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- PDB-6giq: Saccharomyces cerevisiae respiratory supercomplex III2IV -

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Basic information

Entry
Database: PDB / ID: 6giq
TitleSaccharomyces cerevisiae respiratory supercomplex III2IV
Components
  • (Cytochrome b-c1 complex subunit ...) x 2
  • (Cytochrome c oxidase ...) x 5
  • BJ4_G0001550.mRNA.1.CDS.1
  • BJ4_G0018620.mRNA.1.CDS.1
  • BJ4_G0023510.mRNA.1.CDS.1
  • BJ4_G0024040.mRNA.1.CDS.1
  • BJ4_G0028260.mRNA.1.CDS.1
  • BJ4_G0035470.mRNA.1.CDS.1
  • BJ4_G0038800.mRNA.1.CDS.1
  • BJ4_G0043230.mRNA.1.CDS.1
  • BJ4_G0046460.mRNA.1.CDS.1
  • BJ4_G0049990.mRNA.1.CDS.1
  • Complex III subunit 7
  • Cytochrome b
  • HLJ1_G0021680.mRNA.1.CDS.1
  • QCR6 isoform 1
  • Unknown Cox subunit
KeywordsELECTRON TRANSPORT / Respiratory chain / supercomplex / bc1 complex / cytochrome c oxidase
Function / homology
Function and homology information


Complex III assembly / : / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / mitochondrial respiratory chain complex III assembly / respiratory chain complex IV ...Complex III assembly / : / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / mitochondrial respiratory chain complex III assembly / respiratory chain complex IV / cellular respiration / cytochrome-c oxidase / respiratory chain complex III / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / ubiquinone binding / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / nuclear periphery / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / metal ion binding / membrane / cytosol
Similarity search - Function
: / Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c oxidase, subunit Va/VI ...: / Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c oxidase, subunit Va/VI / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / 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 / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / 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 / 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 c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur 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 / 3-layer Sandwich / 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 / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / 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. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit I
Similarity search - Domain/homology
Chem-6PH / Chem-7PH / Chem-8PE / Chem-9PE / Chem-CN3 / Chem-CN5 / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A ...Chem-6PH / Chem-7PH / Chem-8PE / Chem-9PE / Chem-CN3 / Chem-CN5 / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Chem-UQ6 / Cytochrome c oxidase subunit 3 / Cytochrome b / Cytochrome c oxidase subunit 2 / quinol--cytochrome-c reductase / : / : / : / : / : / BJ4_G0018620.mRNA.1.CDS.1 / : / : / : / : / : / : / : / : / : / : / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 8, mitochondrial / Cytochrome c oxidase subunit 7, mitochondrial / Cytochrome b-c1 complex subunit 9, mitochondrial / Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome b-c1 complex subunit 10, mitochondrial / Cytochrome c oxidase subunit 12, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsRathore, S. / Berndtsson, J. / Conrad, J. / Ott, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Cryo-EM structure of the yeast respiratory supercomplex.
Authors: Sorbhi Rathore / Jens Berndtsson / Lorena Marin-Buera / Julian Conrad / Marta Carroni / Peter Brzezinski / Martin Ott /
Abstract: Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes ...Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes IIIIV and IIIIV, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.
History
DepositionMay 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 2.0Oct 9, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_admin / entity / entity_name_com / entity_src_nat / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Assembly

Deposited unit
A: BJ4_G0001550.mRNA.1.CDS.1
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: BJ4_G0049990.mRNA.1.CDS.1
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: QCR6 isoform 1
G: Complex III subunit 7
H: BJ4_G0028260.mRNA.1.CDS.1
I: HLJ1_G0021680.mRNA.1.CDS.1
L: BJ4_G0001550.mRNA.1.CDS.1
M: Cytochrome b-c1 complex subunit 2, mitochondrial
N: Cytochrome b
O: BJ4_G0049990.mRNA.1.CDS.1
P: Cytochrome b-c1 complex subunit Rieske, mitochondrial
Q: QCR6 isoform 1
R: Complex III subunit 7
S: BJ4_G0028260.mRNA.1.CDS.1
T: HLJ1_G0021680.mRNA.1.CDS.1
U: BJ4_G0023510.mRNA.1.CDS.1
V: BJ4_G0023510.mRNA.1.CDS.1
a: Cytochrome c oxidase subunit 1
b: Cytochrome c oxidase subunit 2
c: Cytochrome c oxidase subunit 3
d: BJ4_G0018620.mRNA.1.CDS.1
e: BJ4_G0046460.mRNA.1.CDS.1
f: BJ4_G0024040.mRNA.1.CDS.1
g: BJ4_G0043230.mRNA.1.CDS.1
h: BJ4_G0038800.mRNA.1.CDS.1
i: Cytochrome c oxidase polypeptide VIIA
j: BJ4_G0035470.mRNA.1.CDS.1
k: Cytochrome c oxidase subunit
m: Unknown Cox subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)736,65258
Polymers721,68332
Non-polymers14,96926
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Other experiment performed that support the state of this assembly is native gel electrophoresis and co-purification combined with determination of enzyme quantity.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area128830 Å2
ΔGint-1044 kcal/mol
Surface area224990 Å2
MethodPISA

