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- EMDB-9335: Bacillus PS3 ATP synthase class 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-9335
TitleBacillus PS3 ATP synthase class 3
Map dataATP synthase class 3
Sample
  • Complex: Bacillus PS3 ATP synthase class 3
    • Protein or peptide: x 9 types
  • Ligand: x 4 types
KeywordsBacterial ATP synthase / HYDROLASE
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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 delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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, alpha subunit nucleotide-binding domain / 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 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 / C-terminal domain of V and A type ATP synthase / 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
ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase subunit beta / ATP synthase epsilon chain / ATP synthase subunit c
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria) / Bacillus sp. (strain PS3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 14, 2018-
Header (metadata) releaseNov 28, 2018-
Map releaseFeb 20, 2019-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n30
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9335.png

Downloads & links

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Map

FileDownload / File: emd_9335.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationATP synthase class 3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-4.4751334 - 7.6815343
Average (Standard dev.)0.009195564 (±0.17053707)
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-4.4757.6820.009

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Supplemental data

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Mask #1

Fileemd_9335_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ATP synthase class 3

Fileemd_9335_half_map_1.map
AnnotationATP synthase class 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ATP synthase class 3

Fileemd_9335_half_map_2.map
AnnotationATP synthase class 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacillus PS3 ATP synthase class 3

EntireName: Bacillus PS3 ATP synthase class 3
Components
  • Complex: Bacillus PS3 ATP synthase class 3
    • Protein or peptide: Bacillus PS3 ATP synthase subunit b
    • Protein or peptide: Bacillus PS3 ATP synthase subunit b
    • Protein or peptide: Bacillus PS3 ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: Bacillus PS3 ATP synthase subunit delta
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Bacillus PS3 ATP synthase class 3

SupramoleculeName: Bacillus PS3 ATP synthase class 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 520 kDa/nm

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Macromolecule #1: Bacillus PS3 ATP synthase subunit b

MacromoleculeName: Bacillus PS3 ATP synthase subunit b / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 18.735764 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EAAHGISGGT IIYQLLMFII LLALLRKFAW QPLMNIMKQR EEHIANEIDQ AEKRRQEAEK LLEEQRELMK QSRQEAQALI ENARKLAEE QKEQIVASAR AEAERVKETA KKEIEREKEQ AMAALREQVA SLSVLIASKV I(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) ...String:
EAAHGISGGT IIYQLLMFII LLALLRKFAW QPLMNIMKQR EEHIANEIDQ AEKRRQEAEK LLEEQRELMK QSRQEAQALI ENARKLAEE QKEQIVASAR AEAERVKETA KKEIEREKEQ AMAALREQVA SLSVLIASKV I(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)K DVQEVGGARM

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Macromolecule #2: Bacillus PS3 ATP synthase subunit b

MacromoleculeName: Bacillus PS3 ATP synthase subunit b / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 19.380344 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 QEVGGARM

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Macromolecule #3: Bacillus PS3 ATP synthase subunit a

MacromoleculeName: Bacillus PS3 ATP synthase subunit a / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
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 #4: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. (strain 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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Macromolecule #5: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bacillus sp. (strain PS3) (bacteria) / Strain: PS3
Molecular weightTheoretical: 54.848598 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSIRAEEISA LIKQQIENYE SQIQVSDVGT VIQVGDGIAR AHGLDNVMSG ELVEFANGVM GMALNLEENN VGIVILGPYT GIKEGDEVR RTGRIMEVPV GEALIGRVVN PLGQPVDGLG PVETTETRPI ESPAPGVMDR RSVHEPLQTG IKAIDALVPI G RGQRELII ...String:
MSIRAEEISA LIKQQIENYE SQIQVSDVGT VIQVGDGIAR AHGLDNVMSG ELVEFANGVM GMALNLEENN VGIVILGPYT GIKEGDEVR RTGRIMEVPV GEALIGRVVN PLGQPVDGLG PVETTETRPI ESPAPGVMDR RSVHEPLQTG IKAIDALVPI G RGQRELII GDRQTGKTSV AIDTIINQKD QNMISIYVAI GQKESTVRTV VETLRKHGAL DYTIVVTASA SQPAPLLFLA PY AGVAMGE YFMYKGKHVL VVYDDLSKQA AAYRELSLLL RRPPGREAYP GDIFYLHSRL LERAAKLSDA KGGGSLTALP FVE TQAGDI SAYIPTNVIS ITDGQIFLQS DLFFSGVRPA INAGLSVSRV GGAAQIKAMK KVAGTLRLDL AAYRELEAFA QFGS DLDKA TQAKLARGAR TVEVLKQDLH QPIPVEKQVL IIYALTRGFL DDIPVEDVRR FEKEFYLFLD QNGQHLLEHI RTTKD LPNE DDLNKAIEAF KKTFVVSQ

