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- PDB-8jr1: Cryo-EM structure of Mycobacterium tuberculosis ATP synthase Fo i... -

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Basic information

Entry
Database: PDB / ID: 8jr1
TitleCryo-EM structure of Mycobacterium tuberculosis ATP synthase Fo in complex with TBAJ-587
Components
  • ATP synthase subunit a
  • ATP synthase subunit c
KeywordsMEMBRANE PROTEIN / ATP synthase / Mycobacterium tuberculosis / cryo-EM
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsZhang, Y. / Lai, Y. / Liu, F. / Rao, Z. / 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
DepositionJun 15, 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
1: ATP synthase subunit c
2: ATP synthase subunit c
3: ATP synthase subunit c
4: ATP synthase subunit c
5: ATP synthase subunit c
6: ATP synthase subunit c
7: ATP synthase subunit c
8: ATP synthase subunit c
9: ATP synthase subunit c
a: ATP synthase subunit a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,31617
Polymers100,01410
Non-polymers4,3027
Water0
1


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

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Components

#1: Protein
ATP synthase subunit c /


Mass: 8058.423 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: atpE / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A045H4W8
#2: Protein ATP synthase subunit a / / ATP synthase F0 sector subunit a / F-ATPase subunit 6


Mass: 27488.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: atpB, ERS007657_00358, ERS007661_00092, ERS007663_00105, ERS007665_00910, ERS007670_00031, ERS007679_03316, ERS007681_03471, ERS007688_02939, ERS007703_00159, ERS007720_03212, ERS007722_00190, ...Gene: atpB, ERS007657_00358, ERS007661_00092, ERS007663_00105, ERS007665_00910, ERS007670_00031, ERS007679_03316, ERS007681_03471, ERS007688_02939, ERS007703_00159, ERS007720_03212, ERS007722_00190, ERS007739_02359, ERS007741_03568, ERS024276_02583, ERS027646_02991, ERS027659_00329, ERS027661_00021, SAMEA2683035_01568
Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A045J1C5
#3: Chemical
ChemComp-UTI / (1~{S},2~{S})-1-(6-bromanyl-2-methoxy-quinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2-fluoranyl-3-methoxy-phenyl)butan-2-ol / TBAJ-587


Mass: 614.503 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C30H33BrFN3O5
Has ligand of interestN

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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: Mycobacterium tuberculosis ATP synthase / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis (bacteria)
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: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81528 / Symmetry type: POINT

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