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- PDB-8pw7: A respirasome from murine liver -

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Basic information

Entry
Database: PDB / ID: 8pw7
TitleA respirasome from murine liver
Components
  • (Cytochrome b-c1 complex subunit ...) x 8
  • (Cytochrome c oxidase subunit ...) x 13
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 12
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 3
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 7
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein, mitochondrial
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
KeywordsMEMBRANE PROTEIN / Respiratory chain super complex / mammalian mitochondria
Function / homology
Function and homology information


Complex IV assembly / response to D-galactosamine / Complex III assembly / TP53 Regulates Metabolic Genes / response to cobalamin / Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / mesenchymal stem cell proliferation / reproductive system development / blastocyst hatching ...Complex IV assembly / response to D-galactosamine / Complex III assembly / TP53 Regulates Metabolic Genes / response to cobalamin / Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / mesenchymal stem cell proliferation / reproductive system development / blastocyst hatching / sperm glycocalyx / perinuclear theca / psychomotor behavior / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Mitochondrial ribosome-associated quality control / Cytoprotection by HMOX1 / circulatory system development / Mitochondrial translation termination / Respiratory electron transport / respiratory chain complex IV assembly / response to mercury ion / mesenchymal stem cell differentiation / subthalamus development / pons development / protein insertion into mitochondrial inner membrane / response to light intensity / respiratory system process / cerebellar Purkinje cell layer development / : / mitochondrial respiratory chain complex III assembly / mitochondrial processing peptidase complex / sperm head-tail coupling apparatus / thalamus development / adult walking behavior / Mitochondrial protein degradation / pyramidal neuron development / respiratory chain complex IV / stem cell division / response to alkaloid / response to glucagon / mitochondrial large ribosomal subunit assembly / mitochondrial ATP synthesis coupled electron transport / protein lipoylation / cytochrome complex assembly / cellular response to oxygen levels / adult behavior / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / neural precursor cell proliferation / ubiquinone biosynthetic process / respiratory chain complex / gliogenesis / cytochrome-c oxidase / respiratory chain complex III / negative regulation of non-canonical NF-kappaB signal transduction / cellular respiration / response to hydroperoxide / cardiac muscle tissue development / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / oxidative phosphorylation / positive regulation of mitochondrial membrane potential / [2Fe-2S] cluster assembly / quinol-cytochrome-c reductase activity / oxygen sensor activity / sperm principal piece / cellular response to glucocorticoid stimulus / midbrain development / multicellular organism growth / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / iron-sulfur cluster assembly / response to copper ion / hypothalamus development / dopamine metabolic process / sperm end piece / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / animal organ regeneration / mitochondrial electron transport, NADH to ubiquinone / positive regulation of ATP biosynthetic process / proton motive force-driven mitochondrial ATP synthesis / electron transport coupled proton transport / acyl binding / regulation of protein phosphorylation / neuron development / mitochondrial respiratory chain complex I assembly / response to hyperoxia / response to electrical stimulus / response to cadmium ion / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / cerebellum development / reactive oxygen species metabolic process / respiratory chain complex I / positive regulation of execution phase of apoptosis / NADH dehydrogenase (ubiquinone) activity
Similarity search - Function
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / NmrA-like domain / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / NmrA-like family / Cytochrome C oxidase chain VIIB / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Globular protein, non-globular alpha/beta subunit / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Complex1_LYR-like / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Cytochrome c oxidase subunit III-like superfamily / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome c/quinol oxidase subunit II / Cytochrome b / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome C oxidase subunit II, transmembrane domain superfamily / : / Cytochrome c1 / Cytochrome C1 family / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH-ubiquinone oxidoreductase 1 subunit C1 / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / : / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome b/b6, C-terminal / Cytochrome c oxidase-like, subunit I domain / Cytochrome b(C-terminal)/b6/petD / Cytochrome oxidase subunit I profile.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / : / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / TRISTEAROYLGLYCEROL / Chem-ZMP / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 6A1, mitochondrial / Cytochrome c oxidase subunit 7A2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Cytochrome c oxidase subunit 8A, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Cytochrome b-c1 complex subunit 9 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Cytochrome c oxidase subunit 6C / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 10 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / Cytochrome b-c1 complex subunit 8 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Cytochrome b-c1 complex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome c1, heme protein, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsVercellino, I. / Sazanov, L.A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101020697European Union
Citation
Journal: Nat Struct Mol Biol / Year: 2024
Title: SCAF1 drives the compositional diversity of mammalian respirasomes.
Authors: Irene Vercellino / Leonid A Sazanov /
Abstract: Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies ...Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the 'canonical' respirasome (the C-respirasome, CICIIICIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the 'back' of CI, instead of the 'toe'. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Afonine, P.V. / Adams, P.D.
History
DepositionJul 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 2.0Oct 2, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / em_admin / em_entity_assembly / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_contact_author / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update / _em_entity_assembly.entity_id_list / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity_name_com.entity_id / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Sequence discrepancy
Details: The previous model erroneously featured subunits COX6A2 and COX8B (expressed in the heart) instead of COX6A1 and COX8A (expressed in the liver)
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
n: Cytochrome c oxidase subunit 1
o: Cytochrome c oxidase subunit 2
p: Cytochrome c oxidase subunit 3
q: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
r: Cytochrome c oxidase subunit 5A, mitochondrial
s: Cytochrome c oxidase subunit 5B, mitochondrial
t: Cytochrome c oxidase subunit 6A1, mitochondrial
u: Cytochrome c oxidase subunit 6B1
v: Cytochrome c oxidase subunit 6C
x: Cytochrome c oxidase subunit 7B, mitochondrial
y: Cytochrome c oxidase subunit 7C, mitochondrial
w: Cytochrome c oxidase subunit 7A2, mitochondrial
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
L: Cytochrome b-c1 complex subunit 1, mitochondrial
M: Cytochrome b-c1 complex subunit 2, mitochondrial
N: Cytochrome b
O: Cytochrome c1, heme protein, mitochondrial
P: Cytochrome b-c1 complex subunit Rieske, mitochondrial
Q: Cytochrome b-c1 complex subunit 7
R: Cytochrome b-c1 complex subunit 8
S: Cytochrome b-c1 complex subunit 6, mitochondrial
U: Cytochrome b-c1 complex subunit 9
V: Cytochrome b-c1 complex subunit 10
T: Cytochrome b-c1 complex subunit Rieske, mitochondrial
6: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
C1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
D1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
2: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
3: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
P1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
Q1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
7: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
S1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
T1: Acyl carrier protein, mitochondrial
V1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
W1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
q1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
r1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
s1: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
A1: NADH-ubiquinone oxidoreductase chain 3
H1: NADH-ubiquinone oxidoreductase chain 1
J1: NADH-ubiquinone oxidoreductase chain 6
K1: NADH-ubiquinone oxidoreductase chain 4L
L1: NADH-ubiquinone oxidoreductase chain 5
M1: NADH-ubiquinone oxidoreductase chain 4
N1: NADH-ubiquinone oxidoreductase chain 2
O1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
U1: Acyl carrier protein, mitochondrial
X1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Y1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Z1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
a1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
b1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
c1: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
d1: NADH dehydrogenase [ubiquinone] 1 subunit C2
e1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
f1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
g1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
h1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
i1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
j1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
k1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
l1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
m1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
n1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
o1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
p1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
z: Cytochrome c oxidase subunit 8A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,884,372169
Polymers1,816,75879
Non-polymers67,61490
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Cytochrome c oxidase subunit ... , 13 types, 13 molecules nopqrstuvxywz