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Components

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Protein , 14 types, 22 molecules ALCNDOFQGRHSITUVdefghj

#1: Protein BJ4_G0001550.mRNA.1.CDS.1 / COR1 isoform 1 / Cytochrome b-c1 complex subunit 1 / mitochondrial / Y55_G0001550.mRNA.1.CDS.1


Mass: 50282.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3X1, UniProt: P07256*PLUS
#3: Protein Cytochrome b


Mass: 43686.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A0G3F5W7, UniProt: P00163*PLUS
#4: Protein BJ4_G0049990.mRNA.1.CDS.1 / CYT1 isoform 1 / Cytochrome c1 / heme protein / mitochondrial / HLJ1_G0050000.mRNA.1.CDS.1 / JXXY16. ...CYT1 isoform 1 / Cytochrome c1 / heme protein / mitochondrial / HLJ1_G0050000.mRNA.1.CDS.1 / JXXY16.1_G0049800.mRNA.1.CDS.1 / SX2_G0049550.mRNA.1.CDS.1 / Y55_G0049920.mRNA.1.CDS.1


Mass: 34097.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A5B9RH60, UniProt: P07143*PLUS
#6: Protein QCR6 isoform 1 / Y55_G0017620.mRNA.1.CDS.1


Mass: 17276.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q022, UniProt: P00127*PLUS
#7: Protein Complex III subunit 7


Mass: 14583.755 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q2H4, UniProt: P00128*PLUS
#8: Protein BJ4_G0028260.mRNA.1.CDS.1 / EM14S01-3B_G0028260.mRNA.1.CDS.1 / HLJ1_G0028200.mRNA.1.CDS.1 / HN1_G0028080.mRNA.1.CDS.1 / JXXY16. ...EM14S01-3B_G0028260.mRNA.1.CDS.1 / HLJ1_G0028200.mRNA.1.CDS.1 / HN1_G0028080.mRNA.1.CDS.1 / JXXY16.1_G0025710.mRNA.1.CDS.1 / QCR8 isoform 1 / SX2_G0028380.mRNA.1.CDS.1 / XXYS1_G0028300.mRNA.1.CDS.1 / Y55_G0028450.mRNA.1.CDS.1


Mass: 10987.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PU80, UniProt: P08525*PLUS
#9: Protein HLJ1_G0021680.mRNA.1.CDS.1 / HN1_G0021630.mRNA.1.CDS.1 / SX2_G0021700.mRNA.1.CDS.1 / Y55_G0021900.mRNA.1.CDS.1


Mass: 7485.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0Z0I8, UniProt: P22289*PLUS
#10: Protein BJ4_G0023510.mRNA.1.CDS.1 / EM14S01-3B_G0023320.mRNA.1.CDS.1 / HLJ1_G0023290.mRNA.1.CDS.1 / HN1_G0023260.mRNA.1.CDS.1 / JXXY16. ...EM14S01-3B_G0023320.mRNA.1.CDS.1 / HLJ1_G0023290.mRNA.1.CDS.1 / HN1_G0023260.mRNA.1.CDS.1 / JXXY16.1_G0041640.mRNA.1.CDS.1 / XXYS1_G0023360.mRNA.1.CDS.1 / Y55_G0023430.mRNA.1.CDS.1


Mass: 8602.913 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0ZE60, UniProt: P37299*PLUS
#14: Protein BJ4_G0018620.mRNA.1.CDS.1 / COX4 isoform 1 / Cytochrome c oxidase subunit 4 / mitochondrial / EM14S01-3B_G0018320.mRNA.1.CDS.1 ...COX4 isoform 1 / Cytochrome c oxidase subunit 4 / mitochondrial / EM14S01-3B_G0018320.mRNA.1.CDS.1 / HLJ1_G0018360.mRNA.1.CDS.1 / HN1_G0018250.mRNA.1.CDS.1 / JXXY16.1_G0018520.mRNA.1.CDS.1 / SX2_G0018350.mRNA.1.CDS.1 / XXYS1_G0018320.mRNA.1.CDS.1 / Y55_G0018590.mRNA.1.CDS.1


Mass: 17164.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PV33, UniProt: P04037*PLUS
#15: Protein BJ4_G0046460.mRNA.1.CDS.1 / COX5A isoform 1 / Cytochrome c oxidase subunit 5A / mitochondrial / HLJ1_G0046380.mRNA.1.CDS.1 / ...COX5A isoform 1 / Cytochrome c oxidase subunit 5A / mitochondrial / HLJ1_G0046380.mRNA.1.CDS.1 / HN1_G0046310.mRNA.1.CDS.1 / SX2_G0046080.mRNA.1.CDS.1 / Y55_G0046480.mRNA.1.CDS.1


