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- PDB-8zsk: Complex I from respirasome closed state 1 bound by metformin and ... -

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Basic information

Entry
Database: PDB / ID: 8zsk
TitleComplex I from respirasome closed state 1 bound by metformin and CoQ10, alternative orientation (SC-MetC1-ii)
Components
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 6
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein
  • Complex I-30kD
  • Complex I-B14.5a
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
  • NADH:ubiquinone oxidoreductase subunit V3
KeywordsMEMBRANE PROTEIN / Metformin / electron transport chain / Respirasome / mammalia
Function / homology
Function and homology information


Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Mitochondrial protein import / : / RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Mitochondrial protein degradation / Neutrophil degranulation / cellular response to oxygen levels ...Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Mitochondrial protein import / : / RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Mitochondrial protein degradation / Neutrophil degranulation / cellular response to oxygen levels / mesenchymal stem cell proliferation / reproductive system development / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / mesenchymal stem cell differentiation / circulatory system development / cardiac muscle tissue development / neural precursor cell proliferation / [2Fe-2S] cluster assembly / oxidoreductase activity, acting on NAD(P)H / oxygen sensor activity / stem cell division / acyl binding / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / response to cAMP / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / muscle contraction / reactive oxygen species metabolic process / aerobic respiration / regulation of mitochondrial membrane potential / respiratory electron transport chain / DNA damage response, signal transduction by p53 class mediator / kidney development / electron transport chain / fatty acid metabolic process / brain development / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / multicellular organism growth / NAD binding / cellular senescence / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / gene expression / mitochondrial inner membrane / nuclear speck / nuclear body / mitochondrial matrix / ubiquitin protein ligase binding / structural molecule activity / mitochondrion / nucleoplasm / metal ion binding / membrane
Similarity search - Function
NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / 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 flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Tim17/Tim22/Tim23/Pmp24 family / NADH-ubiquinone oxidoreductase, subunit 10 ...NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / 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 flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Tim17/Tim22/Tim23/Pmp24 family / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / 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 NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / : / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / 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: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-ubiquinone oxidoreductase MWFE subunit / : / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / 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-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / 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 / Deoxynucleoside kinase domain / Deoxynucleoside kinase / 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 / : / SLBB domain / : / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / 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 / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH ubiquinone oxidoreductase, F subunit / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / ADENOSINE-5'-DIPHOSPHATE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Metformin / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX ...1,2-Distearoyl-sn-glycerophosphoethanolamine / ADENOSINE-5'-DIPHOSPHATE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Metformin / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / IRON/SULFUR CLUSTER / UBIQUINONE-10 / Chem-ZMP / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Acyl carrier protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH:ubiquinone oxidoreductase subunit V3 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsTeng, F. / He, Z.X. / Hu, Y.Q. / Xu, C.Y. / Guo, R.Y. / Zhou, L.
Funding support1items
OrganizationGrant numberCountry
Other governmentZJU100 Young Professor
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Hydrophilic metformin and hydrophobic biguanides inhibit mitochondrial complex I by distinct mechanisms.
Authors: Zhaoxiang He / Fei Teng / Yanqing Yang / Ruiyang Guo / Mengchen Wu / Fangzhu Han / Hongtao Tian / Jiawei Wang / Yiqi Hu / Yangwei Jiang / Leili Zhang / Chenyang Xu / Fan Yang / Jiancang Zhou ...Authors: Zhaoxiang He / Fei Teng / Yanqing Yang / Ruiyang Guo / Mengchen Wu / Fangzhu Han / Hongtao Tian / Jiawei Wang / Yiqi Hu / Yangwei Jiang / Leili Zhang / Chenyang Xu / Fan Yang / Jiancang Zhou / Shan Zhang / James A Letts / Ruhong Zhou / Long Zhou /
Abstract: Metformin is the only antihyperglycemic biguanide targeting type 2 diabetes mellitus with proven safety. Although a mechanism of action involving tight inhibition of the respiratory complex I has ...Metformin is the only antihyperglycemic biguanide targeting type 2 diabetes mellitus with proven safety. Although a mechanism of action involving tight inhibition of the respiratory complex I has been proposed for hydrophobic biguanides, it remains elusive for the hydrophilic metformin, whose excellent pharmacological tolerance depends on weak complex I inhibition without competitive nature. Here we solved cryo-electron microscopy structures of the metformin-bound porcine respirasome. Our structural and kinetic data are consistent with a model in which metformin enters complex I only in its open state and becomes trapped at the ubiquinone redox site by ubiquinone-induced conformational closing of the enzyme. By contrast, the hydrophobic proguanil alone occupies both the entrance and the redox site of the ubiquinone channel in open and closed complex I and is kinetically consistent with competitive inhibition with conformation-dependent affinities. Our data provide the molecular basis for metformin's well-known superior properties, such as a wide therapeutic window and positive ubiquinone cooperativity, leading to its clinical success and facilitating future therapeutic developments.
History
DepositionJun 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
4L: NADH-ubiquinone oxidoreductase chain 4L
A1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
A2: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
A3: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
A5: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
A6: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
A7: Complex I-B14.5a
A8: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
A9: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
AB: Acyl carrier protein
AC: Acyl carrier protein
AK: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
AL: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
AM: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
AN: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
B1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
B2: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
B3: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
B4: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
B5: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
B6: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
B7: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
B8: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
B9: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
BK: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
BL: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
CA: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
CB: NADH dehydrogenase [ubiquinone] 1 subunit C2
N1: NADH-ubiquinone oxidoreductase chain 1
N2: NADH-ubiquinone oxidoreductase chain 2
N3: NADH-ubiquinone oxidoreductase chain 3
N4: NADH-ubiquinone oxidoreductase chain 4
N5: NADH-ubiquinone oxidoreductase chain 5
N6: NADH-ubiquinone oxidoreductase chain 6
S1: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
S2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
S3: Complex I-30kD
S4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
S5: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
S6: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
S7: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
S8: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
V1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
V2: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
V3: NADH:ubiquinone oxidoreductase subunit V3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)997,789107
Polymers948,30345
Non-polymers49,48662
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules 4LN1N2N3N4N5N6

