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- PDB-7zm8: CryoEM structure of mitochondrial complex I from Chaetomium therm... -

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Basic information

Entry
Database: PDB / ID: 7zm8
TitleCryoEM structure of mitochondrial complex I from Chaetomium thermophilum (inhibited by DDM) - membrane arm
Components
  • (NADH dehydrogenase ...) x 4
  • (NADH-ubiquinone oxidoreductase chain ...) x 6
  • (NADH-ubiquinone oxidoreductase-like ...) x 2
  • Acyl carrier protein
  • Complex I-B22
  • Complex I-ESSS
  • 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)
KeywordsOXIDOREDUCTASE / Proton transporter / Mitochondrial membrane protein / Complex
Function / homology
Function and homology information


NADH dehydrogenase complex / 5'-flap endonuclease activity / replication fork reversal / single-stranded DNA helicase activity / acyl binding / ubiquinone binding / electron transport coupled proton transport / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly ...NADH dehydrogenase complex / 5'-flap endonuclease activity / replication fork reversal / single-stranded DNA helicase activity / acyl binding / ubiquinone binding / electron transport coupled proton transport / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / aerobic respiration / electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / 4 iron, 4 sulfur cluster binding / DNA helicase / mitochondrial inner membrane / DNA repair / mitochondrion / DNA binding / ATP binding / metal ion binding / nucleus / membrane
Similarity search - Function
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 / 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 ...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 / 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 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / PD-(D/E)XK endonuclease-like domain superfamily / Helix Hairpins - #3510 / DNA2/NAM7 helicase, helicase domain / AAA domain / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / DNA2/NAM7-like helicase / : / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / 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 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / GRIM-19 / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, chain 5-like / Complex 1 LYR protein domain / NADH:ubiquinone oxidoreductase / Complex 1 protein (LYR family) / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Helix Hairpins / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-ZMP / NADH dehydrogenase (Ubiquinone)-like protein / NADH-ubiquinone oxidoreductase 9.5 kDa subunit / NADH-ubiquinone oxidoreductase-like protein / NADH-ubiquinone oxidoreductase / NADH-ubiquinone oxidoreductase-like protein / NADH-ubiquinone oxidoreductase-like protein ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-ZMP / NADH dehydrogenase (Ubiquinone)-like protein / NADH-ubiquinone oxidoreductase 9.5 kDa subunit / NADH-ubiquinone oxidoreductase-like protein / NADH-ubiquinone oxidoreductase / NADH-ubiquinone oxidoreductase-like protein / NADH-ubiquinone oxidoreductase-like protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase B15 subunit / Uncharacterized protein / Uncharacterized protein / 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] 1 alpha subcomplex subunit 13 / Acyl carrier protein / NADH-ubiquinone oxidoreductase-like protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / 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: 2.76 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
Revision 1.2Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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)
D: Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I)
J: NADH-ubiquinone oxidoreductase-like protein
L: NADH-ubiquinone oxidoreductase chain 4L
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
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)
g: Subunit NDUFA3 of NADH-ubiquinone oxidoreductase (Complex I)
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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)724,62957
Polymers701,19526
Non-polymers23,43531
Water10,953608
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 chain ... , 6 types, 6 molecules 13456L

#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 ND1 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 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)

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NADH dehydrogenase ... , 4 types, 4 molecules 28Wa

#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
#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
#16: 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
#18: Protein NADH dehydrogenase (Ubiquinone)-like protein / Subunit NDUFB8 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 89210.109 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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Protein , 13 types, 13 molecules 9DQRSUbcdgijn

#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
#9: 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)
#12: Protein Acyl carrier protein / Subunit NDUFAB1 of NADH-ubiquinone oxidoreductase (Complex I)


Mass: 15593.649 Da / Num. of mol.: 1 / 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
#13: 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
#14: 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
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAN0, DNA helicase
#15: 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
#19: 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
#20: 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
#21: 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
#23: 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
#24: 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
#25: 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
#26: 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

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NADH-ubiquinone oxidoreductase-like ... , 2 types, 2 molecules JX

#10: 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
#17: 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

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Protein/peptide / Sugars , 2 types, 15 molecules e

#22: 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)
#29: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 625 molecules

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


Mass: 748.065 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#28: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#30: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#31: 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.: 1 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#32: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Mitochondrial NADH:ubiquinone oxidoreductase in DDM / Type: COMPLEX / Entity ID: #1-#26 / 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 chlorideNaCl1
30.015 % [w/v]n-dodecyl beta-D-maltosideDDM1
SpecimenConc.: 3.6 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 FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 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: 1996
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1.13CTF correction
7UCSF Chimera1.12model fitting
9PHENIX1.19model refinement
10Coot0.9.2model refinement
11RELION3.0.8initial Euler assignment
13RELION3.0.8classification
14cryoSPARC3.0.1classification
15cryoSPARC3.0.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 126638
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37767 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16RFR

6rfr

16RFR1PDBexperimental model
26RFQ

6rfq

16RFQ2PDBexperimental model

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