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- EMDB-39663: Vo domain of V/A-ATPase from Thermus thermophilus state3 -

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Basic information

Entry
Database: EMDB / ID: EMD-39663
TitleVo domain of V/A-ATPase from Thermus thermophilus state3
Map data
Sample
  • Complex: Vo domain of V/A-ATPase from thermus thermophilus.
    • Protein or peptide: V-type ATP synthase subunit C
    • Protein or peptide: V-type ATP synthase subunit I
    • Protein or peptide: V-type ATP synthase, subunit K
KeywordsV/A-ATPase / ATP synthase / MOTOR PROTEIN
Function / homology
Function and homology information


proton-transporting V-type ATPase, V0 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
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 / : / 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 ...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 / : / 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-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 C / 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: 3.6 Å
AuthorsNishida Y / Kishikawa J / Nakano A / Yokoyama K
Funding support Japan, 4 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)22H0595 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101001 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 3, 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_39663.png

Downloads & links

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Map

FileDownload / File: emd_39663.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 400 pix.
= 352. Å		0.88 Å/pix.
x 400 pix.
= 352. Å		0.88 Å/pix.
x 400 pix.
= 352. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0121
Minimum - Maximum-0.015656449 - 0.036230408
Average (Standard dev.)0.00006858961 (±0.0014633518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39663_msk_1.map
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Additional map: #1

Fileemd_39663_additional_1.map
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Half map: #2

Fileemd_39663_half_map_1.map
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Half map: #1

Fileemd_39663_half_map_2.map
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Sample components

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Entire : Vo domain of V/A-ATPase from thermus thermophilus.

EntireName: Vo domain of V/A-ATPase from thermus thermophilus.
Components
  • Complex: Vo domain of V/A-ATPase from thermus thermophilus.
    • Protein or peptide: V-type ATP synthase subunit C
    • Protein or peptide: V-type ATP synthase subunit I
    • Protein or peptide: V-type ATP synthase, subunit K

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Supramolecule #1: Vo domain of V/A-ATPase from thermus thermophilus.

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

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Macromolecule #1: V-type ATP synthase subunit C

MacromoleculeName: V-type ATP synthase subunit C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 35.66918 KDa
Recombinant expressionOrganism: Thermus thermophilus HB8 (bacteria)
SequenceString: DDFAYLNARV RVRRGTLLKE SFFQEALDLS FADFLRLLSE TVYGGELAGQ GLPDVDRAVL RTQAKLVGDL PRLVTGEARE AVRLLLLRN DLHNLQALLR AKATGRPFEE VLLLPGTLRE EVWRQAYEAQ DPAGMAQVLA VPGHPLARAL RAVLRETQDL A RVEALLAK ...String:
DDFAYLNARV RVRRGTLLKE SFFQEALDLS FADFLRLLSE TVYGGELAGQ GLPDVDRAVL RTQAKLVGDL PRLVTGEARE AVRLLLLRN DLHNLQALLR AKATGRPFEE VLLLPGTLRE EVWRQAYEAQ DPAGMAQVLA VPGHPLARAL RAVLRETQDL A RVEALLAK RFFEDVAKAA KGLDQPALRD YLALEVDAEN LRTAFKLQGS GLAPDAFFLK GGRFVDRVRF ARLMEGDYAV LD ELSGTPF SGLSGVRDLK ALERGLRCVL LKEAKKGVQD PLGVGLVLAY VKEREWEAVR LRLLARRAYF GLPRAQVEEE VVC

UniProtKB: V-type ATP synthase subunit C

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Macromolecule #2: V-type ATP synthase subunit I

MacromoleculeName: V-type ATP synthase subunit I / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 71.875969 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 RPFKSVR

UniProtKB: V-type ATP synthase subunit I

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Macromolecule #3: V-type ATP synthase, subunit K

MacromoleculeName: V-type ATP synthase, subunit K / type: protein_or_peptide / ID: 3
Details: 3 His residues on the c-terminal are purification tag.
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 7.222547 KDa
Recombinant expressionOrganism: Thermus thermophilus HB8 (bacteria)
SequenceString:
GGLDRGLIAV GMGLAVGLAA LGTGVAQARI GAAGVGAIAE DRSNFGTALI FLLLPETLVI FGLLIAFILN GRL

UniProtKB: V-type ATP synthase, subunit K

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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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.105 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1671397
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6r0y

Final reconstructionNumber classes used: 2 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.01) / Number images used: 26525
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.01)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 4.01)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6qum


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

PDB-8yy1:
Vo domain of V/A-ATPase from Thermus thermophilus state3

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