[English] 日本語
Yorodumi
- PDB-6zmr: Porcine ATP synthase Fo domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zmr
TitlePorcine ATP synthase Fo domain
Components(ATP synthase ...) x 10
KeywordsHYDROLASE / mitochondrion / ATP synthase / porcine / complex
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / proton-transporting ATP synthase complex / : / : / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity ...Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / proton-transporting ATP synthase complex / : / : / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / mitochondrial membrane / lipid binding
Similarity search - Function
ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / Mitochondrial proteolipid / ATP synthase protein 8, metazoa ...ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / Mitochondrial proteolipid / ATP synthase protein 8, metazoa / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
CARDIOLIPIN / ATP synthase subunit b / ATP synthase subunit d, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase membrane subunit 6.8PL / ATP synthase membrane subunit K, mitochondrial / ATP synthase lipid-binding protein / ATP synthase subunit / ATP synthase protein 8 / ATP synthase subunit a ...CARDIOLIPIN / ATP synthase subunit b / ATP synthase subunit d, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase membrane subunit 6.8PL / ATP synthase membrane subunit K, mitochondrial / ATP synthase lipid-binding protein / ATP synthase subunit / ATP synthase protein 8 / ATP synthase subunit a / ATP synthase subunit f, mitochondrial / ATP synthase subunit e, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsSpikes, T.E. / Montgomery, M.G. / Walker, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009858/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of the dimeric ATP synthase from bovine mitochondria.
Authors: Tobias E Spikes / Martin G Montgomery / John E Walker /
Abstract: The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial ...The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer-monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer-monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains.
History
DepositionJul 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-0668
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0668
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
8: ATP synthase protein 8
K: ATP synthase F(0) complex subunit C1, mitochondrial
L: ATP synthase F(0) complex subunit C1, mitochondrial
M: ATP synthase F(0) complex subunit C1, mitochondrial
N: ATP synthase F(0) complex subunit C1, mitochondrial
O: ATP synthase F(0) complex subunit C1, mitochondrial
P: ATP synthase F(0) complex subunit C1, mitochondrial
Q: ATP synthase F(0) complex subunit C1, mitochondrial
R: ATP synthase F(0) complex subunit C1, mitochondrial
a: ATP synthase subunit a
b: ATP synthase peripheral stalk-membrane subunit b
d: ATP synthase subunit d, mitochondrial
e: ATP synthase subunit e, mitochondrial
f: ATP synthase subunit f, mitochondrial
g: ATP synthase g subunit
j: ATP synthase j subunit (6.8PL)
k: ATP synthase membrane subunit DAPIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,42918
Polymers179,96517
Non-polymers1,4641
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
ATP synthase ... , 10 types, 17 molecules 8KLMNOPQRabdefgjk

#1: Protein ATP synthase protein 8 / A6L / F-ATPase subunit 8


Mass: 7954.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q35914
#2: Protein
ATP synthase F(0) complex subunit C1, mitochondrial


Mass: 7653.034 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: Reside 43 is trimethyl-lysine. A post-translational modification.
Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWF6
#3: Protein ATP synthase subunit a / F-ATPase protein 6


Mass: 25054.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q35915
#4: Protein ATP synthase peripheral stalk-membrane subunit b


Mass: 24508.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZYM6
#5: Protein ATP synthase subunit d, mitochondrial


Mass: 18542.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287A2Y4, UniProt: A0A287B0C3*PLUS
#6: Protein ATP synthase subunit e, mitochondrial / ATPase subunit e / ATP synthase membrane subunit e


Mass: 8115.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q9MYT8
#7: Protein ATP synthase subunit f, mitochondrial / ATP synthase membrane subunit f


Mass: 10197.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q95339
#8: Protein ATP synthase g subunit / ATP synthase g subunit


Mass: 11198.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ATP synthase g subunit / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SAK7
#9: Protein ATP synthase j subunit (6.8PL) / ATP synthase j subunit (6.8PL)


Mass: 6867.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ATP synthase j subunit (6.8PL) / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TX70
#10: Protein ATP synthase membrane subunit DAPIT


Mass: 6302.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RFD4

-
Non-polymers , 1 types, 1 molecules

#11: 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.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: porcine ATP synthase Fo domain / Type: COMPLEX / Details: Reinterpretation of EMD-0668. / Entity ID: #1-#10 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refinedev_3916refinement
PHENIXdev_3916refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167954 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6B2Z

6b2z

RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 62.72 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006110031
ELECTRON MICROSCOPYf_angle_d0.761313565
ELECTRON MICROSCOPYf_chiral_restr0.04181582
ELECTRON MICROSCOPYf_plane_restr0.00551644
ELECTRON MICROSCOPYf_dihedral_angle_d18.36331444

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more