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- PDB-8h9l: Human ATP synthase F1 domain, state 3a -

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Basic information

Entry
Database: PDB / ID: 8h9l
TitleHuman ATP synthase F1 domain, state 3a
Components
  • (ATP synthase subunit ...) x 4
  • ATPase inhibitor, mitochondrial
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / regulation of protein targeting to mitochondrion / Cristae formation / positive regulation of proteolysis involved in protein catabolic process / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity ...mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / regulation of protein targeting to mitochondrion / Cristae formation / positive regulation of proteolysis involved in protein catabolic process / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / ATP biosynthetic process / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / mitochondrial depolarization / ATPase inhibitor activity / positive regulation of type 2 mitophagy / Mitochondrial protein import / cellular response to interleukin-7 / oxidative phosphorylation / heme biosynthetic process / response to muscle activity / proton-transporting ATP synthase complex / negative regulation of endothelial cell proliferation / MHC class I protein binding / proton motive force-driven ATP synthesis / enzyme inhibitor activity / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / positive regulation of blood vessel endothelial cell migration / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / Mitochondrial protein degradation / proton-transporting ATP synthase activity, rotational mechanism / cellular response to nitric oxide / proton transmembrane transport / cellular response to dexamethasone stimulus / reactive oxygen species metabolic process / erythrocyte differentiation / generation of precursor metabolites and energy / regulation of intracellular pH / Transcriptional activation of mitochondrial biogenesis / mitochondrial membrane / ADP binding / lipid metabolic process / osteoblast differentiation / ATPase binding / protease binding / angiogenesis / response to ethanol / mitochondrial inner membrane / calmodulin binding / mitochondrial matrix / membrane raft / enzyme binding / cell surface / protein-containing complex / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / 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, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit ...Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / 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, 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, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / 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 / 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 / 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 subunit beta, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATPase inhibitor, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsLai, Y. / Zhang, Y. / Liu, F. / Gao, Y. / Gong, H. / Rao, Z.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)813300237 China
National Natural Science Foundation of China (NSFC)32100976 China
National Natural Science Foundation of China (NSFC)82222042 China
CitationJournal: Mol Cell / Year: 2023
Title: Structure of the human ATP synthase.
Authors: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / ...Authors: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / Zihe Rao / Hongri Gong /
Abstract: Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main ...Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase using cryoelectron microscopy. These structures reveal that the release of ADP occurs when the β subunit of FF-ATP synthase is in the open conformation, showing how ADP binding is coordinated during synthesis. The accommodation of the symmetry mismatch between F and F motors is resolved by the torsional flexing of the entire complex, especially the γ subunit, and the rotational substep of the c subunit. Water molecules are identified in the inlet and outlet half-channels, suggesting that the proton transfer in these two half-channels proceed via a Grotthus mechanism. Clinically relevant mutations are mapped to the structure, showing that they are mainly located at the subunit-subunit interfaces, thus causing instability of the complex.
History
DepositionOct 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 5, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase subunit alpha, mitochondrial
B: ATP synthase subunit alpha, mitochondrial
C: ATP synthase subunit alpha, mitochondrial
E: ATP synthase subunit beta, mitochondrial
F: ATP synthase subunit beta, mitochondrial
D: ATP synthase subunit beta, mitochondrial
G: ATP synthase subunit gamma, mitochondrial
J: ATPase inhibitor, mitochondrial
O: ATP synthase subunit O, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,44519
Polymers381,9479
Non-polymers2,49710
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase subunit ... , 4 types, 8 molecules ABCEFDGO

#1: Protein ATP synthase subunit alpha, mitochondrial / ATP synthase F1 subunit alpha


Mass: 55276.160 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25705
#2: Protein ATP synthase subunit beta, mitochondrial / ATP synthase F1 subunit beta


Mass: 51821.965 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P06576, H+-transporting two-sector ATPase
#3: Protein ATP synthase subunit gamma, mitochondrial / ATP synthase F1 subunit gamma / F-ATPase gamma subunit


Mass: 30207.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36542
#5: Protein ATP synthase subunit O, mitochondrial / ATP synthase peripheral stalk subunit OSCP / Oligomycin sensitivity conferral protein / OSCP


Mass: 20904.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48047

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Protein , 1 types, 1 molecules J

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


Mass: 9540.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UII2

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Non-polymers , 3 types, 10 molecules

#6: 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
#7: Chemical
ChemComp-MG / MAGNESIUM ION


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


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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Human ATP synthase / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightValue: 0.6 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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 FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45418 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0124303
ELECTRON MICROSCOPYf_angle_d0.76632873
ELECTRON MICROSCOPYf_dihedral_angle_d16.33614807
ELECTRON MICROSCOPYf_chiral_restr0.0533827
ELECTRON MICROSCOPYf_plane_restr0.0054249

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