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- EMDB-9327: Bacillus PS3 ATP synthase membrane region -

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Basic information

Entry
Database: EMDB / ID: EMD-9327
TitleBacillus PS3 ATP synthase membrane region
Map dataATP synthase membrane region
Sample
  • Complex: Membrane-embedded region of Bacillus PS3 ATP synthase
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit c
KeywordsHYDROLASE
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGuo H / Rubinstein JL
Funding support Canada, Japan, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 81294 Canada
Japan Society for the Promotion of Science (JSPS)JP18H02409 Japan
CitationJournal: Elife / Year: 2019
Title: Structure of a bacterial ATP synthase.
Authors: Hui Guo / Toshiharu Suzuki / John L Rubinstein /
Abstract: ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest ...ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest form of the enzyme and because of the relative ease of genetic manipulation of these complexes. We expressed the PS3 ATP synthase in , purified it, and imaged it by cryo-EM, allowing us to build atomic models of the complex in three rotational states. The position of subunit shows how it is able to inhibit ATP hydrolysis while allowing ATP synthesis. The architecture of the membrane region shows how the simple bacterial ATP synthase is able to perform the same core functions as the equivalent, but more complicated, mitochondrial complex. The structures reveal the path of transmembrane proton translocation and provide a model for understanding decades of biochemical analysis interrogating the roles of specific residues in the enzyme.
History
DepositionNov 12, 2018-
Header (metadata) releaseNov 28, 2018-
Map releaseFeb 20, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.042
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n2d
  • Surface level: 0.042
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9327.png

Downloads & links

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Map

FileDownload / File: emd_9327.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationATP synthase membrane region
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.042 / Movie #1: 0.042
Minimum - Maximum-0.1912876 - 0.2656591
Average (Standard dev.)-0.000497399 (±0.005217133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z339.200339.200339.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1910.266-0.000

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Supplemental data

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Mask #1

Fileemd_9327_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ATP synthase membrane region

Fileemd_9327_half_map_1.map
AnnotationATP synthase membrane region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ATP synthase membrane region

Fileemd_9327_half_map_2.map
AnnotationATP synthase membrane region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Membrane-embedded region of Bacillus PS3 ATP synthase

EntireName: Membrane-embedded region of Bacillus PS3 ATP synthase
Components
  • Complex: Membrane-embedded region of Bacillus PS3 ATP synthase
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit c

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Supramolecule #1: Membrane-embedded region of Bacillus PS3 ATP synthase

SupramoleculeName: Membrane-embedded region of Bacillus PS3 ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 110 kDa/nm

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Macromolecule #1: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria) / Strain: PS3
Molecular weightTheoretical: 19.249148 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EAAHGISGGT IIYQLLMFII LLALLRKFAW QPLMNIMKQR EEHIANEIDQ AEKRRQEAEK LLEEQRELMK QSRQEAQALI ENARKLAEE QKEQIVASAR AEAERVKETA KKEIEREKEQ AMAALREQVA SLSVLIASKV IEKELTEQDQ RKLIEAYIKD V QEVGGAR

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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: Bacillus sp. PS3 (bacteria) / Strain: PS3
Molecular weightTheoretical: 26.44932 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEHKAPLVEF LGLTFNLSDM LMITITCLIV FIIAVAATRS LQLRPTGMQN FMEWVFDFVR GIINSTMDWQ TGGRFLTLGV TLIMYVFVA NMLGLPFSVH VNGELWWKSP TADATVTLTL AVMVVALTHY YGVKMKGASD YLRDYTRPVA WLFPLKIIEE F ANTLTLGL ...String:
MEHKAPLVEF LGLTFNLSDM LMITITCLIV FIIAVAATRS LQLRPTGMQN FMEWVFDFVR GIINSTMDWQ TGGRFLTLGV TLIMYVFVA NMLGLPFSVH VNGELWWKSP TADATVTLTL AVMVVALTHY YGVKMKGASD YLRDYTRPVA WLFPLKIIEE F ANTLTLGL RLFGNIYAGE ILLGLLASLG THYGVLGAVG AAIPMMVWQA FSIFVGTIQA FIFTMLTMVY MAHKVSHDH

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Macromolecule #3: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 3 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria) / Strain: PS3
Molecular weightTheoretical: 7.33778 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSLGVLAAAI AVGLGALGAG IGNGLIVSRT IEGIARQPEL RPVLQTTMFI GVALVEALPI IGVVFSFIYL GR

UniProtKB: ATP synthase subunit c

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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

Concentration10 mg/mL
BufferpH: 7.4
GridMaterial: COPPER/RHODIUM / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 132075 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 60.0 sec. / Average electron dose: 0.71 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1238140
Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 895574
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 91.12
Output model

PDB-6n2d:
Bacillus PS3 ATP synthase membrane region

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