[English] 日本語
Yorodumi
- EMDB-11127: Fo domain of Ovine ATP synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11127
TitleFo domain of Ovine ATP synthase
Map dataMap of Fo domain, combined states
Sample
  • Complex: Fo domain of purified ATP synthase from sheep heart mitochondria
    • Protein or peptide: x 10 types
  • Ligand: x 3 types
Function / homology
Function and homology information


ATP biosynthetic process / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial inner membrane ...ATP biosynthetic process / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial inner membrane / lipid binding / mitochondrion
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
ATP synthase protein 8 / ATP synthase subunit a / ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase membrane subunit DAPIT / ATP synthase subunit ATP5MPL, mitochondrial / ATP synthase subunit e, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit / ATP synthase subunit f, mitochondrial / ATP synthase subunit b
Similarity search - Component
Biological speciesOvis aries (sheep) / Sheep (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsPinke G / Zhou L / Sazanov LA
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structure of the entire mammalian F-type ATP synthase.
Authors: Gergely Pinke / Long Zhou / Leonid A Sazanov /
Abstract: The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain ...The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the 'proton translocation cluster' attached to the c-ring and a more distant 'hook apparatus' holding subunit e. Unexpectedly, this subunit is anchored to a lipid 'plug' capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.
History
DepositionJun 5, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6za9
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11127.png

Downloads & links

-
Map

FileDownload / File: emd_11127.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of Fo domain, combined states
Voxel sizeX=Y=Z: 1.061 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.21077946 - 0.32944193
Average (Standard dev.)0.007973522 (±0.031167299)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions115122100
Spacing100115122
CellA: 106.1 Å / B: 122.015 Å / C: 129.442 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z100115122
origin x/y/z0.0000.0000.000
length x/y/z106.100122.015129.442
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ100115122
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS122115100
D min/max/mean-0.2110.3290.008

-
Supplemental data

-
Sample components

+
Entire : Fo domain of purified ATP synthase from sheep heart mitochondria

EntireName: Fo domain of purified ATP synthase from sheep heart mitochondria
Components
  • Complex: Fo domain of purified ATP synthase from sheep heart mitochondria
    • Protein or peptide: ATP synthase F(0) complex subunit C1, mitochondrial
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit d, mitochondrial
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase membrane subunit DAPIT
    • Protein or peptide: ATP synthase membrane subunit 6.8PL
    • Protein or peptide: ATP synthase protein 8
    • Protein or peptide: ATP synthase membrane subunit f
    • Protein or peptide: ATP synthase subunit
    • Protein or peptide: ATP synthase subunit e, mitochondrial
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: CARDIOLIPIN
  • Ligand: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine

+
Supramolecule #1: Fo domain of purified ATP synthase from sheep heart mitochondria

SupramoleculeName: Fo domain of purified ATP synthase from sheep heart mitochondria
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Ovis aries (sheep)

+
Macromolecule #1: ATP synthase F(0) complex subunit C1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit C1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 14.201577 KDa
SequenceString:
MQTTGALLIS PALIRSCTRG LIRPVSASFL SRPEIPSVQP SYSSGPLQVA RREFQTSVVS RDIDTAAKFI GAGAATVGVA GSGAGIGTV FGSLIIGYAR NPSLKQQLFS YAILGFALSE AMGLFCLMVA FLILFAM

+
Macromolecule #2: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 2 / Details: XP_004002367.2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 28.84457 KDa
SequenceString: MLSRVVLSAA AAAAPSLKNA AFLGPGVLQA TRIFHTGQPS LAPVPPLPEH GGKVRFGLIP EEFFQFLYPK TGVTGPYVLG TGLILYLLS KEIYVITPET FSAISTIGFL VYVVKKYGAS VGEFADKLNE QKIAQLEEVK QASIKQIQDA IDMEKSQQAL V QKRHYLFD ...String:
MLSRVVLSAA AAAAPSLKNA AFLGPGVLQA TRIFHTGQPS LAPVPPLPEH GGKVRFGLIP EEFFQFLYPK TGVTGPYVLG TGLILYLLS KEIYVITPET FSAISTIGFL VYVVKKYGAS VGEFADKLNE QKIAQLEEVK QASIKQIQDA IDMEKSQQAL V QKRHYLFD VQRNNIAMAL EVTYRERLHR VYREVKNRLD YHISVQNMMR QKEQEHMINW VEKHVVQSIS AQQEKETIAK CI ADLKLLA KKAQAQPVM

