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- EMDB-39644: The isolated Vo domain of V/A-ATPase from Thermus thermophilus. -

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Basic information

Entry
Database: EMDB / ID: EMD-39644
TitleThe isolated Vo domain of V/A-ATPase from Thermus thermophilus.
Map dataRefined map
Sample
  • Complex: The isolated Vo domain of V/A-ATPase from Thermus thermophilus
    • Protein or peptide: V-type ATP synthase subunit I
    • Protein or peptide: V-type ATP synthase, subunit K
    • Protein or peptide: V-type ATP synthase subunit C
    • Protein or peptide: V-type ATP synthase, subunit (VAPC-THERM)
    • Protein or peptide: V-type ATP synthase subunit E
  • Ligand: water
KeywordsROTARY ATPASE / V/A-ATPASE / MOLECULAR MOTOR / MOTOR PROTEIN
Function / homology
Function and homology information


proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATPase binding / ATP binding / metal ion binding
Similarity search - Function
V-type ATP synthase subunit I, N-terminal / Vacuolar ATPase subunit I, N-terminal proximal lobe / Vacuolar ATPase Subunit I N-terminal proximal lobe / V-type ATPase subunit I, N-terminal domain / ATPase, V0 complex, c subunit / : / Vacuolar (H+)-ATPase G subunit / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily ...V-type ATP synthase subunit I, N-terminal / Vacuolar ATPase subunit I, N-terminal proximal lobe / Vacuolar ATPase Subunit I N-terminal proximal lobe / V-type ATPase subunit I, N-terminal domain / ATPase, V0 complex, c subunit / : / Vacuolar (H+)-ATPase G subunit / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
V-type ATP synthase subunit E / V-type ATP synthase subunit C / V-type ATP synthase, subunit (VAPC-THERM) / V-type ATP synthase subunit I / V-type ATP synthase, subunit K
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKishikawa J / Nishida Y / Nakano A / Yokoyama K
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
Japan Society for the Promotion of Science (JSPS)20K06514 Japan
Japan Society for the Promotion of Science (JSPS)22H02595 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101001 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
Japan Science and TechnologyJPMJCR1865 Japan
CitationJournal: Nat Commun / Year: 2024
Title: Rotary mechanism of the prokaryotic V motor driven by proton motive force.
Authors: Jun-Ichi Kishikawa / Yui Nishida / Atsuki Nakano / Takayuki Kato / Kaoru Mitsuoka / Kei-Ichi Okazaki / Ken Yokoyama /
Abstract: ATP synthases play a crucial role in energy production by utilizing the proton motive force (pmf) across the membrane to rotate their membrane-embedded rotor c-ring, and thus driving ATP synthesis in ...ATP synthases play a crucial role in energy production by utilizing the proton motive force (pmf) across the membrane to rotate their membrane-embedded rotor c-ring, and thus driving ATP synthesis in the hydrophilic catalytic hexamer. However, the mechanism of how pmf converts into c-ring rotation remains unclear. This study presents a 2.8 Å cryo-EM structure of the V domain of V/A-ATPase from Thermus thermophilus, revealing precise orientations of glutamate (Glu) residues in the c-ring. Three Glu residues face a water channel, with one forming a salt bridge with the Arginine in the stator (a/Arg). Molecular dynamics (MD) simulations show that protonation of specific Glu residues triggers unidirectional Brownian motion of the c-ring towards ATP synthesis. When the key Glu remains unprotonated, the salt bridge persists, blocking rotation. These findings suggest that asymmetry in the protonation of c/Glu residues biases c-ring movement, facilitating rotation and ATP synthesis.
History
DepositionApr 1, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39644.png

Downloads & links

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Map

FileDownload / File: emd_39644.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 320 pix.
= 281.6 Å		0.88 Å/pix.
x 320 pix.
= 281.6 Å		0.88 Å/pix.
x 320 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-3.336584 - 5.29456
Average (Standard dev.)0.003421247 (±0.12681663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39644_msk_1.map
Projections & Slices
AxesZYX

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Half map: half map A

Fileemd_39644_half_map_1.map
Annotationhalf map A
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_39644_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : The isolated Vo domain of V/A-ATPase from Thermus thermophilus

EntireName: The isolated Vo domain of V/A-ATPase from Thermus thermophilus
Components
  • Complex: The isolated Vo domain of V/A-ATPase from Thermus thermophilus
    • Protein or peptide: V-type ATP synthase subunit I
    • Protein or peptide: V-type ATP synthase, subunit K
    • Protein or peptide: V-type ATP synthase subunit C
    • Protein or peptide: V-type ATP synthase, subunit (VAPC-THERM)
    • Protein or peptide: V-type ATP synthase subunit E
  • Ligand: water

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Supramolecule #1: The isolated Vo domain of V/A-ATPase from Thermus thermophilus

SupramoleculeName: The isolated Vo domain of V/A-ATPase from Thermus thermophilus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: V-type ATP synthase subunit I

