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- PDB-8ugr: In-situ structure of typeX supercomplex in respiratory chain (com... -

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Basic information

Entry
Database: PDB / ID: 8ugr
TitleIn-situ structure of typeX supercomplex in respiratory chain (composite)
Components
  • (Cytochrome b-c1 complex subunit ...) x 7
  • (Cytochrome c oxidase subunit ...) x 14
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 10
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 10
  • (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
  • (NADH:ubiquinone oxidoreductase subunit ...) x 4
  • Cytochrome b
  • Cytochrome c1
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
  • Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
KeywordsELECTRON TRANSPORT / in-situ cryo-EM structure / mammalian / mitochondria / respiratory supercomplex / proton pumping / membrane protein
Function / homology
Function and homology information


Complex IV assembly / Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / respiratory chain complex IV assembly / mitochondrial respirasome assembly / RHOG GTPase cycle ...Complex IV assembly / Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / respiratory chain complex IV assembly / mitochondrial respirasome assembly / RHOG GTPase cycle / pyramidal neuron development / Complex I biogenesis / thalamus development / Respiratory electron transport / Neutrophil degranulation / Mitochondrial protein degradation / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / respiratory chain complex III / oxidative phosphorylation / cardiac muscle tissue development / quinol-cytochrome-c reductase / oxidoreductase activity, acting on NAD(P)H / mitochondrial electron transport, cytochrome c to oxygen / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / hypothalamus development / midbrain development / ubiquinone binding / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / response to cAMP / enzyme regulator activity / positive regulation of vasoconstriction / reactive oxygen species metabolic process / aerobic respiration / hippocampus development / central nervous system development / respiratory electron transport chain / electron transport chain / brain development / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / fatty acid biosynthetic process / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / oxidoreductase activity / nuclear speck / nuclear body / mitochondrial matrix / copper ion binding / heme binding / mitochondrion / proteolysis / nucleoplasm / metal ion binding / membrane
Similarity search - Function
NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / 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 / : ...NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / 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 / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / 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 III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / 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 C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / 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 c oxidase subunit III-like superfamily / 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 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Cytochrome c/quinol oxidase subunit II / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / : / Cytochrome c1 / Cytochrome C1 family / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / N-ACETYLMETHIONINE / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / GUANOSINE-5'-TRIPHOSPHATE / HEME-A ...1,2-Distearoyl-sn-glycerophosphoethanolamine / N-ACETYLMETHIONINE / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / GUANOSINE-5'-TRIPHOSPHATE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / : / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-PEK / Chem-PGV / PHOSPHATE ION / Chem-PSC / IRON/SULFUR CLUSTER / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Cytochrome b-c1 complex subunit 7 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Cytochrome c oxidase subunit / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Cytochrome c1 / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 alpha 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 / Cytochrome c oxidase subunit 4 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Cytochrome c oxidase subunit 6C / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Cytochrome b-c1 complex subunit 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Cytochrome b-c1 complex subunit 8 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 6 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Cytochrome c oxidase subunit NDUFA4 / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Cytochrome b-c1 complex subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase chain 2 / Cytochrome c oxidase subunit 1 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / Cytochrome b / Cytochrome c oxidase subunit 7C, mitochondrial / Complex III subunit 9 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 7A1, mitochondrial / NADH-ubiquinone oxidoreductase chain 5
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsZheng, W. / Zhang, K. / Zhu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM142959 United States
CitationJournal: Nature / Year: 2024
Title: High-resolution in situ structures of mammalian respiratory supercomplexes.
Authors: Wan Zheng / Pengxin Chai / Jiapeng Zhu / Kai Zhang /
Abstract: Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in ...Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: IIIIIV, IIIIIV, IIIIIV and IIIIIV, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.
History
DepositionOct 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
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Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / em_admin / em_entity_assembly_naturalsource / em_imaging / em_software / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine_ls_restr / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _em_admin.last_update / _em_entity_assembly_naturalsource.organism / _em_imaging.microscope_model / _em_software.fitting_id / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _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.seq_align_beg / _struct_ref_seq.seq_align_end
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: NADH-ubiquinone oxidoreductase chain 3
1B: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
1C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
1D: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
1E: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
1F: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
1G: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
1H: NADH-ubiquinone oxidoreductase chain 1
1I: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
1J: NADH-ubiquinone oxidoreductase chain 6
1K: NADH-ubiquinone oxidoreductase chain 4L
1L: NADH-ubiquinone oxidoreductase chain 5
1M: NADH-ubiquinone oxidoreductase chain 4
1N: NADH-ubiquinone oxidoreductase chain 2
1O: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
