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- EMDB-37243: Structure of the human ATP synthase bound to bedaquiline (membran... -

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Basic information

Entry
Database: EMDB / ID: EMD-37243
TitleStructure of the human ATP synthase bound to bedaquiline (membrane domain)
Map data
Sample
  • Complex: human ATP synthase
    • Protein or peptide: x 12 types
  • Ligand: x 1 types
KeywordsATP synthase / Human / cryo-EM / Membrane protein
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase, stator stalk / oxidative phosphorylation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / response to copper ion / mitochondrial proton-transporting ATP synthase complex ...Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase, stator stalk / oxidative phosphorylation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / response to copper ion / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / response to hyperoxia / aerobic respiration / substantia nigra development / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / nuclear membrane / mitochondrial inner membrane / hydrolase activity / mitochondrial matrix / lipid binding / mitochondrion / RNA binding / membrane / nucleus
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 F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals ...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 F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f / : / 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 / 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. / 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, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
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 F(0) complex subunit B1, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial ...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 F(0) complex subunit B1, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit e, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsLai Y / Zhang Y / Gong H
Funding support China, 3 items
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 21, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37243.png

Downloads & links

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Map

FileDownload / File: emd_37243.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.73 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.47485363 - 0.75829154
Average (Standard dev.)0.00009921204 (±0.016136695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37243_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37243_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human ATP synthase

EntireName: human ATP synthase
Components
  • Complex: human ATP synthase
    • Protein or peptide: ATP synthase F(0) complex subunit C1, mitochondrial
    • Protein or peptide: ATP synthase subunit gamma, mitochondrial
    • Protein or peptide: ATP synthase subunit delta, mitochondrial
    • Protein or peptide: ATP synthase subunit epsilon, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit B1, mitochondrial
    • Protein or peptide: ATP synthase subunit d, mitochondrial
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit ATP5MJ, mitochondrial
    • Protein or peptide: ATP synthase protein 8
    • Protein or peptide: ATP synthase subunit f, mitochondrial
    • Protein or peptide: ATP synthase subunit g, mitochondrial
    • Protein or peptide: ATP synthase subunit e, mitochondrial
  • Ligand: Bedaquiline

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Supramolecule #1: human ATP synthase

SupramoleculeName: human ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ATP synthase F(0) complex subunit C1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit C1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.610954 KDa
SequenceString:
DIDTAAKFIG AGAATVGVAG SGAGIGTVFG SLIIGYARNP SLKQQLFSYA ILGFALSEAM GLFCLMVAFL ILFAM

UniProtKB: ATP synthase F(0) complex subunit C1, mitochondrial

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Macromolecule #2: ATP synthase subunit gamma, mitochondrial

MacromoleculeName: ATP synthase subunit gamma, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.207752 KDa
SequenceString: ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARIYGLGSLA LYEKADIKGP EDKKKHLLIG VSSDRGLCGA IHSSIAKQM KSEVATLTAA GKEVMLVGIG DKIRGILYRT HSDQFLVAFK EVGRKPPTFG DASVIALELL NSGYEFDEGS I IFNKFRSV ...String:
ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARIYGLGSLA LYEKADIKGP EDKKKHLLIG VSSDRGLCGA IHSSIAKQM KSEVATLTAA GKEVMLVGIG DKIRGILYRT HSDQFLVAFK EVGRKPPTFG DASVIALELL NSGYEFDEGS I IFNKFRSV ISYKTEEKPI FSLNTVASAD SMSIYDDIDA DVLQNYQEYN LANIIYYSLK ESTTSEQSAR MTAMDNASKN AS EMIDKLT LTFNRTRQAV ITKELIEIIS GAAALD

UniProtKB: ATP synthase subunit gamma, mitochondrial

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Macromolecule #3: ATP synthase subunit delta, mitochondrial

MacromoleculeName: ATP synthase subunit delta, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.029817 KDa
SequenceString:
AEAAAAPAAA SGPNQMSFTF ASPTQVFFNG ANVRQVDVPT LTGAFGILAA HVPTLQVLRP GLVVVHAEDG TTSKYFVSSG SIAVNADSS VQLLAEEAVT LDMLDLGAAK ANLEKAQAEL VGTADEATRA EIQIRIEANE ALVKALE

UniProtKB: ATP synthase subunit delta, mitochondrial

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Macromolecule #4: ATP synthase subunit epsilon, mitochondrial

MacromoleculeName: ATP synthase subunit epsilon, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.790779 KDa
SequenceString:
MVAYWRQAGL SYIRYSQICA KAVRDALKTE FKANAEKTSG SNVKIVKVKK E

