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- EMDB-35982: Cryo-EM structure of Mycobacterium tuberculosis ATP synthase Fo i... -

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Basic information

Entry
Database: EMDB / ID: EMD-35982
TitleCryo-EM structure of Mycobacterium tuberculosis ATP synthase Fo in complex with bedaquiline(BDQ)
Map data
Sample
  • Complex: Mycobacterium tuberculosis ATP synthase Fo with bedaquiline(BDQ)
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit a
  • Ligand: Bedaquiline
KeywordsATP synthase / Mycobacterium tuberculosis / cryo-EM / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / lipid binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site ...ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / 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 c / ATP synthase subunit a
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsZhang Y / Lai Y / Liu F / Rao Z / 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
DepositionApr 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_35982.png

Downloads & links

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Map

FileDownload / File: emd_35982.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: 0.15
Minimum - Maximum-0.56068224 - 0.9729998
Average (Standard dev.)0.000089192894 (±0.020686053)
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: #2

Fileemd_35982_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35982_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 : Mycobacterium tuberculosis ATP synthase Fo with bedaquiline(BDQ)

EntireName: Mycobacterium tuberculosis ATP synthase Fo with bedaquiline(BDQ)
Components
  • Complex: Mycobacterium tuberculosis ATP synthase Fo with bedaquiline(BDQ)
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit a
  • Ligand: Bedaquiline

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Supramolecule #1: Mycobacterium tuberculosis ATP synthase Fo with bedaquiline(BDQ)

SupramoleculeName: Mycobacterium tuberculosis ATP synthase Fo with bedaquiline(BDQ)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 8.058423 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MDPTIAAGAL IGGGLIMAGG AIGAGIGDGV AGNALISGVA RQPEAQGRLF TPFFITVGLV EAAYFINLAF MALFVFATPV K

UniProtKB: ATP synthase subunit c

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Macromolecule #2: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 27.488436 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MTETILAAQI EVGEHHTATW LGMTVNTDTV LSTAIAGLIV IALAFYLRAK VTSTDVPGGV QLFFEAITIQ MRNQVESAIG MRIAPFVLP LAVTIFVFIL ISNWLAVLPV QYTDKHGHTT ELLKSAAADI NYVLALALFV FVCYHTAGIW RRGIVGHPIK L LKGHVTLL ...String:
MTETILAAQI EVGEHHTATW LGMTVNTDTV LSTAIAGLIV IALAFYLRAK VTSTDVPGGV QLFFEAITIQ MRNQVESAIG MRIAPFVLP LAVTIFVFIL ISNWLAVLPV QYTDKHGHTT ELLKSAAADI NYVLALALFV FVCYHTAGIW RRGIVGHPIK L LKGHVTLL APINLVEEVA KPISLSLRLF GNIFAGGILV ALIALFPPYI MWAPNAIWKA FDLFVGAIQA FIFALLTILY FS QAMELEE EHH

UniProtKB: ATP synthase subunit a

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Macromolecule #3: Bedaquiline

MacromoleculeName: Bedaquiline / type: ligand / ID: 3 / Number of copies: 7 / 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: OTHER / Details: AlphaFold
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96592

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