#1: Protein Cytochrome c oxidase subunit 1 / Cytochrome c oxidase polypeptide I


Mass: 56945.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P00397, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II


Mass: 25993.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P00405, cytochrome-c oxidase
#3: Protein Cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 29948.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P00416, cytochrome-c oxidase
#4: Protein Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase polypeptide IV / Cytochrome c oxidase subunit IV isoform 1 / COX IV-1


Mass: 19558.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P19783
#5: Protein Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase polypeptide Va


Mass: 16123.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P12787
#6: Protein Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase polypeptide Vb


Mass: 13831.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P19536
#7: Protein Cytochrome c oxidase subunit 6A1, mitochondrial / Cytochrome c oxidase polypeptide VIa-liver


Mass: 12372.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P43024
#8: Protein Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1


Mass: 10086.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P56391
#9: Protein Cytochrome c oxidase subunit 6C / Cytochrome c oxidase polypeptide VIc


Mass: 8484.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPQ1
#10: Protein Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase polypeptide VIIb


Mass: 9023.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P56393
#11: Protein Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase polypeptide VIIc


Mass: 7344.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P17665
#12: Protein Cytochrome c oxidase subunit 7A2, mitochondrial / Cytochrome c oxidase subunit VIIa-liver/heart / Cytochrome c oxidase subunit VIIa-L


