[English] 日本語
Yorodumi
- PDB-9pew: Porcine ATP synthase with inhibitory protein IF1, DP-state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9pew
TitlePorcine ATP synthase with inhibitory protein IF1, DP-state
Components
  • (ATP synthase ...) x 15
  • ATPase inhibitor, mitochondrial
KeywordsMEMBRANE PROTEIN / TRANSLOCASE / ATP synthesis / Complex V / mitochondria / oxidative-phosphorylation
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex binding / : / : / mitochondrial depolarization / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / ATP biosynthetic process / positive regulation of type 2 mitophagy ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex binding / : / : / mitochondrial depolarization / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / ATP biosynthetic process / positive regulation of type 2 mitophagy / ATPase inhibitor activity / Mitochondrial translation termination / Mitochondrial protein degradation / proton channel activity / negative regulation of hydrolase activity / negative regulation of endothelial cell proliferation / heme biosynthetic process / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / negative regulation of cardiac muscle cell apoptotic process / response to ischemia / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / erythrocyte differentiation / ADP binding / mitochondrial membrane / ATPase binding / calmodulin binding / mitochondrial inner membrane / lipid binding / cell surface / protein-containing complex / mitochondrion / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / 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 G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / 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 / 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, F0 complex, subunit A, bacterial/mitochondria / 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 / 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. / 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, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / 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 / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / 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 subunit beta / ATP synthase subunit b / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F1 subunit epsilon / ATP synthase subunit gamma / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase F(0) complex subunit g, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta / ATP synthase subunit b / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F1 subunit epsilon / ATP synthase subunit gamma / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase F(0) complex subunit g, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase F(0) complex subunit 8 / ATP synthase F(0) complex subunit a / ATP synthase lipid-binding protein / ATP synthase F(0) complex subunit f, mitochondrial / ATP synthase F(0) complex subunit e, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsMnatsakanyan, N. / Mello, J.F.R. / Palles, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG072484 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS137275 United States
CitationJournal: To Be Published
Title: Porcine ATP synthase with inhibitory protein IF1, DP-state
Authors: Mnatsakanyan, N. / Mello, J.F.R. / Palles, C.
History
DepositionJul 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: ATP synthase lipid-binding protein
2: ATP synthase lipid-binding protein
3: ATP synthase lipid-binding protein
4: ATP synthase lipid-binding protein
5: ATP synthase lipid-binding protein
6: ATP synthase lipid-binding protein
7: ATP synthase lipid-binding protein
8: ATP synthase lipid-binding protein
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 subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase subunit gamma
H: ATP synthase F(1) complex subunit delta, mitochondrial
I: ATP synthase F1 subunit epsilon
J: ATPase inhibitor, mitochondrial
K: ATP synthase subunit b
L: ATP synthase peripheral stalk subunit F6, mitochondrial
M: ATP synthase peripheral stalk subunit d, mitochondrial
N: ATP synthase subunit a
O: ATP synthase peripheral stalk subunit OSCP, mitochondrial
Q: ATP synthase F(0) complex subunit 8
R: ATP synthase F(0) complex subunit f, mitochondrial
S: ATP synthase F(0) complex subunit g, mitochondrial
T: ATP synthase F(0) complex subunit e, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)555,19038
Polymers552,18527
Non-polymers3,00511
Water00
1


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

-
Components

-
ATP synthase ... , 15 types, 26 molecules 12345678ABCDEFGHIKLMNOQRST

#1: Protein
ATP synthase lipid-binding protein / ATPase protein 9 / ATPase subunit c


Mass: 7426.718 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q4VT52
#2: Protein ATP synthase F(1) complex subunit alpha, mitochondrial / ATP synthase F1 subunit alpha / ATP synthase subunit alpha heart isoform / mitochondrial / ATP ...ATP synthase F1 subunit alpha / ATP synthase subunit alpha heart isoform / mitochondrial / ATP synthase subunit alpha liver isoform


Mass: 55100.027 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P80021
#3: Protein ATP synthase subunit beta


Mass: 50677.730 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A481D232, H+-transporting two-sector ATPase
#4: Protein ATP synthase subunit gamma


Mass: 30121.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1SNA2
#5: Protein ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F1 subunit delta / F-ATPase delta subunit


Mass: 13852.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VPE5
#6: Protein/peptide ATP synthase F1 subunit epsilon


Mass: 5242.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0X6E8
#8: Protein ATP synthase subunit b


Mass: 22079.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TA12
#9: Protein ATP synthase peripheral stalk subunit F6, mitochondrial / ATPase subunit F6 / ATP synthase peripheral stalk subunit F6


Mass: 8018.009 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P13618
#10: Protein ATP synthase peripheral stalk subunit d, mitochondrial / ATPase subunit d


Mass: 16904.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1TS79
#11: 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
#12: Protein ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase subunit O / Oligomycin sensitivity conferral protein / OSCP


Mass: 20561.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN81
#13: Protein/peptide ATP synthase F(0) complex subunit 8 / A6L / F-ATPase subunit 8


Mass: 2639.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q35914
#14: Protein ATP synthase F(0) complex subunit f, mitochondrial / ATP synthase membrane subunit f


Mass: 9940.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q95339
#15: Protein ATP synthase F(0) complex subunit g, mitochondrial / ATPase subunit g


Mass: 8852.386 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SAK7
#16: Protein ATP synthase F(0) complex subunit e, mitochondrial / ATPase subunit e / ATP synthase membrane subunit e


Mass: 6361.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q9MYT8

-
Protein , 1 types, 1 molecules J

#7: Protein ATPase inhibitor, mitochondrial / ATP synthase F1 subunit epsilon / Inhibitor of F(1)F(o)-ATPase / IF(1) / IF1


Mass: 5810.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q29307

-
Non-polymers , 3 types, 11 molecules

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


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#18: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#19: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mitochondrial ATP synthase / Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.8
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
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 magnification: 81000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 15.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105447 / Symmetry type: POINT
Atomic model buildingDetails: Genome annotation and AlphaFold / Source name: Other / Type: integrative model
RefinementHighest resolution: 2.69 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00239311
ELECTRON MICROSCOPYf_angle_d0.48853161
ELECTRON MICROSCOPYf_dihedral_angle_d5.8135463
ELECTRON MICROSCOPYf_chiral_restr0.046193
ELECTRON MICROSCOPYf_plane_restr0.0056791

+
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