MacromoleculeName: V-type ATP synthase subunit I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 72.204289 KDa
Recombinant expressionOrganism: Thermus thermophilus HB8 (bacteria)
SequenceString: MIAPMEKLVL AGPKGRAKEL LQSLQQAGVV HLETLRPEAL SAYQLSPEER AELRRWEAVS AGAEHTLSLL GLEAEPARPF PEGLEAAEK ALSPIQAHAE GLTRQKQELE EELALAQAYL EPLERLAALA HGLDKSPFLR VIPFLLTEKE LPLVEEALRK A LEDRYLLA ...String:
MIAPMEKLVL AGPKGRAKEL LQSLQQAGVV HLETLRPEAL SAYQLSPEER AELRRWEAVS AGAEHTLSLL GLEAEPARPF PEGLEAAEK ALSPIQAHAE GLTRQKQELE EELALAQAYL EPLERLAALA HGLDKSPFLR VIPFLLTEKE LPLVEEALRK A LEDRYLLA HEAYAGGVAA LVVVHRKEVD QAKAALSRAG VAELRLPGAL GELPLSEAAR RLKERAEAAP RELSEVRQHL AK LARESAS TLQSLWTRAQ DEVARLKALE ELASGRFGFA LLGYVPVKAK PKVEEALARH KESVVYAFEP VDEHHEADRI PVV LDNPPW AKPFELLVSF LNTPKYGTFD PTPVVPVFFP FWFGMIVGDI GYALLFYLVG RWLSGYVKRN EPLVIDLFAL KLKP QVIGK LVHILNWMVF WTVVWGVIYG EFFGTFLEHL GVFGTPEHPG LIPILIHRID TAKTANLLIL LSVAFGVVLV FFGLA LRAY LGLKHRHMAH FWEGVGYLGG LVGVLALAAS YLGNLQAGWL QGLMYLGFGV FLLAVLMSRI WLMIPEIFTQ AGHILS HIR IYAVGAAGGI LAGLLTDVGF ALAERLGLLG VLLGLLVAGV LHLLILLLTT LGHMLQPIRL LWVEFFTKFG FYEENGR PY RPFKSVREAQ

UniProtKB: V-type ATP synthase subunit I

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Macromolecule #2: V-type ATP synthase, subunit K

MacromoleculeName: V-type ATP synthase, subunit K / type: protein_or_peptide / ID: 2
Details: 3 His residues on the c-terminal are purification tag.
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 10.256154 KDa
Recombinant expressionOrganism: Thermus thermophilus HB8 (bacteria)
SequenceString:
MKKLLVTVLL AVFGALAFAA EEAAASGGLD RGLIAVGMGL AVGLAALGTG VAQARIGAAG VGAIAEDRSN FGTALIFLLL PETLVIFGL LIAFILNGRL HHH

UniProtKB: V-type ATP synthase, subunit K

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Macromolecule #3: V-type ATP synthase subunit C

MacromoleculeName: V-type ATP synthase subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 35.96857 KDa
Recombinant expressionOrganism: Thermus thermophilus HB8 (bacteria)
SequenceString: MADDFAYLNA RVRVRRGTLL KESFFQEALD LSFADFLRLL SETVYGGELA GQGLPDVDRA VLRTQAKLVG DLPRLVTGEA REAVRLLLL RNDLHNLQAL LRAKATGRPF EEVLLLPGTL REEVWRQAYE AQDPAGMAQV LAVPGHPLAR ALRAVLRETQ D LARVEALL ...String:
MADDFAYLNA RVRVRRGTLL KESFFQEALD LSFADFLRLL SETVYGGELA GQGLPDVDRA VLRTQAKLVG DLPRLVTGEA REAVRLLLL RNDLHNLQAL LRAKATGRPF EEVLLLPGTL REEVWRQAYE AQDPAGMAQV LAVPGHPLAR ALRAVLRETQ D LARVEALL AKRFFEDVAK AAKGLDQPAL RDYLALEVDA ENLRTAFKLQ GSGLAPDAFF LKGGRFVDRV RFARLMEGDY AV LDELSGT PFSGLSGVRD LKALERGLRC VLLKEAKKGV QDPLGVGLVL AYVKEREWEA VRLRLLARRA YFGLPRAQVE EEV VCP

UniProtKB: V-type ATP synthase subunit C

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Macromolecule #4: V-type ATP synthase, subunit (VAPC-THERM)

MacromoleculeName: V-type ATP synthase, subunit (VAPC-THERM) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 13.166218 KDa
Recombinant expressionOrganism: Thermus thermophilus HB8 (bacteria)
SequenceString:
MTGGLVLNAI SRAGGAMGGL GLIKSLAEKE KQLLERLEAA KKEAEERVKR AEAEAKALLE EAEAKAKALE AQYRERERAE TEALLARYR ERAEAEAKAV REKAMARLDE AVALVLKEVL P

UniProtKB: V-type ATP synthase, subunit (VAPC-THERM)

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Macromolecule #5: V-type ATP synthase subunit E

MacromoleculeName: V-type ATP synthase subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 20.645582 KDa
Recombinant expressionOrganism: Thermus thermophilus HB8 (bacteria)
SequenceString:
MSKLEAILSQ EVEAEIQALL QEAEAKAEAV KREAEEKAKA LLQARERALE AQYRAALRRA ESAGELLVAT ARTQARGEVL EEVRRRVRE ALEALPQKPE WPEVVRKLAL EALEALPGAK ALVANPEDLP HLEALARERG VELQAEPALR LGVRAVGAEG K TQVENSLL ARLDRAWDAL SSKVAQALWG

UniProtKB: V-type ATP synthase subunit E

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 70 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration3.00 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
150.0 mMsodium chlorideNaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 9341 / Average exposure time: 0.05 sec. / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.043 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
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: 4391283
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ly9

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 370215
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ly9


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: Coot
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8ywt:
The isolated Vo domain of V/A-ATPase from Thermus thermophilus.

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