Mass: 9304.892 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P48771
#67: Protein Cytochrome c oxidase subunit 8A, mitochondrial / Cytochrome c oxidase polypeptide VIII-liver / Cytochrome c oxidase subunit 8-2


Mass: 7659.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q64445

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Cytochrome b-c1 complex subunit ... , 8 types, 17 molecules ALBMEPTFQGRHSJUKV

#13: Protein Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome-c reductase complex core protein 1


Mass: 52910.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZ13
#14: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


Mass: 48289.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DB77
#17: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Rieske protein UQCRFS1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 29406.635 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR68, quinol-cytochrome-c reductase
#18: Protein Cytochrome b-c1 complex subunit 7


Mass: 13587.532 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQB4
#19: Protein Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa ...Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 9783.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ69
#20: Protein Cytochrome b-c1 complex subunit 6, mitochondrial / Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / ...Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 11 kDa protein


Mass: 10452.694 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P99028
#21: Protein Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol- ...Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol-cytochrome c reductase complex 7.2 kDa protein


Mass: 7457.526 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8R1I1
#22: Protein Cytochrome b-c1 complex subunit 10 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 6.4 kDa protein


Mass: 6546.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPX8

+
Protein , 4 types, 7 molecules CNDO3T1U1

#15: Protein Cytochrome b / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 43240.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P00158
#16: Protein Cytochrome c1, heme protein, mitochondrial / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol- ...Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


Mass: 35374.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0M3, quinol-cytochrome-c reductase
#28: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Complex I-75kD / CI-75kD


Mass: 79866.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q91VD9, NADH:ubiquinone reductase (H+-translocating)
#34: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 17390.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR21

+
NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules 6C1D19Q17e1

#23: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Complex I-20kD / CI-20kD / NADH-ubiquinone oxidoreductase 20 kDa subunit


Mass: 24715.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9DC70, NADH:ubiquinone reductase (H+-translocating)
#24: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Complex I-30kD / CI-30kD / NADH-ubiquinone oxidoreductase 30 kDa subunit


Mass: 30191.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9DCT2, NADH:ubiquinone reductase (H+-translocating)
#25: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / Complex I-49kD / CI-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 52720.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q91WD5, NADH:ubiquinone reductase (H+-translocating)
#29: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Complex I-23kD / CI-23kD / NADH-ubiquinone oxidoreductase 23 kDa subunit


Mass: 24068.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q8K3J1, NADH:ubiquinone reductase (H+-translocating)
#31: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-18 kDa / CI-18 kDa / Complex I-AQDQ / CI-AQDQ / NADH-ubiquinone oxidoreductase 18 kDa subunit


Mass: 19814.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CXZ1
#32: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Complex I-13kD-A / CI-13kD-A / NADH-ubiquinone oxidoreductase 13 kDa-A subunit


Mass: 13041.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P52503
#55: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Complex I-15 kDa / CI-15 kDa / NADH-ubiquinone oxidoreductase 15 kDa subunit


Mass: 12675.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99LY9

+
NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules 21s1

#26: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase 24 kDa subunit


Mass: 27318.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9D6J6, NADH:ubiquinone reductase (H+-translocating)
#27: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-51kD / CI-51kD / NADH-ubiquinone oxidoreductase 51 kDa subunit


Mass: 50904.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q91YT0, NADH:ubiquinone reductase (H+-translocating)
#39: Protein NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Complex I-9kD / CI-9kD / NADH-ubiquinone oxidoreductase 9 kDa subunit


Mass: 11833.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BK30

+
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 12 molecules P1S1V1W1q1r1O1X1Y1Z1a1b1

#30: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / CI-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


Mass: 42588.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DC69
#33: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Complex I-B8 / CI-B8 / NADH-ubiquinone oxidoreductase B8 subunit


Mass: 10932.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ75
#35: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Complex I subunit B13 / Complex I-13kD-B / CI-13kD-B / NADH-ubiquinone oxidoreductase 13 kDa-B subunit


Mass: 13380.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPP6
#36: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / CI-B14 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 15311.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQZ5
#37: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Complex I-B17.2 / CI-B17.2 / CIB17.2 / NADH-ubiquinone oxidoreductase subunit B17.2


Mass: 17112.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q7TMF3
#38: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Complex I-B14.5a / CI-B14.5a / NADH-ubiquinone oxidoreductase subunit B14.5a


