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- EMDB-60251: mouse TMEM63b in LMNG-CHS micelle with YN9303-24 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-60251
Titlemouse TMEM63b in LMNG-CHS micelle with YN9303-24 Fab
Map datafull map
Sample
  • Complex: mouse TMEM63B
KeywordsScramblase / LIPID TRANSPORT
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsMiyata Y / Takahashi K / Lee Y / Sultan CS / Kuribayashi R / Takahashi M / Hata K / Bamba T / Izumi Y / Liu K ...Miyata Y / Takahashi K / Lee Y / Sultan CS / Kuribayashi R / Takahashi M / Hata K / Bamba T / Izumi Y / Liu K / Uemura T / Nomura N / Iwata S / Nagata S / Nishizawa T / Segawa K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Mechanosensitive channel TMEM63B functions as a plasma membrane lipid scramblase
Authors: Miyata Y / Takahashi K / Lee Y / Sultan CS / Kuribayashi R / Takahashi M / Hata K / Bamba T / Izumi Y / Liu K / Uemura T / Nomura N / Iwata S / Nagata S / Nishizawa T / Segawa K
History
DepositionMay 23, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60251.png

Downloads & links

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Map

FileDownload / File: emd_60251.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 128 pix.
= 212.48 Å		1.66 Å/pix.
x 128 pix.
= 212.48 Å		1.66 Å/pix.
x 128 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.221
Minimum - Maximum-0.5465773 - 1.0601434
Average (Standard dev.)0.0031266783 (±0.033206873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60251_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_60251_msk_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: halmap 2

Fileemd_60251_half_map_1.map
Annotationhalmap_2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halmap 1

Fileemd_60251_half_map_2.map
Annotationhalmap_1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mouse TMEM63B

EntireName: mouse TMEM63B
Components
  • Complex: mouse TMEM63B

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Supramolecule #1: mouse TMEM63B

SupramoleculeName: mouse TMEM63B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 100 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration5 mg/mL
BufferpH: 8
GridModel: Quantifoil R0.6/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 408554
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

twi9


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model

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