UniProtKB: ATP synthase subunit alpha

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Macromolecule #6: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bacillus sp. (strain PS3) (bacteria) / Strain: PS3
Molecular weightTheoretical: 51.911969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTRGRVIQVM GPVVDVKFEN GHLPAIYNAL KIQHKARNEN EVDIDLTLEV ALHLGDDTVR TIAMASTDGL IRGMEVIDTG APISVPVGE VTLGRVFNVL GEPIDLEGDI PADARRDPIH RPAPKFEELA TEVEILETGI KVVDLLAPYI KGGKIGLFGG A GVGKTVLI ...String:
MTRGRVIQVM GPVVDVKFEN GHLPAIYNAL KIQHKARNEN EVDIDLTLEV ALHLGDDTVR TIAMASTDGL IRGMEVIDTG APISVPVGE VTLGRVFNVL GEPIDLEGDI PADARRDPIH RPAPKFEELA TEVEILETGI KVVDLLAPYI KGGKIGLFGG A GVGKTVLI QELIHNIAQE HGGISVFAGV GERTREGNDL YHEMKDSGVI SKTAMVFGQM NEPPGARMRV ALTGLTMAEY FR DEQGQDV LLFIDNIFRF TQAGSEVSAL LGRMPSAVGY QPTLATEMGQ LQERITSTAK GSITSIQAIY VPADDYTDPA PAT TFSHLD ATTNLERKLA EMGIYPAVDP LASTSRALAP EIVGEEHYQV ARKVQQTLQR YKELQDIIAI LGMDELSDED KLVV HRARR IQFFLSQNFH VAEQFTGQPG SYVPVKETVR GFKEILEGKY DHLPEDAFRL VGRIEEVVEK AKAMGVEV

UniProtKB: ATP synthase subunit beta

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Macromolecule #7: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. (strain PS3) (bacteria) / Strain: PS3
Molecular weightTheoretical: 31.859523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAS PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL ...String:
MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAS PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL YMYYNHYVSA IQQEVTERKL LPLTDLAENK QRTVYEFEPS QEEILDVLLP QYAESLIYGA LLDAKASEHA AR MTAMKNA TDNANELIRT LTLSYNRARQ AAITQEITEI VAGANALQ

UniProtKB: ATP synthase gamma chain

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Macromolecule #8: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. (strain PS3) (bacteria) / Strain: PS3
Molecular weightTheoretical: 14.585905 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKTIHVSVVT PDGPVYEDDV EMVSVKAKSG ELGILPGHIP LVAPLEISAA RLKKGGKTQY IAVSGGFLEV RPDKVTILAQ AAERAEDID VLRAKAAKER AERRLQSQQD DIDFKRAELA LKRAMNRLSV AEMK

UniProtKB: ATP synthase epsilon chain

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Macromolecule #9: Bacillus PS3 ATP synthase subunit delta

MacromoleculeName: Bacillus PS3 ATP synthase subunit delta / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 19.790689 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNQEVIAKRY ASALFQIALE QGQLDRIEED VRAVRQALAE NGEFLSLLSY PKLSLDQKKA LIAEAFAGVS TPVQNTLLLL LERHRFGLV PELAEQFLAL VDDARGIAKA VAYSARPLTD EELRALSDVF AQKVGKQTLE IENIIDPELI GGVRLRIGNR I YDGSVSGQ LERIRRQLIG

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Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #12: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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
GridDetails: unspecified
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
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 132075 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1238140
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.0) / Number images used: 175694
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6n30:
Bacillus PS3 ATP synthase class 3

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