+
Macromolecule #3: ATP synthase subunit d, mitochondrial

MacromoleculeName: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 18.747508 KDa
SequenceString:
MAGRKLALKT IDWVAFGEII PRNQKAVANS LKSWNETLTS RLATLPEKPP AIDWAYYKAN VTKAGLVDDF EKKFNALKVP IPEDKYTAQ VDAEEKEDVK SCAEFLIQSK TRIQEYEKEL EKMRNIIPFD QMTIEDLNEV FPETKLDKKK YPYWPHRPIE S L

+
Macromolecule #4: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 24.81185 KDa
SequenceString: MNENLFASFI TPMMFGLPLV TLIVLFPSLL FPTSNRLVNN RLISLQQWML QLVSKQMMSI HNTKGQTWAL MLMSLILFIG STNLLGLLP HSFTPTTQLS MNLGMAIPLW GGAVITGFRN KTKASLAHFL PQGTPTPLIP MLVIIETISL FIQPVALAVR L TANITAGH ...String:
MNENLFASFI TPMMFGLPLV TLIVLFPSLL FPTSNRLVNN RLISLQQWML QLVSKQMMSI HNTKGQTWAL MLMSLILFIG STNLLGLLP HSFTPTTQLS MNLGMAIPLW GGAVITGFRN KTKASLAHFL PQGTPTPLIP MLVIIETISL FIQPVALAVR L TANITAGH LLIHLIGGAT LALMSINTTT ALITFIILIL LTVLEFAVAM IQAYVFTLLV SLYLHDNT

+
Macromolecule #5: ATP synthase membrane subunit DAPIT

MacromoleculeName: ATP synthase membrane subunit DAPIT / type: protein_or_peptide / ID: 5 / Details: ATP synthase membrane subunit DAPIT / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 6.443579 KDa
SequenceString:
MAGPEADAQF HFTGIKKYFN SYTLTGRMNC VLATYGSIAL IVLYFKLRSK KTPAVKAT

+
Macromolecule #6: ATP synthase membrane subunit 6.8PL

MacromoleculeName: ATP synthase membrane subunit 6.8PL / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 6.846093 KDa
SequenceString:
MLQSLIKKVW IPMKPYYTQA YQEIWVGTGL MAYIVYKIRS ADKRSKALKA SSAAPAHGHH

+
Macromolecule #7: ATP synthase protein 8

MacromoleculeName: ATP synthase protein 8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 7.918443 KDa
SequenceString:
MPQLDTSTWL TMILSMFLVL FIIFQLKISK HNFYHNPELM TTKTPKQNTP WETKWTKIYL PLSLPL

+
Macromolecule #8: ATP synthase membrane subunit f

MacromoleculeName: ATP synthase membrane subunit f / type: protein_or_peptide / ID: 8 / Details: ATP synthase subunit f, XP_004016938.3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 10.315207 KDa
SequenceString:
MASVVPLKEK KLLEVKLGEL PSWILMRDFT PSGIAGAFQR GYYRYYNKYV NVKKGSIAGL SMVLAAYVFL NYCRSYKELK HERLRKYH

+
Macromolecule #9: ATP synthase subunit

MacromoleculeName: ATP synthase subunit / type: protein_or_peptide / ID: 9 / Details: XP_011950914.1, ATP synthase subunit g / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 11.428407 KDa
SequenceString:
MAQFVRNLAE KAPALVNAAV TYSKPRLATF WYYAKVELVP PTPAEIPTAI QSLKKIINSA KTGSFKQLTV KEALLNGLVA TEVWMWFYV GEIIGKRGII GYDV

+
Macromolecule #10: ATP synthase subunit e, mitochondrial

MacromoleculeName: ATP synthase subunit e, mitochondrial / type: protein_or_peptide / ID: 10 / Details: XP_027827162.1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 8.336688 KDa
SequenceString:
MVPPVQVSPL IKLGRYSALF LGMAYGAKRY NYLKPRAEEE RRLAAEEKKK RDEQKRIERE LAEAQEDTIL K

+
Macromolecule #11: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 11 / Number of copies: 6 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM / Phosphatidylglycerol

+
Macromolecule #12: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 12 / Number of copies: 3 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

+
Macromolecule #13: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}p...

MacromoleculeName: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine
type: ligand / ID: 13 / Number of copies: 1 / Formula: S12
Molecular weightTheoretical: 523.597 Da
Chemical component information

ChemComp-S12:
O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.8 mg/mL
BufferpH: 7.4
Details: 20 mM HEPES pH7.4, 35 mM NaCl, 2 mM EDTA, 1% sucrose, 1 mM DTT, 0.1% LMNG, 0.2% CHAPS
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.4 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 131951 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 3053 / Average exposure time: 1.0 sec. / Average electron dose: 106.0 e/Å2 / Details: 40 frames per movie
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 809000
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ara

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 217266
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5ara

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 77
Output model

PDB-6za9:
Fo domain of Ovine ATP synthase

+
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