1P: NADH:ubiquinone oxidoreductase subunit A9
1Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
1R: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
1S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
1T: NADH:ubiquinone oxidoreductase subunit AB1
1U: NADH:ubiquinone oxidoreductase subunit AB1
1V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1
1W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
1X: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
1Y: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
1Z: NADH:ubiquinone oxidoreductase subunit A13
1a: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
1b: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
1c: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
1d: NADH dehydrogenase [ubiquinone] 1 subunit C2
1e: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
1f: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
1g: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
1h: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
1i: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
1j: NADH:ubiquinone oxidoreductase subunit B2
1k: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
1l: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
1m: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
1n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
1o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
1p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
1q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
1r: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
1s: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
3A: Cytochrome b-c1 complex subunit 1, mitochondrial
3B: Cytochrome b-c1 complex subunit 2, mitochondrial
3C: Cytochrome b
3D: Cytochrome c1
3E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
3F: Cytochrome b-c1 complex subunit 7
3G: Cytochrome b-c1 complex subunit 8
3H: Cytochrome b-c1 complex subunit 6, mitochondrial
3I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
3J: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
3N: Cytochrome b-c1 complex subunit 1, mitochondrial
3O: Cytochrome b-c1 complex subunit 2, mitochondrial
3P: Cytochrome b
3Q: Cytochrome c1
3R: Cytochrome b-c1 complex subunit Rieske, mitochondrial
3S: Cytochrome b-c1 complex subunit 7
3T: Cytochrome b-c1 complex subunit 8
3U: Cytochrome b-c1 complex subunit 6, mitochondrial
3V: Cytochrome b-c1 complex subunit Rieske, mitochondrial
3W: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
3X: Cytochrome b-c1 complex subunit 10
3Y: Cytochrome b-c1 complex subunit 10
4A: Cytochrome c oxidase subunit 1
4B: Cytochrome c oxidase subunit 2
4C: Cytochrome c oxidase subunit 3
4D: Cytochrome c oxidase subunit 4
4E: Cytochrome c oxidase subunit 5A, mitochondrial
4F: Cytochrome c oxidase subunit 5B, mitochondrial
4G: Cytochrome c oxidase subunit 6A2
4H: Cytochrome c oxidase subunit 6B1
4I: Cytochrome c oxidase subunit 6C
4J: Cytochrome c oxidase subunit 7A1, mitochondrial
4K: Cytochrome c oxidase subunit 7B
4L: Cytochrome c oxidase subunit 7C, mitochondrial
4M: Cytochrome c oxidase subunit 8
4N: Cytochrome c oxidase subunit NDUFA4
5A: NADH-ubiquinone oxidoreductase chain 3
5B: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
5C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
5D: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
5E: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
5F: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
5G: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
5H: NADH-ubiquinone oxidoreductase chain 1
5I: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
5J: NADH-ubiquinone oxidoreductase chain 6
5K: NADH-ubiquinone oxidoreductase chain 4L
5L: NADH-ubiquinone oxidoreductase chain 5
5M: NADH-ubiquinone oxidoreductase chain 4
5N: NADH-ubiquinone oxidoreductase chain 2
5O: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
5P: NADH:ubiquinone oxidoreductase subunit A9
5Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
5R: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
5S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
5T: NADH:ubiquinone oxidoreductase subunit AB1
5U: NADH:ubiquinone oxidoreductase subunit AB1
5V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1
5W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
5X: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
5Y: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
5Z: NADH:ubiquinone oxidoreductase subunit A13
5a: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
5b: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
5c: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
5d: NADH dehydrogenase [ubiquinone] 1 subunit C2
5e: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
5f: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
5g: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
5h: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
5i: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
5j: NADH:ubiquinone oxidoreductase subunit B2
5k: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
5l: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
5m: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
5n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
5o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
5p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
5q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
5r: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
5s: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
6A: Cytochrome b-c1 complex subunit 1, mitochondrial
6B: Cytochrome b-c1 complex subunit 2, mitochondrial
6C: Cytochrome b
6D: Cytochrome c1
6E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
6F: Cytochrome b-c1 complex subunit 7
6G: Cytochrome b-c1 complex subunit 8
6H: Cytochrome b-c1 complex subunit 6, mitochondrial
6I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
6J: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
6N: Cytochrome b-c1 complex subunit 1, mitochondrial
6O: Cytochrome b-c1 complex subunit 2, mitochondrial
6P: Cytochrome b
6Q: Cytochrome c1
6R: Cytochrome b-c1 complex subunit Rieske, mitochondrial
6S: Cytochrome b-c1 complex subunit 7
6T: Cytochrome b-c1 complex subunit 8
6U: Cytochrome b-c1 complex subunit 6, mitochondrial
6V: Cytochrome b-c1 complex subunit Rieske, mitochondrial
6W: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
6X: Cytochrome b-c1 complex subunit 10
6Y: Cytochrome b-c1 complex subunit 10
8A: Cytochrome c oxidase subunit 1
8B: Cytochrome c oxidase subunit 2
8C: Cytochrome c oxidase subunit 3
8D: Cytochrome c oxidase subunit 4
8E: Cytochrome c oxidase subunit 5A, mitochondrial
8F: Cytochrome c oxidase subunit 5B, mitochondrial
8G: Cytochrome c oxidase subunit 6A2
8H: Cytochrome c oxidase subunit 6B1
8I: Cytochrome c oxidase subunit 6C
8J: Cytochrome c oxidase subunit 7A1, mitochondrial
8K: Cytochrome c oxidase subunit 7B
8L: Cytochrome c oxidase subunit 7C, mitochondrial
8M: Cytochrome c oxidase subunit 8
8N: Cytochrome c oxidase subunit NDUFA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,906,272331
Polymers3,792,411162
Non-polymers113,861169
Water00
1


