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- PDB-8ki3: Structure of the human ATP synthase bound to bedaquiline (composite) -

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Basic information

Entry
Database: PDB / ID: 8ki3
TitleStructure of the human ATP synthase bound to bedaquiline (composite)
Components
  • (ATP synthase F(0) complex subunit ...) x 2
  • (ATP synthase subunit ...) x 12
  • ATP synthase protein 8
  • ATP synthase-coupling factor 6, mitochondrial
  • ATPase inhibitor, mitochondrial
KeywordsMEMBRANE PROTEIN / ATP synthase / Human / cryo-EM
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 / regulation of protein targeting to mitochondrion / Formation of ATP by chemiosmotic coupling / Cristae formation / positive regulation of proteolysis involved in protein catabolic process / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / ATP biosynthetic process / angiostatin binding ...mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / negative regulation of cell adhesion involved in substrate-bound cell migration / regulation of protein targeting to mitochondrion / Formation of ATP by chemiosmotic coupling / Cristae formation / positive regulation of proteolysis involved in protein catabolic process / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / ATP biosynthetic process / angiostatin binding / ATPase inhibitor activity / mitochondrial depolarization / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / Mitochondrial protein import / negative regulation of ATP-dependent activity / mitochondrial proton-transporting ATP synthase complex assembly / negative regulation of hydrolase activity / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / enzyme inhibitor activity / proton-transporting ATP synthase complex / cellular response to interleukin-7 / oxidative phosphorylation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / response to muscle activity / response to copper ion / heme biosynthetic process / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / negative regulation of endothelial cell proliferation / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / cellular response to nitric oxide / response to hyperoxia / proton-transporting ATP synthase complex, catalytic core F(1) / positive regulation of blood vessel endothelial cell migration / MHC class I protein binding / aerobic respiration / H+-transporting two-sector ATPase / substantia nigra development / proton-transporting ATPase activity, rotational mechanism / reactive oxygen species metabolic process / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / cellular response to dexamethasone stimulus / erythrocyte differentiation / generation of precursor metabolites and energy / ADP binding / regulation of intracellular pH / mitochondrial membrane / Transcriptional activation of mitochondrial biogenesis / lipid metabolic process / osteoblast differentiation / ATPase binding / angiogenesis / response to ethanol / nuclear membrane / mitochondrial inner membrane / protease binding / calmodulin binding / hydrolase activity / mitochondrial matrix / membrane raft / lipid binding / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
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 ATPase inhibitor / Mitochondrial F1-F0 ATP synthase subunit F, predicted ...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 ATPase inhibitor / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial ATPase inhibitor, IATP / Mitochondrial F1F0-ATP synthase, subunit f / 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 delta/epsilon subunit, C-terminal domain superfamily / 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, 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, 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 / 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 / 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 / Bedaquiline / ATP synthase subunit d, mitochondrial / ATP synthase subunit g, mitochondrial / ATP synthase subunit a / ATP synthase protein 8 / ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase subunit beta, mitochondrial / ATP synthase-coupling factor 6, mitochondrial ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Bedaquiline / ATP synthase subunit d, mitochondrial / ATP synthase subunit g, mitochondrial / ATP synthase subunit a / ATP synthase protein 8 / ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase subunit beta, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit e, mitochondrial / ATPase inhibitor, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsLai, Y. / Zhang, Y. / Gong, H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)32100976 China
National Natural Science Foundation of China (NSFC)82222042 China
CitationJournal: To Be Published
Title: Structure of Mycobacterium tuberculosis ATP synthase
Authors: Zhang, Y. / Lai, Y. / Liu, F. / Rao, Z. / Gong, H.
History
DepositionAug 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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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
D: ATP synthase subunit beta, mitochondrial
E: ATP synthase subunit beta, mitochondrial
F: ATP synthase subunit beta, mitochondrial
G: ATP synthase subunit gamma, mitochondrial
J: ATPase inhibitor, mitochondrial
O: ATP synthase subunit O, mitochondrial
1: ATP synthase F(0) complex subunit C1, mitochondrial
2: ATP synthase F(0) complex subunit C1, mitochondrial
3: ATP synthase F(0) complex subunit C1, mitochondrial
4: ATP synthase F(0) complex subunit C1, mitochondrial
5: ATP synthase F(0) complex subunit C1, mitochondrial
6: ATP synthase F(0) complex subunit C1, mitochondrial
7: ATP synthase F(0) complex subunit C1, mitochondrial
8: ATP synthase F(0) complex subunit C1, mitochondrial
H: ATP synthase subunit delta, mitochondrial
I: ATP synthase subunit epsilon, mitochondrial
K: ATP synthase F(0) complex subunit B1, mitochondrial
M: ATP synthase subunit d, mitochondrial
N: ATP synthase subunit a
P: ATP synthase subunit ATP5MJ, mitochondrial
Q: ATP synthase protein 8
R: ATP synthase subunit f, mitochondrial
S: ATP synthase subunit g, mitochondrial
T: ATP synthase subunit e, mitochondrial
L: ATP synthase-coupling factor 6, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)591,92539
Polymers588,87228
Non-polymers3,05311
Water0
1


