydrogenase (Ubiquinone)-like protein / Subunit NDUFA9 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 43800.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids added according to map density, genome sequence and MS data.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SB35
#31: Protein NADH dehydrogenase (Ubiquinone)-like protein / Subunit NDUFB8 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 23239.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids removed and added according to map density, genome sequence and MS data.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RXU4

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Oxidoreductase-like ... , 2 types, 2 molecules Io

#17: Protein Oxidoreductase-like protein / Subunit NDUFS8 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 25415.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence renumbered (compared to entry sequence).
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SBG8
#42: Protein Oxidoreductase-like domain-containing protein / Subunit Ct-NDUFV3 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 41609.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S982

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Protein/peptide , 1 types, 1 molecules e

#35: Protein/peptide Subunit NDUFB2 of NADH-ubiquinone oxidoreductase (Complex I) / Subunit NDUFB2 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 5278.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: No entry (not annotated). Sequence modelled according to map density, genome sequence and MS data.
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719

-
Non-polymers , 11 types, 1639 molecules

#43: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#44: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#45: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#46: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
#47: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#48: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#49: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#50: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#51: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#52: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#53: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1593 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

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Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Mitochondrial NADH:ubiquinone oxidoreductase in LMNG / Type: COMPLEX / Entity ID: #1-#42 / Source: NATURAL
Molecular weightValue: 0.97 MDa / Experimental value: NO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (pH adjusted with sodium hydroxide)Hepes/NaOH1
2100 mMsodium chlorideNaClSodium chloride1
30.0015 % [w/v]lauryl maltose neopentyl glycolLMNG1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.11 sec. / Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6503
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV

-
Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1.13CTF correction
7UCSF Chimera1.12model fitting
9PHENIX1.19model refinement
10Coot0.9.2model refinement
11cryoSPARC3.0.1initial Euler assignment
13RELION3.0.8classification
14cryoSPARC3.0.1classification
15cryoSPARC3.0.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1087651
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21989 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-ID
16RFR

6rfr

1
26RFQ

6rfq

1
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00469849
ELECTRON MICROSCOPYf_angle_d0.61594548
ELECTRON MICROSCOPYf_dihedral_angle_d28.66310242
ELECTRON MICROSCOPYf_chiral_restr0.04310304
ELECTRON MICROSCOPYf_plane_restr0.00511875

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