[English] 日本語
Yorodumi
- PDB-9vpd: Cryo-EM structure of the IF1 bound bovine ATP synthase monomer: r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vpd
TitleCryo-EM structure of the IF1 bound bovine ATP synthase monomer: rotary state 1, F1 focused map
Components
  • (ATP synthase F(1) complex subunit ...) x 4
  • (ATP synthase peripheral stalk subunit ...) x 4
  • ATP synthase F(1) complex catalytic subunit beta, mitochondrial
  • ATPase inhibitor, mitochondrial
KeywordsMEMBRANE PROTEIN / ATP synthase/hydrolase / oligomer / membrane bending / mammalian mitochondria / motor protein
Function / homology
Function and homology information


negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / heme biosynthetic process / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / erythrocyte differentiation / aerobic respiration / ADP binding / ATPase binding / protein homotetramerization / calmodulin binding / mitochondrial inner membrane / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) ...Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / 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 delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / 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, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase peripheral stalk subunit d, mitochondrial ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsNakano, A. / Jiko, C. / Yamashita, E. / Yokoyama, K. / Gerle, C.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22ama121003 Japan
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
Citation
Journal: Cell Death Differ / Year: 2026
Title: A planar dimer of bovine ATP synthase.
Authors: Chimari Jiko / Atsuki Nakano / Yosuke Teshirogi / Eiki Yamashita / Genji Kurisu / Daron Standley / Tohru Terada / Kaoru Mitsuoka / Ken Yokoyama / Christoph Gerle /
Abstract: Mammalian mitochondrial ATP synthase typically organizes into rows of V-shaped dimers that impose significant membrane curvature essential for mitochondrial cristae formation. Using gentle, column- ...Mammalian mitochondrial ATP synthase typically organizes into rows of V-shaped dimers that impose significant membrane curvature essential for mitochondrial cristae formation. Using gentle, column-free purification combined with single-particle cryo-electron microscopy, we have identified a previously unrecognized planar dimeric form of bovine ATP synthase exhibiting minimal membrane bending. This planar dimer is characterized structurally by anti-parallel arrangement of two ATP synthase complexes linked by a straight conformation of inhibitory factor 1 (IF1), a sharp contrast to the kinked IF1 observed in tetrameric assemblies. Molecular dynamics simulations confirm that transitioning between straight and kinked IF1 conformations occurs without significant energetic barriers. The planar dimer also displays distinct peripheral stalk positioning relative to its adjacent α subunit. These structural divergences suggest a specialized function and a distinct localization for planar ATP synthase dimers, providing structural support for a division of labor within mitochondrial ATP synthase populations.
History
DepositionJul 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.1Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP synthase F(1) complex subunit alpha, mitochondrial
B: ATP synthase F(1) complex subunit alpha, mitochondrial
C: ATP synthase F(1) complex subunit alpha, mitochondrial
D: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
E: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
F: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
G: ATP synthase F(1) complex subunit gamma, mitochondrial
H: ATP synthase F(1) complex subunit delta, mitochondrial
I: ATP synthase F(1) complex subunit epsilon, mitochondrial
J: ATPase inhibitor, mitochondrial
S: ATP synthase peripheral stalk subunit OSCP, mitochondrial
b: ATP synthase peripheral stalk subunit b, mitochondrial
d: ATP synthase peripheral stalk subunit d, mitochondrial
h: ATP synthase peripheral stalk subunit F6, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)503,67825
Polymers500,75414
Non-polymers2,92511
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
ATP synthase F(1) complex subunit ... , 4 types, 6 molecules ABCGHI

#1: Protein ATP synthase F(1) complex subunit alpha, mitochondrial / ATP synthase F1 subunit alpha


Mass: 59795.492 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P19483
#3: Protein ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase subunit gamma / ATP synthase F1 subunit gamma / F-ATPase gamma subunit


Mass: 33119.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05631
#4: Protein ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase subunit delta / ATP synthase F1 subunit delta / F-ATPase delta subunit


Mass: 17626.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05630
#5: Protein ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase subunit epsilon / ATPase subunit epsilon / ATP synthase F1 subunit epsilon


Mass: 5793.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05632

-
Protein , 2 types, 4 molecules DEFJ

#2: Protein ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase subunit beta / ATP synthase F1 subunit beta


Mass: 56340.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P00829, H+-transporting two-sector ATPase
#6: Protein ATPase inhibitor, mitochondrial / ATPase inhibitory factor 1 (IF1) / ATP synthase F1 subunit epsilon / Inhibitor of F(1)F(o)-ATPase / ...ATPase inhibitory factor 1 (IF1) / ATP synthase F1 subunit epsilon / Inhibitor of F(1)F(o)-ATPase / IF(1) / IF1


Mass: 12326.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P01096

-
ATP synthase peripheral stalk subunit ... , 4 types, 4 molecules Sbdh

#7: Protein ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase oligomycin sensitivity conferral protein (OSCP) / ATP synthase subunit O / Oligomycin ...ATP synthase oligomycin sensitivity conferral protein (OSCP) / ATP synthase subunit O / Oligomycin sensitivity conferral protein / OSCP


Mass: 23351.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13621
#8: Protein ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase subunit b / ATP synthase F(0) complex subunit B1 / mitochondrial / ATP synthase ...ATP synthase subunit b / ATP synthase F(0) complex subunit B1 / mitochondrial / ATP synthase peripheral stalk-membrane subunit b / ATP synthase subunit b / ATPase subunit b


Mass: 28859.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13619
#9: Protein ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase subunit d / ATPase subunit d / ATP synthase peripheral stalk subunit d


Mass: 18719.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13620
#10: Protein ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase subunit F6 / ATPase subunit F6 / ATP synthase peripheral stalk subunit F6


Mass: 12549.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02721

-
Non-polymers , 4 types, 28 molecules

#11: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#12: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: IF1 bound bovine ATP synthase monomer isolated from heart muscle tissue mitochondria
Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightValue: 0.6 MDa / Experimental value: NO
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.3
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameCategory
1Topazparticle selection
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 398620 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6YY0

6yy0


Accession code: 6YY0 / Source name: PDB / Type: experimental model

+
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