[English] 日本語
Yorodumi
- PDB-2ybb: Fitted model for bovine mitochondrial supercomplex I1III2IV1 by s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ybb
TitleFitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)
Components
  • (CYTOCHROME B-C1 COMPLEX SUBUNIT ...) x 9
  • (CYTOCHROME C OXIDASE SUBUNIT ...) x 12
  • (NADH-QUINONE OXIDOREDUCTASE SUBUNIT ...) x 10
  • (NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT ...) x 2
  • CYTOCHROME B
  • CYTOCHROME C
  • CYTOCHROME C OXIDASE POLYPEPTIDE VIA, CYTOCHROME C OXIDASE POLYPEPTIDE VB
  • CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE / SUPERCOMPLEX B / MITOCHONDRIA / RESPIRATORY CHAIN / AMPHIPOL A8-35 / RANDOM CONICAL TILT
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / : / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / : / cytochrome-c oxidase / : / oxidative phosphorylation / quinol-cytochrome-c reductase / molybdopterin cofactor binding / respiratory chain complex I / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / iron-sulfur cluster assembly / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / NADH dehydrogenase activity / : / ubiquinone binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / respiratory electron transport chain / ferric iron binding / central nervous system development / mitochondrial membrane / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / electron transfer activity / iron ion binding / copper ion binding / apoptotic process / heme binding / mitochondrion / proteolysis / membrane / metal ion binding / plasma membrane
Similarity search - Function
NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Frataxin/CyaY superfamily / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII ...NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Frataxin/CyaY superfamily / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / : / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Molybdopterin oxidoreductase Fe4S4 domain / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit Va/VI / Globular protein, non-globular alpha/beta subunit / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Molybdopterin oxidoreductase Fe4S4 domain / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / 4Fe-4S binding domain / Cytochrome C oxidase subunit II, transmembrane domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / 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 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c, class IA/ IB / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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 b / Cytochrome c/quinol oxidase subunit II / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature.
Similarity search - Domain/homology
CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / STIGMATELLIN A ...CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / STIGMATELLIN A / UBIQUINONE-1 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome b-c1 complex subunit 10 / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome c / Cytochrome c oxidase subunit 2 / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 / NADH-quinone oxidoreductase subunit 9 / NADH-quinone oxidoreductase subunit 15
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
BOS TAURUS (cattle)
ESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 19 Å
AuthorsAlthoff, T. / Mills, D.J. / Popot, J.-L. / Kuehlbrandt, W.
Citation
Journal: EMBO J / Year: 2011
Title: Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1.
Authors: Thorsten Althoff / Deryck J Mills / Jean-Luc Popot / Werner Kühlbrandt /
Abstract: The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. ...The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. A 19-Å 3D map of the 1.7-MDa amphipol-solubilized supercomplex I(1)III(2)IV(1) from bovine heart obtained by single-particle electron cryo-microscopy reveals an amphipol belt replacing the membrane lipid bilayer. A precise fit of the X-ray structures of complex I, the complex III dimer, and monomeric complex IV indicates distances of 13 nm between the ubiquinol-binding sites of complexes I and III, and of 10-11 nm between the cytochrome c binding sites of complexes III and IV. The arrangement of respiratory chain complexes suggests two possible pathways for efficient electron transfer through the supercomplex, of which the shorter branch through the complex III monomer proximal to complex I may be preferred.
#1: Journal: Ph D Thesis / Year: 2011
Title: Strukturelle Untersuchungen Am Superkomplex I1III2Iv1 Der Atmungskette Mittels Kryoelektronenmikroskopie
Authors: Althoff, T.
History
DepositionMar 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2Aug 30, 2017Group: Advisory / Data collection / Category: em_software / pdbx_distant_solvent_atoms
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: cell / struct_conn / struct_ref_seq
Item: _cell.Z_PDB / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1876
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links