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- PDB-7vb7: Matrix arm of active state CI from DQ-NADH dataset -

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Entry
Database: PDB / ID: 7vb7
TitleMatrix arm of active state CI from DQ-NADH dataset
Components
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 6
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 3
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 6
  • Acyl carrier protein, mitochondrial
  • NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitochondrial
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
KeywordsELECTRON TRANSPORT / Respiratory / Complex
Function / homology
Function and homology information


RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Mitochondrial protein degradation / oxidoreductase activity, acting on NAD(P)H / cardiac muscle tissue development / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : ...RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Mitochondrial protein degradation / oxidoreductase activity, acting on NAD(P)H / cardiac muscle tissue development / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / negative regulation of intrinsic apoptotic signaling pathway / ATP synthesis coupled electron transport / quinone binding / : / respiratory electron transport chain / reactive oxygen species metabolic process / electron transport chain / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / nuclear body / mitochondrion / membrane / metal ion binding / cytosol
Similarity search - Function
NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / : / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / 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 / GRIM-19 ...NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / : / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / 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 / GRIM-19 / GRIM-19 protein / NDUFA6, LYR domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / 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 / : / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / 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 / 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. / 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 / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NAD-dependent epimerase/dehydratase / NuoE domain / NAD dependent epimerase/dehydratase family / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Acyl carrier protein (ACP) / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Phosphopantetheine attachment site / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Phosphopantetheine attachment site. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-8Q1 / CARDIOLIPIN / Chem-DCQ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-NDP / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / IRON/SULFUR CLUSTER ...Chem-8Q1 / CARDIOLIPIN / Chem-DCQ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-NDP / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / IRON/SULFUR CLUSTER / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsGu, J.K. / Yang, M.J.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504600 and 2016YFA0501100 China
National Natural Science Foundation of China (NSFC)31625008, 32030056, 21532004, 31570733, 31800620 China
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: The coupling mechanism of mammalian mitochondrial complex I.
Authors: Jinke Gu / Tianya Liu / Runyu Guo / Laixing Zhang / Maojun Yang /
Abstract: Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in ...Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in mitochondria. In the present study, we report cryo-electron microscopy structures of CI from Sus scrofa in six treatment conditions at a resolution of 2.4-3.5 Å, in which CI structures of each condition can be classified into two biochemical classes (active or deactive), with a notably higher proportion of active CI particles. These structures illuminate how hydrophobic ubiquinone-10 (Q10) with its long isoprenoid tail is bound and reduced in a narrow Q chamber comprising four different Q10-binding sites. Structural comparisons of active CI structures from our decylubiquinone-NADH and rotenone-NADH datasets reveal that Q10 reduction at site 1 is not coupled to proton pumping in the membrane arm, which might instead be coupled to Q10 oxidation at site 2. Our data overturn the widely accepted previous proposal about the coupling mechanism of CI.
History
DepositionAug 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
B: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
E: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
F: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
G: Acyl carrier protein, mitochondrial
H: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
I: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
J: NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitochondrial
K: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
L: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
M: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
N: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
O: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
P: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
T: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)411,53237
Polymers402,41218
Non-polymers9,12019
Water13,259736
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 [ubiquinone] flavoprotein ... , 3 types, 3 molecules AKO

#1: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 47434.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: F1RVN1, NADH:ubiquinone reductase (H+-translocating)
#10: Protein/peptide NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH-ubiquinone oxidoreductase 9 kDa subunit / Complex I-9kD


Mass: 5193.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TFI3
#14: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase 24 kDa subunit


Mass: 23826.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BG40

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 6 types, 6 molecules BCLPQT

#2: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH-ubiquinone oxidoreductase 23 kDa subunit / Complex I-23kD


Mass: 20207.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BDC0
#3: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH-ubiquinone oxidoreductase 20 kDa subunit / Complex I-20kD


Mass: 17874.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LK43
#11: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-18 kDa / NADH-ubiquinone oxidoreductase 18 kDa subunit


Mass: 14442.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: G8IFA6
#15: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH-ubiquinone oxidoreductase 30 kDa subunit / Complex I-30kD


Mass: 24521.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNN4
#16: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH-ubiquinone oxidoreductase 49 kDa subunit / Complex I-49kD


Mass: 44127.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JYS1
#17: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 10567.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S031

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 6 types, 6 molecules EFHINW

#4: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6


Mass: 13812.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480VKQ8
#5: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 9841.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RGE3
#7: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Complex I-13kD-B / NADH-ubiquinone oxidoreductase 13 kDa-B subunit / Complex I subunit B13


Mass: 12949.106 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2RN85
#8: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-ubiquinone oxidoreductase subunit B14.5a / Complex I-B14.5a


Mass: 12517.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VLA2
#13: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17031.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SQP4
#18: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH-ubiquinone oxidoreductase B16.6 subunit / Complex I-B16.6


Mass: 3204.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S6Q1

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Protein , 3 types, 3 molecules GJM

#6: Protein Acyl carrier protein, mitochondrial


Mass: 10133.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: D0G781
#9: Protein NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitochondrial


Mass: 38954.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480QJC4
#12: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial


Mass: 75770.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SHD7

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Non-polymers , 14 types, 755 molecules

#19: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#23: Chemical ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H89NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#24: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N2O8PS / Feature type: SUBJECT OF INVESTIGATION
#25: 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.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#26: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical ChemComp-UQ / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical ChemComp-DCQ / 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione / decylubiquinone


Mass: 322.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O4 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#32: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Respiratory complex I / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 462013 / Symmetry type: POINT

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