Mass: 12637.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9Z1P6
#47: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-42kD / CI-42kD / NADH-ubiquinone oxidoreductase 42 kDa subunit


Mass: 40657.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99LC3
#48: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-19kD / CI-19kD / Complex I-PGIV / CI-PGIV / NADH-ubiquinone oxidoreductase 19 kDa subunit


Mass: 20025.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DCJ5
#49: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Complex I-B14.7 / NADH-ubiquinone oxidoreductase subunit B14.7


Mass: 14928.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: G5E814
#50: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic ...Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic and interferon-induced mortality 19 protein / Gene associated with retinoic and IFN-induced mortality 19 protein / NADH-ubiquinone oxidoreductase B16.6 subunit


Mass: 16881.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9ERS2
#51: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Complex I-MWFE / CI-MWFE / NADH-ubiquinone oxidoreductase MWFE subunit


Mass: 8149.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O35683
#52: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Complex I-B9 / CI-B9 / NADH-ubiquinone oxidoreductase B9 subunit


Mass: 9380.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ91

+
NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules A1H1J1K1L1M1N1

#40: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 13251.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03899, NADH:ubiquinone reductase (H+-translocating)
#41: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 36105.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03888, NADH:ubiquinone reductase (H+-translocating)
#42: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 18656.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03925, NADH:ubiquinone reductase (H+-translocating)
#43: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10637.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03903, NADH:ubiquinone reductase (H+-translocating)
#44: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68547.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03921, NADH:ubiquinone reductase (H+-translocating)
#45: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 51943.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03911, NADH:ubiquinone reductase (H+-translocating)
#46: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 38800.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03893, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules c1d1

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


Mass: 8636.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQY9
#54: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2 / Complex I-B14.5b / CI-B14.5b / NADH-ubiquinone oxidoreductase subunit B14.5b


Mass: 14185.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ54

+
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules f1g1h1i1j1k1l1m1n1o1p1

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


Mass: 6965.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P0DN34
#57: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / CI-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit / Neuronal protein 15.6 / p15.6


Mass: 17463.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O09111
#58: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / Complex I-SGDH / CI-SGDH / NADH-ubiquinone oxidoreductase SGDH subunit


Mass: 21742.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQH3
#59: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / CI-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 15582.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3UIU2
#60: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Complex I-AGGG / CI-AGGG / NADH-ubiquinone oxidoreductase AGGG subunit


Mass: 11982.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPU2
#61: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Complex I-B12 / CI-B12 / NADH-ubiquinone oxidoreductase B12 subunit


Mass: 11714.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQZ6
#62: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / CI-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 21903.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D6J5
#63: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Complex I-B15 / CI-B15 / NADH-ubiquinone oxidoreductase B15 subunit


Mass: 15105.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQC7
#64: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / CI-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 22020.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQJ8
#65: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Complex I-B18 / CI-B18 / NADH-ubiquinone oxidoreductase B18 subunit


Mass: 16360.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR61
#66: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Complex I-PDSW / CI-PDSW / NADH-ubiquinone oxidoreductase PDSW subunit


Mass: 21054.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DCS9

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Non-polymers , 19 types, 90 molecules

#68: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#69: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#70: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#71: 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.: 33 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#72: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#73: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#74: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#75: Chemical ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL


Mass: 891.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C57H110O6
#76: 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.: 16 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#77: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#78: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#79: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#80: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#81: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#83: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#84: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#85: 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
#86: 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

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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: A respirasome from murine liver / Type: COMPLEX / Entity ID: #1-#67 / Source: NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Strain: CD1 / Organ: liver / Organelle: mitochondria
Buffer solutionpH: 7.7
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium chlorideNaCl1
220 mMHEPESC8H18N2O4S1
32 mMEDTAC10H16N2O81
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R0.6/1
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: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.4 sec. / Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9453

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Processing

EM softwareName: PHENIX / Version: 1.19_4092: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1758187
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57506 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Details: initial fitting done in chimera
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetails (eV)Initial refinement model-ID
16g2j

6g2j

6g2jCI1
27o3c

7o3c

7o3cCIII and CIV2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009118510
ELECTRON MICROSCOPYf_angle_d0.918160510
ELECTRON MICROSCOPYf_dihedral_angle_d8.94817885
ELECTRON MICROSCOPYf_chiral_restr0.05417396
ELECTRON MICROSCOPYf_plane_restr0.00720129

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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