UniProtKB: ATP synthase subunit epsilon, mitochondrial

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Macromolecule #5: ATP synthase F(0) complex subunit B1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit B1, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.658586 KDa
SequenceString: PVPPLPEYGG KVRYGLIPEE FFQFLYPKTG VTGPYVLGTG LILYALSKEI YVISAETFTA LSVLGVMVYG IKKYGPFVAD FADKLNEQK LAQLEEAKQA SIQHIQNAID TEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLYRVYK EVKNRLDYHI S VQNMMRRK ...String:
PVPPLPEYGG KVRYGLIPEE FFQFLYPKTG VTGPYVLGTG LILYALSKEI YVISAETFTA LSVLGVMVYG IKKYGPFVAD FADKLNEQK LAQLEEAKQA SIQHIQNAID TEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLYRVYK EVKNRLDYHI S VQNMMRRK EQEHMINWVE KHVVQSISTQ QEKETIAKCI ADLKLLAKKA QAQPVM

UniProtKB: ATP synthase F(0) complex subunit B1, mitochondrial

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Macromolecule #6: ATP synthase subunit d, mitochondrial

MacromoleculeName: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.383982 KDa
SequenceString:
AGRKLALKTI DWVAFAEIIP QNQKAIASSL KSWNETLTSR LAALPENPPA IDWAYYKANV AKAGLVDDFE KKFNALKVPV PEDKYTAQV DAEEKEDVKS CAEWVSLSKA RIVEYEKEME KMKNLIPFDQ MTIEDLNEAF PETKLDKKKY PYWPHQPIEN L

UniProtKB: ATP synthase subunit d, mitochondrial

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Macromolecule #7: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.833102 KDa
SequenceString: MNENLFASFI APTILGLPAA VLIILFPPLL IPTSKYLINN RLITTQQWLI KLTSKQMMTM HNTKGRTWSL MLVSLIIFIA TTNLLGLLP HSFTPTTQLS MNLAMAIPLW AGTVIMGFRS KIKNALAHFL PQGTPTPLIP MLVIIETISL LIQPMALAVR L TANITAGH ...String:
MNENLFASFI APTILGLPAA VLIILFPPLL IPTSKYLINN RLITTQQWLI KLTSKQMMTM HNTKGRTWSL MLVSLIIFIA TTNLLGLLP HSFTPTTQLS MNLAMAIPLW AGTVIMGFRS KIKNALAHFL PQGTPTPLIP MLVIIETISL LIQPMALAVR L TANITAGH LLMHLIGSAT LAMSTINLPS TLIIFTILIL LTILEIAVAL IQAYVFTLLV SLYLHDNT

UniProtKB: ATP synthase subunit a

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Macromolecule #8: ATP synthase subunit ATP5MJ, mitochondrial

MacromoleculeName: ATP synthase subunit ATP5MJ, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.673053 KDa
SequenceString:
MLQSIIKNIW IPMKPYYTKV YQEIWIGMGL MGFIVYKIRA ADKRSKALKA SAPAPGHH

UniProtKB: ATP synthase subunit ATP5MJ, mitochondrial

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Macromolecule #9: ATP synthase protein 8

MacromoleculeName: ATP synthase protein 8 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.000634 KDa
SequenceString:
MPQLNTTVWP TMITPMLLTL FLITQLKMLN TNYHLPPSPK PMKMKNYNKP WEPKWTKICS LHSLPPQS

UniProtKB: ATP synthase protein 8

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Macromolecule #10: ATP synthase subunit f, mitochondrial

MacromoleculeName: ATP synthase subunit f, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.804686 KDa
SequenceString:
ASVGECPAPV PVKDKKLLEV KLGELPSWIL MRDFSPSGIF GAFQRGYYRY YNKYINVKKG SISGITMVLA CYVLFSYSFS YKHLKHERL RKYH

UniProtKB: ATP synthase subunit f, mitochondrial

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Macromolecule #11: ATP synthase subunit g, mitochondrial

MacromoleculeName: ATP synthase subunit g, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.309226 KDa
SequenceString:
AQFVRNLVEK TPALVNAAVT YSKPRLATFW YYAKVELVPP TPAEIPRAIQ SLKKIVNSAQ TGSFKQLTVK EAVLNGLVAT EVLMWFYVG EIIGKRGIIG YDV

UniProtKB: ATP synthase subunit g, mitochondrial

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Macromolecule #12: ATP synthase subunit e, mitochondrial

MacromoleculeName: ATP synthase subunit e, mitochondrial / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.947215 KDa
SequenceString:
MVPPVQVSPL IKLGRYSALF LGVAYGATRY NYLKPRAEEE RRIAAEEKKK QDELKRIARE LAEDDSILK

UniProtKB: ATP synthase subunit e, mitochondrial

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Macromolecule #13: Bedaquiline

MacromoleculeName: Bedaquiline / type: ligand / ID: 13 / Number of copies: 1 / Formula: BQ1
Molecular weightTheoretical: 555.505 Da
Chemical component information

ChemComp-BQ1:
Bedaquiline / medication, antibiotic*YM / Bedaquiline

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8h9f

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84037

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