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- PDB-8esz: Structure of mitochondrial complex I from Drosophila melanogaster... -

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Entry
Database: PDB / ID: 8esz
TitleStructure of mitochondrial complex I from Drosophila melanogaster, Helix-locked state
Components
  • (NADH dehydrogenase ...) x 29
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein, mitochondrial
  • Complex I-49kD
  • GEO11417p1
  • LD31474p
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
  • RH45008p
KeywordsOXIDOREDUCTASE / NADH:ubiquinone oxidoreductase / TRANSLOCASE
Function / homology
Function and homology information


Mitochondrial protein import / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / Protein lipoylation / Mitochondrial protein degradation / regulation of terminal button organization / Neutrophil degranulation / mitochondrial [2Fe-2S] assembly complex ...Mitochondrial protein import / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / Protein lipoylation / Mitochondrial protein degradation / regulation of terminal button organization / Neutrophil degranulation / mitochondrial [2Fe-2S] assembly complex / ubiquinone-6 biosynthetic process / cellular respiration / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / respiratory chain complex I / : / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / : / aerobic respiration / respiratory electron transport chain / proton transmembrane transport / reactive oxygen species metabolic process / determination of adult lifespan / response to reactive oxygen species / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / protein-containing complex binding / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
NADH:ubiquinone oxidoreductase, subunit NDUFB4 / : / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 ...NADH:ubiquinone oxidoreductase, subunit NDUFB4 / : / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / : / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / : / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / Zinc finger, CHCC-type / Zinc-finger domain / 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:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / GRIM-19 / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NDUFB9, LYR domain / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NDUFA6, LYR domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / Deoxynucleoside kinase domain / Deoxynucleoside kinase / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH-quinone oxidoreductase, chain G, C-terminal / : / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / SLBB domain / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone oxidoreductase chain 4L/K / Complex 1 LYR protein domain / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / Complex 1 protein (LYR family) / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / : / NADH-quinone oxidoreductase, subunit D / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / TETRADECANE / CARDIOLIPIN / DODECANE / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / N-OCTANE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE ...1,2-Distearoyl-sn-glycerophosphoethanolamine / TETRADECANE / CARDIOLIPIN / DODECANE / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / N-OCTANE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / UBIQUINONE-10 / Chem-WSF / Chem-ZMP / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / GH23780p / GEO11417p1 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Acyl carrier protein, mitochondrial / NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / GM23292p / Complex I-49kD / NADH dehydrogenase (ubiquinone) 23 kDa subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase (Ubiquinone) 13 kDa B subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A / LD31474p / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPadavannil, A. / Letts, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137929 United States
CitationJournal: Elife / Year: 2023
Title: Resting mitochondrial complex I from adopts a helix-locked state.
Authors: Abhilash Padavannil / Anjaneyulu Murari / Shauna-Kay Rhooms / Edward Owusu-Ansah / James A Letts /
Abstract: Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the ...Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the evolutionary split between Protostomia and Deuterostomia. Complex I from Deuterostomia including mammals can adopt a biochemically defined off-pathway 'deactive' state, whereas complex I from Protostomia cannot. The presence of off-pathway states complicates the interpretation of structural results and has led to considerable mechanistic debate. Here, we report the structure of mitochondrial complex I from the thoracic muscles of the model protostome . We show that although complex I (-CI) does not have a NEM-sensitive deactive state, it does show slow activation kinetics indicative of an off-pathway resting state. The resting-state structure of -CI from the thoracic muscle reveals multiple conformations. We identify a helix-locked state in which an N-terminal α-helix on the NDUFS4 subunit wedges between the peripheral and membrane arms. Comparison of the -CI structure and conformational states to those observed in bacteria, yeast, and mammals provides insight into the roles of subunits across organisms, explains why the -CI off-pathway resting state is NEM insensitive, and raises questions regarding current mechanistic models of complex I turnover.
History
DepositionOct 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AN: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
S6: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
S1: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
S3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
V2: NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A
S7: LD31474p
S8: NADH dehydrogenase (ubiquinone) 23 kDa subunit
1: NADH-ubiquinone oxidoreductase chain 1
4: NADH-ubiquinone oxidoreductase chain 4
5: NADH-ubiquinone oxidoreductase chain 5
A8: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
A1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
AO: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
S5: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
AM: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
BL: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
B6: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
B4: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
B7: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
B5: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
B9: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
BM: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
B8: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
B3: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
AC: Acyl carrier protein, mitochondrial
C2: NADH dehydrogenase [ubiquinone] 1 subunit C2
B1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
S4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
A9: NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A
B2: GEO11417p1
S2: Complex I-49kD
V3: NADH dehydrogenase [ubiquinone] flavoprotein 3
V1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
2: NADH-ubiquinone oxidoreductase chain 2
A7: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
A3: RH45008p
4L: NADH-ubiquinone oxidoreductase chain 4L
6: NADH-ubiquinone oxidoreductase chain 6
3: NADH-ubiquinone oxidoreductase chain 3
A5: NADH dehydrogenase (Ubiquinone) 13 kDa B subunit
AL: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
A6: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
AB: Acyl carrier protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,074,286111
Polymers1,026,98943
Non-polymers47,29868
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NADH dehydrogenase ... , 29 types, 29 molecules ANS6S3V2S8A8A1AOS5AMBLB6B4B7B5B9BMB8B3C2B1S4A9V3V1A7A5ALA6