#1: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10827.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: P56632, NADH:ubiquinone reductase (H+-translocating)
#28: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35667.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79874, NADH:ubiquinone reductase (H+-translocating)
#29: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39077.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79875, NADH:ubiquinone reductase (H+-translocating)
#30: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 12998.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79880, NADH:ubiquinone reductase (H+-translocating)
#31: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 51853.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q7IIB7, NADH:ubiquinone reductase (H+-translocating)
#32: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 68267.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q71K68, NADH:ubiquinone reductase (H+-translocating)
#33: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 18890.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79882, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 11 types, 11 molecules A1A2A3A5A6A8A9AKALAMAN

#2: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Complex I-MWFE / NADH-ubiquinone oxidoreductase MWFE subunit


Mass: 8034.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GR43
#3: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 9770.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RGE3
#4: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Complex I-B9 / NADH-ubiquinone oxidoreductase B9 subunit


Mass: 9094.372 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VPG4
#5: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5


Mass: 12949.106 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1IJ52
#6: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 13812.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SJP6
#8: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH-ubiquinone oxidoreductase 19 kDa subunit / Complex I-19kD


Mass: 19932.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SLR1
#9: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


Mass: 38840.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SL07
#11: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 36949.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9
#12: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase subunit B14.7 / Complex I-B14.7


Mass: 14555.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM4
#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
#14: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


Mass: 16709.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1NRT6

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Protein , 4 types, 5 molecules A7ABACS1S3

#7: Protein Complex I-B14.5a / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-ubiquinone oxidoreductase subunit 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
#10: Protein Acyl carrier protein


Mass: 10046.488 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AAR5
#34: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial


Mass: 75683.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1V1H9
#36: Protein Complex I-30kD / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / mitochondrial / NADH-ubiquinone ...NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / mitochondrial / NADH-ubiquinone oxidoreductase 30 kDa subunit


