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- EMDB-60252: mouse TMEM63b in DDM-CHS micelle -

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Basic information

Entry
Database: EMDB / ID: EMD-60252
Titlemouse TMEM63b in DDM-CHS micelle
Map data
Sample
  • Complex: mouse TMEM63B
KeywordsScramblase / LIPID TRANSPORT
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.96 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: Nat Struct Mol Biol / Year: 2025
Title: Membrane structure-responsive lipid scrambling by TMEM63B to control plasma membrane lipid distribution.
Authors: Yugo Miyata / Katsuya Takahashi / Yongchan Lee / Cheryl S Sultan / Risa Kuribayashi / Masatomo Takahashi / Kosuke Hata / Takeshi Bamba / Yoshihiro Izumi / Kehong Liu / Tomoko Uemura / ...Authors: Yugo Miyata / Katsuya Takahashi / Yongchan Lee / Cheryl S Sultan / Risa Kuribayashi / Masatomo Takahashi / Kosuke Hata / Takeshi Bamba / Yoshihiro Izumi / Kehong Liu / Tomoko Uemura / Norimichi Nomura / So Iwata / Shigekazu Nagata / Tomohiro Nishizawa / Katsumori Segawa /
Abstract: Phospholipids are asymmetrically distributed in the plasma membrane (PM), with phosphatidylcholine and sphingomyelin abundant in the outer leaflet. However, the mechanisms by which their distribution ...Phospholipids are asymmetrically distributed in the plasma membrane (PM), with phosphatidylcholine and sphingomyelin abundant in the outer leaflet. However, the mechanisms by which their distribution is regulated remain unclear. Here, we show that transmembrane protein 63B (TMEM63B) functions as a membrane structure-responsive lipid scramblase localized at the PM and lysosomes, activating bidirectional lipid translocation upon changes in membrane curvature and thickness. TMEM63B contains two intracellular loops with palmitoylated cysteine residue clusters essential for its scrambling function. TMEM63B deficiency alters phosphatidylcholine and sphingomyelin distributions in the PM. Persons with heterozygous mutations in TMEM63B are known to develop neurodevelopmental disorders. We show that V44M, the most frequent substitution, confers constitutive scramblase activity on TMEM63B, disrupting PM phospholipid asymmetry. We determined the cryo-electron microscopy structures of TMEM63B in its open and closed conformations, uncovering a lipid translocation pathway formed in response to changes in the membrane environment. Together, our results identify TMEM63B as a membrane structure-responsive scramblase that controls PM lipid distribution and we reveal the molecular basis for lipid scrambling and its biological importance.
History
DepositionMay 23, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60252.png

Downloads & links

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Map

FileDownload / File: emd_60252.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
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Contour LevelBy AUTHOR: 0.261
Minimum - Maximum-0.3572302 - 0.7335006
Average (Standard dev.)0.00823462 (±0.04810902)
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_60252_msk_1.map
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Mask #2

Fileemd_60252_msk_2.map
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Half map: #1

Fileemd_60252_half_map_1.map
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Half map: #2

Fileemd_60252_half_map_2.map
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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: 6.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 290946
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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