[English] 日本語
Yorodumi
- PDB-6rd6: CryoEM structure of Polytomella F-ATP synthase, focussed refineme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rd6
TitleCryoEM structure of Polytomella F-ATP synthase, focussed refinement of upper peripheral stalk
Components
  • (Mitochondrial ATP synthase associated protein ...) x 2
  • ASA-2: Polytomella F-ATP synthase associated subunit 2
  • ATP synthase subunit alpha
  • Mitochondrial ATP synthase subunit OSCP
KeywordsPROTON TRANSPORT / mitochondrial ATP synthase dimer flexible coupling cryoEM
Function / homology
Function and homology information


photosynthetic electron transport in photosystem I / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase, catalytic core / photosynthetic electron transport in photosystem II / proton motive force-driven mitochondrial ATP synthesis / chloroplast thylakoid membrane / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / hydrolase activity ...photosynthetic electron transport in photosystem I / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase, catalytic core / photosynthetic electron transport in photosystem II / proton motive force-driven mitochondrial ATP synthesis / chloroplast thylakoid membrane / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / hydrolase activity / ATP binding / plasma membrane
Similarity search - Function
ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain ...ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit alpha / Mitochondrial ATP synthase associated protein ASA4 / Mitochondrial ATP synthase subunit ASA2 / Mitochondrial ATP synthase subunit OSCP / Mitochondrial ATP synthase associated protein ASA7
Similarity search - Component
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsMurphy, B.J. / Klusch, N. / Yildiz, O. / Kuhlbrandt, W.
Funding supporttopol, European Molecular Biology Organization, 2items
OrganizationGrant numberCountry
Max Planck SocietyGermanytopol
1GermanyEuropean Molecular Biology Organization
CitationJournal: Science / Year: 2019
Title: Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F-F coupling.
Authors: Bonnie J Murphy / Niklas Klusch / Julian Langer / Deryck J Mills / Özkan Yildiz / Werner Kühlbrandt /
Abstract: FF-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy ...FF-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy structure of active dimeric ATP synthase from mitochondria of sp. at a resolution of 2.7 to 2.8 angstroms. Separation of 13 well-defined rotary substates by three-dimensional classification provides a detailed picture of the molecular motions that accompany -ring rotation and result in ATP synthesis. Crucially, the F head rotates along with the central stalk and -ring rotor for the first ~30° of each 120° primary rotary step to facilitate flexible coupling of the stoichiometrically mismatched F and F subcomplexes. Flexibility is mediated primarily by the interdomain hinge of the conserved OSCP subunit. A conserved metal ion in the proton access channel may synchronize -ring protonation with rotation.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Data processing / Experimental preparation / Other
Category: atom_sites / em_ctf_correction ...atom_sites / em_ctf_correction / em_image_processing / em_imaging / em_imaging_optics / em_particle_selection / em_sample_support / em_single_particle_entity
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _em_ctf_correction.details / _em_image_processing.details / _em_imaging.details / _em_imaging_optics.chr_aberration_corrector / _em_imaging_optics.phase_plate / _em_imaging_optics.sph_aberration_corrector / _em_particle_selection.details / _em_sample_support.id / _em_sample_support.specimen_id
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.3May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-4807
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4807
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
2: ASA-2: Polytomella F-ATP synthase associated subunit 2
4: Mitochondrial ATP synthase associated protein ASA4
7: Mitochondrial ATP synthase associated protein ASA7
P: Mitochondrial ATP synthase subunit OSCP
T: ATP synthase subunit alpha


Theoretical massNumber of molelcules
Total (without water)182,9675
Polymers182,9675
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21360 Å2
ΔGint-138 kcal/mol
Surface area45080 Å2
MethodPISA

-
Components

-
Protein , 3 types, 3 molecules 2PT

#1: Protein ASA-2: Polytomella F-ATP synthase associated subunit 2


Mass: 44842.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D7P6B9*PLUS
#4: Protein Mitochondrial ATP synthase subunit OSCP


Mass: 25530.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D8V7I1
#5: Protein ATP synthase subunit alpha /


Mass: 60766.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: A0ZW40

-
Mitochondrial ATP synthase associated protein ... , 2 types, 2 molecules 47

#2: Protein Mitochondrial ATP synthase associated protein ASA4


Mass: 31275.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D7NIZ2
#3: Protein Mitochondrial ATP synthase associated protein ASA7


Mass: 20553.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D8V7I2

-
Non-polymers , 1 types, 32 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Dimeric mitochondrial F-type ATP synthase from Polytomella sp. Pringsheim 198.80
Type: COMPLEX
Details: Generated using a symmetry-expanded dataset, with focussed refinement of the upper peripheral stalk region of one monomer
Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Buffer solutionpH: 7.8
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: -5000 nm / Nominal defocus min: -400 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)
Image scansWidth: 4096 / Height: 4096

-
Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1.10CTF correction
7Coot0.8.9.1model fitting
9PHENIX1.14model refinement
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 735197
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 777340 / Symmetry type: POINT
Atomic model buildingSpace: REAL

+
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