Mass: 24521.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNN4

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules B1B2B3B4B5B6B7B8B9BKBL

#15: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Complex I-MNLL / NADH-ubiquinone oxidoreductase MNLL subunit


Mass: 6781.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D2CGH8
#16: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Complex I-AGGG / NADH-ubiquinone oxidoreductase AGGG subunit


Mass: 8201.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2QW32
#17: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Complex I-B12 / NADH-ubiquinone oxidoreductase B12 subunit


Mass: 9042.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VD84
#18: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH-ubiquinone oxidoreductase B15 subunit / Complex I-B15


Mass: 14986.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T6M0
#19: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH-ubiquinone oxidoreductase SGDH subunit / Complex I-SGDH


Mass: 16281.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6
#20: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 15333.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480KM09
#21: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Complex I-B18 / NADH-ubiquinone oxidoreductase B18 subunit


Mass: 15307.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SCH1
#22: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 18608.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWL7
#23: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 21733.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GSE5
#24: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Complex I-PDSW / NADH-ubiquinone oxidoreductase PDSW subunit


Mass: 20944.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1FAG1
#25: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit


Mass: 12113.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1EYI7

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NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules CACB

#26: Protein/peptide NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH-ubiquinone oxidoreductase KFYI subunit / Complex I-KFYI


Mass: 5881.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A1XQS6
#27: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14196.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JRW3

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 6 types, 6 molecules S2S4S5S6S7S8

#35: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / Complex I-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 49234.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S1A8
#37: 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: A0A4X1SN37
#38: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH-ubiquinone oxidoreductase 15 kDa subunit / Complex I-15 kDa


Mass: 12375.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SV23
#39: 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
#40: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Complex I-20kD / NADH-ubiquinone oxidoreductase 20 kDa subunit


Mass: 17874.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1TL60
#41: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Complex I-23kD / NADH-ubiquinone oxidoreductase 23 kDa subunit


Mass: 20207.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BDC0

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules V1V2

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


Mass: 47235.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A4X1SZP7, NADH:ubiquinone reductase (H+-translocating)
#43: 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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Protein/peptide , 1 types, 1 molecules V3

#44: Protein/peptide NADH:ubiquinone oxidoreductase subunit V3


Mass: 5046.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BEK4

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Non-polymers , 16 types, 62 molecules

#45: 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.: 13 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#46: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#47: 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
#48: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#49: 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 / Feature type: SUBJECT OF INVESTIGATION
#50: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#51: 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.: 7 / Source method: obtained synthetically / Formula: C42H89NO8P / Comment: phospholipid*YM
#52: 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.: 3 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#53: Chemical ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H52O8P
#54: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#55: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#57: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#58: Chemical ChemComp-MF8 / Metformin / N,N-Dimethylimidodicarbonimidic diamide


Mass: 129.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11N5 / Feature type: SUBJECT OF INVESTIGATION
#59: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#60: 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

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Details

Has ligand of interestY
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: respirasome closed state 1 bound by metformin and CoQ(alternative orientation),comformation B
Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.4
Details: SEC buffer (20 mM Tris pH 7.4, 50 mM NaCl, 0.002% PMSF, 0.1% GDN (w/v))
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrimethylsilylTris1
250 mMSodium chlorideNaCl1
30.002 %PhenylmethylsulfonylPMSF1
40.1 %Glyco-diosgeninGDN1
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7.8 sec. / Electron dose: 51.9 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
7PHENIX1.20.1model fitting
8Coot0.9.6model fitting
10PHENIX1.20.1model refinement
11cryoSPARCv4.4.1initial Euler assignment
12cryoSPARCv4.4.1final Euler assignment
13cryoSPARCv4.4.1classification
14cryoSPARCv4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30599 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 92.04 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00370793
ELECTRON MICROSCOPYf_angle_d0.501795461
ELECTRON MICROSCOPYf_chiral_restr0.04110218
ELECTRON MICROSCOPYf_plane_restr0.004211849
ELECTRON MICROSCOPYf_dihedral_angle_d12.407227625

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