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

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Components

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ATP synthase subunit ... , 12 types, 16 molecules ABCDEFGOHIMNPRST

#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
#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
#7: Protein ATP synthase subunit delta, mitochondrial / / ATP synthase F1 subunit delta / F-ATPase delta subunit


Mass: 15029.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30049
#8: Protein ATP synthase subunit epsilon, mitochondrial / / ATPase subunit epsilon / ATP synthase F1 subunit epsilon


Mass: 5790.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56381
#10: Protein ATP synthase subunit d, mitochondrial / / ATPase subunit d / ATP synthase peripheral stalk subunit d


Mass: 18383.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75947
#11: Protein ATP synthase subunit a / / F-ATPase protein 6


Mass: 24833.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00846
#12: Protein ATP synthase subunit ATP5MJ, mitochondrial / / 6.8 kDa mitochondrial proteolipid protein / MLQ / ATP synthase membrane subunit 6.8PL


Mass: 6673.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56378
#14: Protein ATP synthase subunit f, mitochondrial / / ATP synthase membrane subunit f


Mass: 10804.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56134
#15: Protein ATP synthase subunit g, mitochondrial / / ATPase subunit g / ATP synthase membrane subunit g


Mass: 11309.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75964
#16: Protein ATP synthase subunit e, mitochondrial / / ATPase subunit e / ATP synthase membrane subunit e


Mass: 7947.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56385

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Protein , 3 types, 3 molecules JQL

#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
#13: Protein ATP synthase protein 8 / / A6L / F-ATPase subunit 8


Mass: 8000.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P03928
#17: Protein ATP synthase-coupling factor 6, mitochondrial / ATPase subunit F6 / ATP synthase peripheral stalk subunit F6


Mass: 12606.499 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18859

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ATP synthase F(0) complex subunit ... , 2 types, 9 molecules 12345678K

#6: Protein
ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 1 / ATP synthase ...ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 1 / ATP synthase proteolipid P1 / ATP synthase proton-transporting mitochondrial F(0) complex subunit C1 / ATPase protein 9 / ATPase subunit c


Mass: 7610.954 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05496
#9: Protein ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase peripheral stalk-membrane subunit b / ATP synthase proton-transporting mitochondrial ...ATP synthase peripheral stalk-membrane subunit b / ATP synthase proton-transporting mitochondrial F(0) complex subunit B1 / ATP synthase subunit b / ATPase subunit b


Mass: 24658.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P24539

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Non-polymers , 4 types, 11 molecules

#18: 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
#19: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#20: 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
#21: Chemical ChemComp-BQ1 / Bedaquiline / Bedaquiline


Mass: 555.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H31BrN2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*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-#17 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84037 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00539305
ELECTRON MICROSCOPYf_angle_d0.54153181
ELECTRON MICROSCOPYf_dihedral_angle_d6.92623893
ELECTRON MICROSCOPYf_chiral_restr0.0436194
ELECTRON MICROSCOPYf_plane_restr0.0036781

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