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- EMDB-46795: Human V-ATPase Vo subcomplex bound to inhibitor and nanobody -

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Basic information

Entry
Database: EMDB / ID: EMD-46795
TitleHuman V-ATPase Vo subcomplex bound to inhibitor and nanobody
Map dataHuman V-ATPase Vo subcomplex bound to inhibitor and nanobody
Sample
  • Complex: Vo subcomplex from human V-ATPase bound to Nanobody and inhibitor
KeywordsV-ATPase / lipid nanodisc / Vo subcomplex / inhibitor / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsOot RA / Park JB / Roh S-H / Wilkens S
Funding support United States, Korea, Republic Of, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141908 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA228340 United States
Other private73258
National Research Foundation (NRF, Korea)2020R1A6C101A183 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4021220 Korea, Republic Of
CitationJournal: To Be Published
Title: Inhibitor bound Vo subcomplex from human V-ATPase
Authors: Oot RA / Park JB / Roh S-H / Wilkens S
History
DepositionAug 29, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46795.png

Downloads & links

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Map

FileDownload / File: emd_46795.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman V-ATPase Vo subcomplex bound to inhibitor and nanobody
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34
Minimum - Maximum-1.3055632 - 2.1351194
Average (Standard dev.)0.00016513046 (±0.06719558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map for cryosparc P14 J99 005 volume map sharp consensus map.mrc

Fileemd_46795_half_map_1.map
Annotationhalf map for cryosparc_P14_J99_005_volume_map_sharp_consensus_map.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map for cryosparc P14 J99 005 volume map sharp consensus map.mrc

Fileemd_46795_half_map_2.map
Annotationhalf map for cryosparc_P14_J99_005_volume_map_sharp_consensus_map.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vo subcomplex from human V-ATPase bound to Nanobody and inhibitor

EntireName: Vo subcomplex from human V-ATPase bound to Nanobody and inhibitor
Components
  • Complex: Vo subcomplex from human V-ATPase bound to Nanobody and inhibitor

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Supramolecule #1: Vo subcomplex from human V-ATPase bound to Nanobody and inhibitor

SupramoleculeName: Vo subcomplex from human V-ATPase bound to Nanobody and inhibitor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Details: Subunit a, isoform 4 (a4) carrying a C-terminal 2x FLAG tag was stably expressed in HEK293F cells. All other subunits present in the complex are endogenously expressed and have formed a ...Details: Subunit a, isoform 4 (a4) carrying a C-terminal 2x FLAG tag was stably expressed in HEK293F cells. All other subunits present in the complex are endogenously expressed and have formed a complex with the FLAG tagged a4. The Nanobody was raised against a4 and used for concentrating the sample for EM. A small molecule inhibitor is also bound to the complex.
Source (natural)Organism: Homo sapiens (human) / Location in cell: Membranes

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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

Concentration2 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMC4H11NO3Tris
0.5 mMC10H14N2Na2O8Ethylenediaminetetraacetic acid
2.0 mMC4H10O2S2Dithiothreitol

Details: 20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 39.96 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.3 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144439
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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