Mass: 17161.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q8F6, UniProt: P00424*PLUS
#16: Protein BJ4_G0024040.mRNA.1.CDS.1 / COX6 isoform 1 / Cytochrome c oxidase subunit 6 / mitochondrial / HLJ1_G0023830.mRNA.1.CDS.1 / SX2_ ...COX6 isoform 1 / Cytochrome c oxidase subunit 6 / mitochondrial / HLJ1_G0023830.mRNA.1.CDS.1 / SX2_G0023870.mRNA.1.CDS.1 / Y55_G0023980.mRNA.1.CDS.1


Mass: 17366.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PUE0, UniProt: P00427*PLUS
#17: Protein BJ4_G0043230.mRNA.1.CDS.1 / COX7 isoform 1 / EM14S01-3B_G0043140.mRNA.1.CDS.1 / HLJ1_G0043160.mRNA.1.CDS.1 / HN1_G0042940.mRNA. ...COX7 isoform 1 / EM14S01-3B_G0043140.mRNA.1.CDS.1 / HLJ1_G0043160.mRNA.1.CDS.1 / HN1_G0042940.mRNA.1.CDS.1 / JXXY16.1_G0040380.mRNA.1.CDS.1 / SX2_G0042750.mRNA.1.CDS.1 / XXYS1_G0042950.mRNA.1.CDS.1 / Y55_G0043120.mRNA.1.CDS.1


Mass: 6942.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PQU1, UniProt: P10174*PLUS
#18: Protein BJ4_G0038800.mRNA.1.CDS.1 / COX8 isoform 1 / HLJ1_G0038810.mRNA.1.CDS.1 / HN1_G0038550.mRNA.1.CDS.1 / SX2_G0038370.mRNA.1.CDS.1


Mass: 8921.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PRD8, UniProt: P04039*PLUS
#20: Protein BJ4_G0035470.mRNA.1.CDS.1 / COX12 isoform 1 / EM14S01-3B_G0035180.mRNA.1.CDS.1 / HLJ1_G0035620.mRNA.1.CDS.1 / HN1_G0035360.mRNA. ...COX12 isoform 1 / EM14S01-3B_G0035180.mRNA.1.CDS.1 / HLJ1_G0035620.mRNA.1.CDS.1 / HN1_G0035360.mRNA.1.CDS.1 / JXXY16.1_G0032480.mRNA.1.CDS.1 / SX2_G0035180.mRNA.1.CDS.1 / XXYS1_G0035020.mRNA.1.CDS.1 / Y55_G0035530.mRNA.1.CDS.1


Mass: 9799.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PU81, UniProt: Q01519*PLUS

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Cytochrome b-c1 complex subunit ... , 2 types, 4 molecules BMEP

#2: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / QCR2 isoform 1


Mass: 40528.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q625, UniProt: P07257*PLUS
#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 23393.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5PX11, UniProt: P08067*PLUS, quinol-cytochrome-c reductase

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Cytochrome c oxidase ... , 5 types, 5 molecules abcik

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


Mass: 58832.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00401, cytochrome-c oxidase
#12: Protein Cytochrome c oxidase subunit 2


Mass: 28585.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A0H3WI21, UniProt: P00410*PLUS
#13: Protein Cytochrome c oxidase subunit 3


Mass: 30383.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A0G3F1J2, UniProt: P00420*PLUS
#19: Protein Cytochrome c oxidase polypeptide VIIA / Cytochrome c oxidase subunit 9 / mitochondrial


Mass: 6974.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q104, UniProt: P07255*PLUS
#21: Protein Cytochrome c oxidase subunit / Cytochrome c oxidase polypeptide VIa


Mass: 15046.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PWA0, UniProt: P32799*PLUS

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Protein/peptide , 1 types, 1 molecules m

#22: Protein/peptide Unknown Cox subunit


Mass: 2656.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 13 types, 26 molecules

#23: Chemical ChemComp-6PH / (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate / PHOSPHATIDIC ACID


Mass: 592.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H61O8P
#24: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#25: Chemical ChemComp-8PE / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 691.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#26: Chemical ChemComp-CN5 / (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate / CARDIOLIPIN


Mass: 634.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H52O13P2
#27: Chemical ChemComp-UQ6 / 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL


Mass: 592.891 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H60O4
#28: Chemical ChemComp-7PH / (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate / PHOSPHATIDIC ACID


Mass: 564.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H57O8P
#29: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#30: Chemical ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P
#31: Chemical ChemComp-9PE / (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 593.773 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H60NO8P / Comment: phospholipid*YM
#32: Chemical ChemComp-CN3 / (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate / CARDIOLIPIN


Mass: 834.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H68O17P2
#33: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#34: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#35: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Saccharomyces cerevisiae Supercomplex (III2IV)COMPLEX#1-#220NATURAL
2Saccharomyces cerevisiae complex IIICOMPLEX#1-#101NATURAL
3Saccharomyces cerevisiae complex IVCOMPLEX#11-#221NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDOrganelle
21Saccharomyces cerevisiae W303 (yeast)580240Mitochondria
32Saccharomyces cerevisiae W303 (yeast)580240Mitochondria
43Saccharomyces cerevisiae W303 (yeast)580240Mitochondria
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
9PHENIX1.13model refinement
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203271 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-Correlation coefficient

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