[English] 日本語
Yorodumi
- EMDB-1357: Structure of the mitochondrial ATP synthase by electron cryomicro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1357
TitleStructure of the mitochondrial ATP synthase by electron cryomicroscopy.
Map data3-D model of detergent solubilized bovine ATP synthase
Sample
  • Sample: Bovine mitochondrial ATP synthase
  • Protein or peptide: x 15 types
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 32.0 Å
AuthorsRubinstein JL / Walker JE / Henderson R
CitationJournal: EMBO J / Year: 2003
Title: Structure of the mitochondrial ATP synthase by electron cryomicroscopy.
Authors: John L Rubinstein / John E Walker / Richard Henderson /
Abstract: We have determined the structure of intact ATP synthase from bovine heart mitochondria by electron cryomicroscopy of single particles. Docking of an atomic model of the F1-c10 subcomplex into a major ...We have determined the structure of intact ATP synthase from bovine heart mitochondria by electron cryomicroscopy of single particles. Docking of an atomic model of the F1-c10 subcomplex into a major segment of the map has allowed the 32 A resolution density to be interpreted as the F1-ATPase, a central and a peripheral stalk and an FO membrane region that is composed of two domains. One domain of FO corresponds to the ring of c-subunits, and the other probably contains the a-subunit, the transmembrane portion of the b-subunit and the remaining integral membrane proteins of FO. The peripheral stalk wraps around the molecule and connects the apex of F1 to the second domain of FO. The interaction of the peripheral stalk with F1-c10 implies that it binds to a non-catalytic alpha-beta interface in F1 and its inclination where it is not attached to F1 suggests that it has a flexible region that can serve as a stator during both ATP synthesis and ATP hydrolysis.
History
DepositionMay 8, 2007-
Header (metadata) releaseMay 9, 2007-
Map releaseMay 9, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.167303869
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.167303869
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-1qo1
  • Surface level: 0.167303869
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1357.gif

Downloads & links

-
Map

FileDownload / File: emd_1357.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3-D model of detergent solubilized bovine ATP synthase
Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level1: 0.0799 / Movie #1: 0.1673039
Minimum - Maximum-0.14835 - 0.899798
Average (Standard dev.)0.01476 (±0.0974465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 358.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1480.9000.015

-
Supplemental data

-
Sample components

+
Entire : Bovine mitochondrial ATP synthase

EntireName: Bovine mitochondrial ATP synthase
Components
  • Sample: Bovine mitochondrial ATP synthase
  • Protein or peptide: alpha
  • Protein or peptide: beta
  • Protein or peptide: gamma
  • Protein or peptide: delta
  • Protein or peptide: epsilon
  • Protein or peptide: a
  • Protein or peptide: b
  • Protein or peptide: c
  • Protein or peptide: d
  • Protein or peptide: e
  • Protein or peptide: f
  • Protein or peptide: g
  • Protein or peptide: F6
  • Protein or peptide: OSCPOffensive Security Certified Professional
  • Protein or peptide: A6L

+
Supramolecule #1000: Bovine mitochondrial ATP synthase

SupramoleculeName: Bovine mitochondrial ATP synthase / type: sample / ID: 1000 / Details: Kept in solution with Brij-35 detergent / Oligomeric state: multisubunit complex / Number unique components: 15
Molecular weightTheoretical: 660 KDa

+
Macromolecule #1: alpha

MacromoleculeName: alpha / type: protein_or_peptide / ID: 1 / Details: 3 copies / Oligomeric state: Multiprotein complex / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow / Tissue: Bovine Heart / Organelle: Mitochondrial / Location in cell: Inner mitochondrial membrane
Molecular weightExperimental: 54.39 KDa / Theoretical: 54.39 KDa

+
Macromolecule #2: beta

MacromoleculeName: beta / type: protein_or_peptide / ID: 2 / Details: 3 copies / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 51.705 KDa / Theoretical: 51.705 KDa

+
Macromolecule #3: gamma

MacromoleculeName: gamma / type: protein_or_peptide / ID: 3 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 30.256 KDa / Theoretical: 30.256 KDa

+
Macromolecule #4: delta

MacromoleculeName: delta / type: protein_or_peptide / ID: 4 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 15.065 KDa / Theoretical: 15.065 KDa

+
Macromolecule #5: epsilon

MacromoleculeName: epsilon / type: protein_or_peptide / ID: 5 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 5.652 KDa / Theoretical: 5.652 KDa

+
Macromolecule #6: a

MacromoleculeName: a / type: protein_or_peptide / ID: 6 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 24.788 KDa / Theoretical: 24.788 KDa

+
Macromolecule #7: b

MacromoleculeName: b / type: protein_or_peptide / ID: 7 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 24.669 KDa / Theoretical: 24.669 KDa

+
Macromolecule #8: c

MacromoleculeName: c / type: protein_or_peptide / ID: 8 / Details: 9-12 copies / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 7.608 KDa / Theoretical: 7.608 KDa

+
Macromolecule #9: d

MacromoleculeName: d / type: protein_or_peptide / ID: 9 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 18.561 KDa / Theoretical: 18.561 KDa

+
Macromolecule #10: e

MacromoleculeName: e / type: protein_or_peptide / ID: 10 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 8.321 KDa / Theoretical: 8.321 KDa

+
Macromolecule #11: f

MacromoleculeName: f / type: protein_or_peptide / ID: 11 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 10.166 KDa / Theoretical: 10.166 KDa

+
Macromolecule #12: g

MacromoleculeName: g / type: protein_or_peptide / ID: 12 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 11.286 KDa / Theoretical: 11.286 KDa

+
Macromolecule #13: F6

MacromoleculeName: F6 / type: protein_or_peptide / ID: 13 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 8.958 KDa / Theoretical: 8.958 KDa

+
Macromolecule #14: OSCP

MacromoleculeName: OSCP / type: protein_or_peptide / ID: 14 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 20.96 KDa / Theoretical: 20.96 KDa

+
Macromolecule #15: A6L

MacromoleculeName: A6L / type: protein_or_peptide / ID: 15 / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 7.937 KDa / Theoretical: 7.937 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 8
Details: Tris-HCl, 20 mM Sucrose, 50 mM Magnesium Sulfate, 2 mM EDTA, 1 mM ADP, 2 mM Brij-35, 0.05%(w/v)
GridDetails: 400 mesh grid coated with a perforated carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Talmon plunger. Carried out in coldroom
Method: Sample applied from one side and blotted from same side

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen / Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: corrected at 175kx magnification
DetailsDigitized with Zeiss SCAI scanner
DateJan 1, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 101 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: See publication
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMAGIC, FREALIGN, ROTAN / Number images used: 5984
DetailsParticles manually selected.

-
Atomic model buiding 1

SoftwareName: O
DetailsProtocol: Eye. Multiple pdb files fit. See publication.
RefinementProtocol: RIGID BODY FIT

+
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