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- EMDB-30015: The membrane-embedded Vo domain of V/A-ATPase from Thermus thermo... -

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Basic information

Entry
Database: EMDB / ID: EMD-30015
TitleThe membrane-embedded Vo domain of V/A-ATPase from Thermus thermophilus
Map dataThe membrane-embedded Vo domain of V/A-ATPase from Thermus thermophilus.
Sample
  • Complex: Membrane-embedded Vo domain
    • 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
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 / plasma membrane
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 / V-ATPase proteolipid 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 / V-ATPase proteolipid 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-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: 3.93 Å
AuthorsKishikawa J / Nakanishi A / Furuta A / Kato T / Namba K / Tamakoshi M / Mitsuoka K / Yokoyama K
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H03648 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)12024046 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101001 Japan
CitationJournal: Elife / Year: 2020
Title: Mechanical inhibition of isolated V from V/A-ATPase for proton conductance.
Authors: Jun-Ichi Kishikawa / Atsuko Nakanishi / Aya Furuta / Takayuki Kato / Keiichi Namba / Masatada Tamakoshi / Kaoru Mitsuoka / Ken Yokoyama /
Abstract: V-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V domain, with proton flow through the V membrane domain, via rotation of the central rotor complex ...V-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V domain, with proton flow through the V membrane domain, via rotation of the central rotor complex relative to the surrounding stator apparatus. Upon dissociation from the V domain, the V domain of the eukaryotic V-ATPase can adopt a physiologically relevant auto-inhibited form in which proton conductance through the V domain is prevented, however the molecular mechanism of this inhibition is not fully understood. Using cryo-electron microscopy, we determined the structure of both the V/A-ATPase and isolated V at near-atomic resolution, respectively. These structures clarify how the isolated V domain adopts the auto-inhibited form and how the complex prevents formation of the inhibited V form.
History
DepositionFeb 13, 2020-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-6ly9
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ly9
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30015.png

Downloads & links

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Map

FileDownload / File: emd_30015.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe membrane-embedded Vo domain of V/A-ATPase from Thermus thermophilus.
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.063989334 - 0.11663879
Average (Standard dev.)0.0005525833 (±0.0044713207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z220.000220.000220.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0640.1170.001

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Supplemental data

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Sample components

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Entire : Membrane-embedded Vo domain

EntireName: Membrane-embedded Vo domain
Components
  • Complex: Membrane-embedded Vo domain
    • 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

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Supramolecule #1: Membrane-embedded Vo domain

SupramoleculeName: Membrane-embedded Vo domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: V/A-type ATPase from Thermus thermophilus
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 260 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
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

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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 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 9.841714 KDa
SequenceString:
MKKLLVTVLL AVFGALAFAA EEAAASGGLD RGLIAVGMGL AVGLAALGTG VAQARIGAAG VGAIAEDRSN FGTALIFLLL PETLVIFGL LIAFILNGRL

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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
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

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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
SequenceString:
MTGGLVLNAI SRAGGAMGGL GLIKSLAEKE KQLLERLEAA KKEAEERVKR AEAEAKALLE EAEAKAKALE AQYRERERAE TEALLARYR ERAEAEAKAV REKAMARLDE AVALVLKEVL P

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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
SequenceString:
MSKLEAILSQ EVEAEIQALL QEAEAKAEAV KREAEEKAKA LLQARERALE AQYRAALRRA ESAGELLVAT ARTQARGEVL EEVRRRVRE ALEALPQKPE WPEVVRKLAL EALEALPGAK ALVANPEDLP HLEALARERG VELQAEPALR LGVRAVGAEG K TQVENSLL ARLDRAWDAL SSKVAQALWG

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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

Concentration3.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTris-HCl
150.0 mMNaClSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was purified from cell membrane of Thermus thermophilus and incorporated into nanodisc.

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-60 / Number real images: 5988 / Average exposure time: 12.0 sec. / Average electron dose: 79.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal magnification: 50000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3140000
Details: The particles selected from manually-selected 3268 micrographs.
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: Previous result of same enzyme.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Software - details: 3.0.7 / Number images used: 157618
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION / Software - details: 3.0.7
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION / Software - details: 3.0.7
Final 3D classificationNumber classes: 100 / Avg.num./class: 10 / Software - Name: RELION / Software - details: 3.0.7
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6qum

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Correlation coefficient
Output model

PDB-6ly9:
The membrane-embedded Vo domain of V/A-ATPase from Thermus thermophilus

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