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- PDB-8h9p: Human ATP synthase F1 domain, state 3b -

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Basic information

Entry
Database: PDB / ID: 8h9p
TitleHuman ATP synthase F1 domain, state 3b
Components(ATP synthase subunit ...) x 4
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / angiostatin binding / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / cellular response to interleukin-7 / proton-transporting ATP synthase complex ...negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / angiostatin binding / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / cellular response to interleukin-7 / proton-transporting ATP synthase complex / oxidative phosphorylation / response to muscle activity / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / negative regulation of endothelial cell proliferation / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / cellular response to nitric oxide / proton-transporting ATP synthase complex, catalytic core F(1) / positive regulation of blood vessel endothelial cell migration / MHC class I protein binding / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / cellular response to dexamethasone stimulus / generation of precursor metabolites and energy / ADP binding / regulation of intracellular pH / mitochondrial membrane / Transcriptional activation of mitochondrial biogenesis / lipid metabolic process / osteoblast differentiation / angiogenesis / response to ethanol / mitochondrial inner membrane / protease binding / mitochondrial matrix / membrane raft / cell surface / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane
Similarity search - Function
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 ...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, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / 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 subunit beta, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit O, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
O: ATP synthase subunit O, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,90418
Polymers372,4078
Non-polymers2,49710
Water0
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 /


Mass: 51821.965 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P06576
#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
#4: 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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Non-polymers , 3 types, 10 molecules

#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine 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
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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-#4 / 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 FIELDBright-field microscopy / 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: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23272 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00523835
ELECTRON MICROSCOPYf_angle_d0.66632235
ELECTRON MICROSCOPYf_dihedral_angle_d14.40914537
ELECTRON MICROSCOPYf_chiral_restr0.0953763
ELECTRON MICROSCOPYf_plane_restr0.0044165

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