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

-
Components

+
NADH-ubiquinone oxidoreductase chain ... , 7 types, 14 molecules 1A5A1H5H1J5J1K5K1L5L1M5M1N5N

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


Mass: 13026.458 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79880, NADH:ubiquinone reductase (H+-translocating)
#8: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 35619.434 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A0U1RS44, NADH:ubiquinone reductase (H+-translocating)
#10: Protein NADH-ubiquinone oxidoreductase chain 6


Mass: 19021.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79882
#11: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10855.263 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: P56632, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68723.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q9TDR1, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 51887.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79881, NADH:ubiquinone reductase (H+-translocating)
#14: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39105.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79875, NADH:ubiquinone reductase (H+-translocating)

+
NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 14 molecules 1B5B1C5C1D5D1I5I1Q5Q1R5R1e5e

#2: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial


Mass: 28500.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VVS8
#3: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial


Mass: 30241.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNN4
#4: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / Complex I-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 52953.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1TTB3
#9: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial


Mass: 27135.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZUN9
#17: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial


Mass: 19746.514 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SN37
#18: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 13348.950 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1THU2
#30: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5


Mass: 12506.591 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VX77

+
NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 6 molecules 1E5E1F5F1s5s

#5: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial


Mass: 27439.533 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VRV3
#6: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 50637.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SZP7
#44: Protein NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial


Mass: 48217.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TE42

+
Protein , 4 types, 14 molecules 1G5G3C3P6C6P3D3Q6D6Q3J3W6J6W

#7: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial


Mass: 79627.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ARY3
#47: Protein
Cytochrome b


Mass: 42840.715 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q1HBG9
#48: Protein
Cytochrome c1


Mass: 35488.930 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AZF9
#53: Protein
Ubiquinol-cytochrome c reductase complex 7.2 kDa protein


Mass: 7412.530 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN79

+
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10 types, 20 molecules 1O5O1S5S1V5V1W5W1X5X1Y5Y1a5a1b5b1q5q1r5r

#15: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 40476.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9
#19: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 11099.798 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1FN21
#21: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1


Mass: 13321.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0UWW0
#22: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6


Mass: 14953.313 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480VKQ8
#23: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8


Mass: 20064.096 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0K6B5
#24: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11


Mass: 14686.894 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM4
#26: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 8034.373 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0TJQ4
#27: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3


Mass: 9225.567 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VQ42
#42: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17162.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SQP4
#43: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7


Mass: 12648.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8W4F7N8

+
NADH:ubiquinone oxidoreductase subunit ... , 4 types, 10 molecules 1P5P1T1U5T5U1Z5Z1j5j

#16: Protein NADH:ubiquinone oxidoreductase subunit A9


Mass: 42606.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1ULW2
#20: Protein
NADH:ubiquinone oxidoreductase subunit AB1


Mass: 17338.211 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1KH26
#25: Protein NADH:ubiquinone oxidoreductase subunit A13


Mass: 16911.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0K655
#35: Protein NADH:ubiquinone oxidoreductase subunit B2


Mass: 11939.366 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1G9F4

+
NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 4 molecules 1c5c1d5d

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


Mass: 8664.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0J7S2
#29: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14327.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JRW3

+
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 10 types, 20 molecules 1f5f1g5g1h5h1i5i1k5k1l5l1m5m1n5n1o5o1p5p

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


Mass: 7044.278 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D2CGH8
#32: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial


Mass: 17384.729 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1EYI7
#33: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial


