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- EMDB-41811: Axle-less Bacillus sp. PS3 F1 ATPase mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-41811
TitleAxle-less Bacillus sp. PS3 F1 ATPase mutant
Map dataSharpened axle-less Bacillus PS3 ATPase map
Sample
  • Complex: Bacillus PS3 F1 ATPase complex, with truncated gamma subunit
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION
KeywordsATPase / ATP synthase / HYDROLASE
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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, 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, 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, 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, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / 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
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsFurlong EJ / Zeng YC / Brown SHJ / Sobti M / Stewart AG
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2016308 Australia
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2024
Title: The molecular structure of an axle-less F-ATPase.
Authors: Emily J Furlong / Ian-Blaine P Reininger-Chatzigiannakis / Yi C Zeng / Simon H J Brown / Meghna Sobti / Alastair G Stewart /
Abstract: FF ATP synthase is a molecular rotary motor that can generate ATP using a transmembrane proton motive force. Isolated F-ATPase catalytic cores can hydrolyse ATP, passing through a series of ...FF ATP synthase is a molecular rotary motor that can generate ATP using a transmembrane proton motive force. Isolated F-ATPase catalytic cores can hydrolyse ATP, passing through a series of conformational states involving rotation of the central γ rotor subunit and the opening and closing of the catalytic β subunits. Cooperativity in F-ATPase has long thought to be conferred through the γ subunit, with three key interaction sites between the γ and β subunits being identified. Single molecule studies have demonstrated that the F complexes lacking the γ axle still "rotate" and hydrolyse ATP, but with less efficiency. We solved the cryogenic electron microscopy structure of an axle-less Bacillus sp. PS3 F-ATPase. The unexpected binding-dwell conformation of the structure in combination with the observed lack of interactions between the axle-less γ and the open β subunit suggests that the complete γ subunit is important for coordinating efficient ATP binding of F-ATPase.
History
DepositionSep 1, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41811.png

Downloads & links

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Map

FileDownload / File: emd_41811.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened axle-less Bacillus PS3 ATPase map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 250 pix.
= 205. Å		0.82 Å/pix.
x 250 pix.
= 205. Å		0.82 Å/pix.
x 250 pix.
= 205. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.40756035 - 0.7364234
Average (Standard dev.)-0.00030877153 (±0.039180398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 205.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41811_msk_1.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 : Bacillus PS3 F1 ATPase complex, with truncated gamma subunit

EntireName: Bacillus PS3 F1 ATPase complex, with truncated gamma subunit
Components
  • Complex: Bacillus PS3 F1 ATPase complex, with truncated gamma subunit
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION

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Supramolecule #1: Bacillus PS3 F1 ATPase complex, with truncated gamma subunit

SupramoleculeName: Bacillus PS3 F1 ATPase complex, with truncated gamma subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: The first 4 and last 25 amino acids have been deleted from the gamma subunit
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 354 KDa

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Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 54.908676 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSIRAEEISA LIKQQIENYE SQIQVSDVGT VIQVGDGIAR AHGLDNVMSG ELVEFANGVM GMALNLEENN VGIVILGPYT GIKEGDEVR RTGRIMEVPV GEALIGRVVN PLGQPVDGLG PVETTETRPI ESRAPGVMDR RSVHEPLQTG IKAIDALVPI G RGQRELII ...String:
MSIRAEEISA LIKQQIENYE SQIQVSDVGT VIQVGDGIAR AHGLDNVMSG ELVEFANGVM GMALNLEENN VGIVILGPYT GIKEGDEVR RTGRIMEVPV GEALIGRVVN PLGQPVDGLG PVETTETRPI ESRAPGVMDR 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 #2: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 53.424625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHHHH HMTRGRVIQV MGPVVDVKFE NGHLPAIYNA LKIQHKARNE NEVDIDLTLE VALHLGDDTV RTIAMASTDG LIRGMEVID TGAPISVPVG EVTLGRVFNV LGEPIDLEGD IPADARRDPI HRPAPKFEEL ATEVEILETG IKVVDLLAPY I KGGKIGLF ...String:
MHHHHHHHHH HMTRGRVIQV MGPVVDVKFE NGHLPAIYNA LKIQHKARNE NEVDIDLTLE VALHLGDDTV RTIAMASTDG LIRGMEVID TGAPISVPVG EVTLGRVFNV LGEPIDLEGD IPADARRDPI HRPAPKFEEL ATEVEILETG IKVVDLLAPY I KGGKIGLF GGAGVGKTVL IQELIHNIAQ EHGGISVFAG VGERTREGND LYHEMKDSGV ISKTAMVFGQ MNEPPGARMR VA LTGLTMA EYFRDEQGQD VLLFIDNIFR FTQAGSEVSA LLGRMPSAVG YQPTLATEMG QLQERITSTA KGSITSIQAI YVP ADDYTD PAPATTFSHL DATTNLERKL AEMGIYPAVD PLASTSRALA PEIVGEEHYQ VARKVQQTLQ RYKELQDIIA ILGM DELSD EDKLVVHRAR RIQFFLSQNF HVAEQFTGQP GSYVPVKETV RGFKEILEGK YDHLPEDAFR LVGRIEEVVE KAKAM GVEV

UniProtKB: ATP synthase subunit beta

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Macromolecule #3: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 3
Details: 4 residues deleted from N-term, 25 residues deleted from C-term, S109C, I212C, Strep-tag II insertion at N197
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 29.677084 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDIKTRINAT KKTSQITKAM EMVSTSKLNR AEQNAKSFVP YMEKIQEVVA NVALGAGGAS HPMLVSRPVK KTGYLVITSD RGLAGAYNS NVLRLVYQTI QKRHACPDEY AIIVIGRVGL SFFRKRNMPV ILDITRLPDQ PSFADIKEIA RKTVGLFADG T FDELYMYY ...String:
MDIKTRINAT KKTSQITKAM EMVSTSKLNR AEQNAKSFVP YMEKIQEVVA NVALGAGGAS HPMLVSRPVK KTGYLVITSD RGLAGAYNS NVLRLVYQTI QKRHACPDEY AIIVIGRVGL SFFRKRNMPV ILDITRLPDQ PSFADIKEIA RKTVGLFADG T FDELYMYY NHYVSAIQQE VTERKLLPLT DLAENWSHPQ FEKQRTVYEF EPSQEECLDV LLPQYAESLI YGALLDAKAS EH AARMTAM KNATDNANEL IRTLTL

UniProtKB: ATP synthase gamma chain

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Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 4 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / 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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Macromolecule #7: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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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

Concentration6 mg/mL
BufferpH: 7
Details: 100 mM Potassium phosphate pH 7, 2 mM EDTA 1 mM AMPPNP was added 20 min prior to freezing
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: Grid was glow discharged using a PELCO easiGlow set to 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
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

Startup modelType of model: OTHER
Details: The startup model was determined by an ab-initio reconstruction in CryoSPARC.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.1) / Number images used: 23813
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsModelAngelo was used to build an initial model into the map
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8u1h:
Axle-less Bacillus sp. PS3 F1 ATPase mutant

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