#1: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 16848.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VQD7
#2: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 14383.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VMU0
#4: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase (Ubiquinone) 30 kDa subunit


Mass: 30013.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
References: UniProt: Q9VZU4, NADH:ubiquinone reductase (H+-translocating)
#5: Protein NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A / NADH dehydrogenase (Ubiquinone) 24 kDa subunit / isoform B


Mass: 26814.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VX36
#7: Protein NADH dehydrogenase (ubiquinone) 23 kDa subunit


Mass: 24609.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
References: UniProt: Q9VF27, NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8


Mass: 19873.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W125
#12: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Complex I-MWFE / NADH-ubiquinone oxidoreductase MWFE subunit


Mass: 14878.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: A8DYC4
#13: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


Mass: 17773.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W402
#14: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Complex I-15 kDa / NADH-ubiquinone oxidoreductase 15 kDa subunit


Mass: 12015.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q7K1C0
#15: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Complex I-B14.7 / NADH-ubiquinone oxidoreductase subunit B14.7


Mass: 18433.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q7JYH3
#16: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10


Mass: 18946.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VQR2
#17: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 19025.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9V3W2
#18: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Complex I-B15 / NADH-ubiquinone oxidoreductase B15 subunit


Mass: 13157.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q6IDF5
#19: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7


Mass: 13905.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VXZ0
#20: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / Complex I-SGDH / NADH-ubiquinone oxidoreductase SGDH subunit


Mass: 22065.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VTU2
#21: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9


Mass: 17416.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VJZ4
#22: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit


Mass: 16988.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9V3L7
#23: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 20229.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W3X7
#24: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Complex I-B12 / NADH-ubiquinone oxidoreductase B12 subunit


Mass: 12113.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W2E8
#26: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 12925.802 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VQM2
#27: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Complex I-MNLL / NADH-ubiquinone oxidoreductase MNLL subunit


Mass: 6232.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W3N7
#28: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial


Mass: 20710.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VWI0
#29: Protein NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A / NADH dehydrogenase (Ubiquinone) 39 kDa subunit / isoform B / TB01457p1


Mass: 46891.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VPE2, NADH dehydrogenase
#32: Protein/peptide NADH dehydrogenase [ubiquinone] flavoprotein 3


Mass: 3166.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
#33: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 51898.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
References: UniProt: Q9VMI3, NADH:ubiquinone reductase (H+-translocating)
#35: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Complex I-B14.5a / NADH-ubiquinone oxidoreductase subunit B14.5a


Mass: 11562.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O97418
#40: Protein NADH dehydrogenase (Ubiquinone) 13 kDa B subunit / RH11203p


Mass: 13808.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VTB4, NADH dehydrogenase
#41: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-42kD / CI-42kD / NADH-ubiquinone oxidoreductase 42 kDa subunit


Mass: 46955.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P91929
#42: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 14921.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q7JZK1

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Protein , 6 types, 7 molecules S1S7ACABB2S2A3

#3: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Complex I-75kD / CI-75kD


Mass: 78724.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
References: UniProt: Q94511, NADH:ubiquinone reductase (H+-translocating)
#6: Protein LD31474p / NADH dehydrogenase (Ubiquinone) 20 kDa subunit / isoform A / isoform B / isoform C


Mass: 24622.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VXK7
#25: Protein Acyl carrier protein, mitochondrial / ACP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit / NADH-ubiquinone oxidoreductase acyl-carrier subunit


Mass: 17257.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q94519
#30: Protein GEO11417p1 / NADH dehydrogenase (Ubiquinone) AGGG subunit / isoform A / isoform B / RH18150p


Mass: 10758.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q7PL91
#31: Protein Complex I-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 52985.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9V4E0
#36: Protein RH45008p / Uncharacterized protein / isoform A / isoform B


Mass: 8412.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W380

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules 14524L63

#8: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 36383.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
References: UniProt: C7DZL9, NADH:ubiquinone reductase (H+-translocating)
#9: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 51383.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
References: UniProt: Q9MDK5, NADH:ubiquinone reductase (H+-translocating)
#10: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 65777.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
References: UniProt: C7DZL4, NADH:ubiquinone reductase (H+-translocating)
#34: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39839.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
References: UniProt: P03896, NADH:ubiquinone reductase (H+-translocating)
#37: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 11363.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
References: UniProt: P18934, NADH:ubiquinone reductase (H+-translocating)
#38: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 20083.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
References: UniProt: P18933, NADH:ubiquinone reductase (H+-translocating)
#39: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 13572.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
References: UniProt: P18930, NADH:ubiquinone reductase (H+-translocating)

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Non-polymers , 15 types, 68 molecules

#43: 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.: 8 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#44: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#45: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#46: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#47: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#48: 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.: 24 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#49: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#50: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H30
#51: 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
#52: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#53: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#54: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#55: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#56: Chemical ChemComp-WSF / (2R)-3-{[(S)-hydroxy(3-methylbutoxy)phosphoryl]oxy}-2-(octanoyloxy)propyl decanoate


Mass: 522.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H51O8P
#57: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3

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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 complex I from the thoracic muscle of Drosophila melanogaster
Type: COMPLEX / Entity ID: #1-#24, #26-#42, #25 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Buffer solutionpH: 7.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 293389 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00569385
ELECTRON MICROSCOPYf_angle_d0.94493563
ELECTRON MICROSCOPYf_dihedral_angle_d10.52710914
ELECTRON MICROSCOPYf_chiral_restr0.0699945
ELECTRON MICROSCOPYf_plane_restr0.00811682

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