Mass: 21587.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6
#34: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 15498.017 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UIV8
#36: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3


Mass: 11128.515 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VD84
#37: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial


Mass: 21658.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: B8Y651
#38: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4


Mass: 15117.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T6M0
#39: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9


Mass: 21864.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GSE5
#40: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Complex I-B18 / NADH-ubiquinone oxidoreductase B18 subunit


Mass: 16356.690 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SCH1
#41: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10


Mass: 20944.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0R7A9

+
Cytochrome b-c1 complex subunit ... , 7 types, 32 molecules 3A3N6A6N3B3O6B6O3E3I3R3V6E6I6R6V3F3S6F6S3G3T6G6T3H3U6H6U3X3Y6X6Y

#45: Protein
Cytochrome b-c1 complex subunit 1, mitochondrial


Mass: 52756.320 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0PK14
#46: Protein
Cytochrome b-c1 complex subunit 2, mitochondrial


Mass: 48262.434 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RPD2
#49: Protein
Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 29492.600 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480EHC1
#50: Protein
Cytochrome b-c1 complex subunit 7


Mass: 13587.549 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZPR8
#51: Protein
Cytochrome b-c1 complex subunit 8


Mass: 9784.339 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0SHY6
#52: Protein
Cytochrome b-c1 complex subunit 6, mitochondrial


Mass: 10685.803 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1JI21
#54: Protein
Cytochrome b-c1 complex subunit 10


Mass: 6560.654 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SDI2

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Cytochrome c oxidase subunit ... , 14 types, 28 molecules 4A8A4B8B4C8C4D8D4E8E4F8F4G8G4H8H4I8I4J8J4K8K4L8L4M8M4N8N

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


Mass: 57020.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79876, cytochrome-c oxidase
#56: Protein Cytochrome c oxidase subunit 2


Mass: 26288.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q69GF7
#57: Protein Cytochrome c oxidase subunit 3


Mass: 29753.361 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q35916
#58: Protein Cytochrome c oxidase subunit 4


Mass: 19670.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T8J9
#59: Protein Cytochrome c oxidase subunit 5A, mitochondrial


Mass: 16771.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SJ34
#60: Protein Cytochrome c oxidase subunit 5B, mitochondrial


Mass: 13801.783 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q5S3G4
#61: Protein Cytochrome c oxidase subunit 6A2


Mass: 10876.370 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AEB7
#62: Protein Cytochrome c oxidase subunit 6B1


Mass: 10204.456 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A1XQT1
#63: Protein Cytochrome c oxidase subunit 6C


Mass: 8617.122 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TXH1
#64: Protein Cytochrome c oxidase subunit 7A1, mitochondrial


Mass: 9028.479 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q8SPJ9
#65: Protein Cytochrome c oxidase subunit 7B


Mass: 9169.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BJ57
#66: Protein Cytochrome c oxidase subunit 7C, mitochondrial


Mass: 7358.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q1W0Y2
#67: Protein Cytochrome c oxidase subunit 8


Mass: 7615.939 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A1XQT4
#68: Protein Cytochrome c oxidase subunit NDUFA4


Mass: 9322.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A1XQS3

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Non-polymers , 23 types, 169 molecules

#69: 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.: 32 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#70: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#71: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#72: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe2S2
#73: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#74: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#75: 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.: 17 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#76: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#77: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#78: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#79: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#80: Chemical
ChemComp-EHZ / ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate


Mass: 584.703 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H49N2O9PS
#81: Chemical ChemComp-AME / N-ACETYLMETHIONINE


Type: L-peptide NH3 amino terminus / Mass: 191.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13NO3S
#82: Chemical...
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#83: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#84: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#85: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#86: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#87: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#88: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#89: Chemical ChemComp-PSC / (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 2-LINOLEOYL-1-PALMITOYL-SN-GYCEROL-3-PHOSPHOCHOLINE


Mass: 759.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H81NO8P / Comment: phospholipid*YM
#90: Chemical
ChemComp-PEK / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE / PHOSPHATIDYLETHANOLAMINE / 2-ARACHIDONOYL-1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE


Mass: 768.055 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C43H78NO8P / Comment: phospholipid*YM
#91: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

-
Experiment

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

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Sample preparation

ComponentName: In-situ cryo-EM structure of respiratory supercomplex by directly imaging mitochondria
Type: COMPLEX / Entity ID: #1-#39, #41-#68 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009120907
ELECTRON MICROSCOPYf_angle_d0.906163447
ELECTRON MICROSCOPYf_dihedral_angle_d7.69518835
ELECTRON MICROSCOPYf_chiral_restr0.04517648
ELECTRON MICROSCOPYf_plane_restr0.00520308

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