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- EMDB-37501: mouse TMEM63b in LMNG-CHS micelle -

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Basic information

Entry
Database: EMDB / ID: EMD-37501
Titlemouse TMEM63b in LMNG-CHS micelle
Map datasharpened map
Sample
  • Complex: mouse TMEM63B
    • Protein or peptide: CSC1-like protein 2,Green fluorescent protein
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
KeywordsScramblase / LIPID TRANSPORT
Function / homology
Function and homology information


alveolar lamellar body membrane / sphingomyelin transfer activity / surfactant secretion / phosphatidylcholine transfer activity / mechanosensitive monoatomic cation channel activity / osmolarity-sensing monoatomic cation channel activity / intestinal stem cell homeostasis / phospholipid scramblase activity / drinking behavior / mechanosensitive monoatomic ion channel activity ...alveolar lamellar body membrane / sphingomyelin transfer activity / surfactant secretion / phosphatidylcholine transfer activity / mechanosensitive monoatomic cation channel activity / osmolarity-sensing monoatomic cation channel activity / intestinal stem cell homeostasis / phospholipid scramblase activity / drinking behavior / mechanosensitive monoatomic ion channel activity / calcium-activated cation channel activity / exocytosis / bioluminescence / generation of precursor metabolites and energy / sensory perception of sound / actin cytoskeleton / early endosome membrane / lysosomal membrane / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
CSC1/OSCA1-like, 7TM region / CSC1/OSCA1-like, cytosolic domain / CSC1/OSCA1-like, N-terminal transmembrane domain / Calcium permeable stress-gated cation channel 1-like / Calcium-dependent channel, 7TM region, putative phosphate / Late exocytosis, associated with Golgi transport / Cytosolic domain of 10TM putative phosphate transporter / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Mechanosensitive cation channel TMEM63B
Similarity search - Component
Biological speciesMus musculus (house mouse) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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
DepositionSep 20, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37501.png

Downloads & links

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Map

FileDownload / File: emd_37501.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 160 pix.
= 249. Å		1.56 Å/pix.
x 160 pix.
= 249. Å		1.56 Å/pix.
x 160 pix.
= 249. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.55625 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.671
Minimum - Maximum-2.3084238 - 3.4690824
Average (Standard dev.)-0.0017334161 (±0.073799685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37501_msk_1.map
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Mask #2

Fileemd_37501_msk_2.map
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Half map: halfmapA

Fileemd_37501_half_map_1.map
AnnotationhalfmapA
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Half map: halfmapB

Fileemd_37501_half_map_2.map
AnnotationhalfmapB
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Sample components

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Entire : mouse TMEM63B

EntireName: mouse TMEM63B
Components
  • Complex: mouse TMEM63B
    • Protein or peptide: CSC1-like protein 2,Green fluorescent protein
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

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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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Macromolecule #1: CSC1-like protein 2,Green fluorescent protein

MacromoleculeName: CSC1-like protein 2,Green fluorescent protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 126.759461 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLPFLLATLG TAALNSSNPK DYCYSARIRS TVLQGLPFGG VPTVLALDFM CFLALLFLFS ILRKVAWDYG RLALVTDADR LRRQERERV EQEYVASAMH GDSHDRYERL TSVSSSVDFD QRDNGF(P1L)SWL TAIFRIKDDE IRDKCGGDAV HYLSFQR HI IGLLVVVGVL ...String:
MLPFLLATLG TAALNSSNPK DYCYSARIRS TVLQGLPFGG VPTVLALDFM CFLALLFLFS ILRKVAWDYG RLALVTDADR LRRQERERV EQEYVASAMH GDSHDRYERL TSVSSSVDFD QRDNGF(P1L)SWL TAIFRIKDDE IRDKCGGDAV HYLSFQR HI IGLLVVVGVL SVGIVLPVNF SGDLLENNAY SFGRTTIANL KSGNNLLWLH TSFAFLYLLL TVYSMRRHTS KMRYKEDD L VKRTLFINGI SKYAESEKIK KHFEEAYPNC TVLEARPCYN VARLMFLDAE RKKAERGKLY FTNLQSKENV PAMINPKPC GHLCCCVVRG CEQVEAIEYY TKLEQRLKED YRREKEKVNE KPLGMAFVTF HNETITAIIL KDFNVCKCQG CTCRGEPRAS SCSEALHIS NWTVTYAPDP QNIYWEHLSI RGFIWWLRCL VINVVLFILL FFLTTPAIII TTMDKFNVTK PVEYLNNPII T QFFPTLLL WCFSALLPTI VYYSAFFEAH WTRSGENRTT MHKCYTFLIF MVLLLPSLGL SSLDLFFRWL FDKKFLAEAA IR FECVFLP DNGAFFVNYV IASAFIGNAM DLLRIPGLLM YMIRLCLARS AAERRNVKRH QAYEFQFGAA YAWMMCVFTV VMT YSITCP IIVPFGLMYM LLKHLVDRYN LYYAYLPAKL DKKIHSGAVN QVVAAPILCL FWLLFFSTMR TGFLAPTSMF TFVV LVITI VICLCHVCFG HFKYLSAHNY KIEHTETDAV SSRSNGRPPT AGAVPKSAKY IAQVLQDSEG DGDGDGAPGS SGDEP PSSS SQDEELLMPP DGLTDTDFQS CEDSLIENEI HQGTENLYFQ GSAAAAVSKG EELFTGVVPI LVELDGDVNG HKFSVS GEG EGDATYGKLT LKFICTTGKL PVPWPTLVTT LTYGVQCFSR YPDHMKQHDF FKSAMPEGYV QERTIFFKDD GNYKTRA EV KFEGDTLVNR IELKGIDFKE DGNILGHKLE YNYNSHNVYI MADKQKNGIK VNFKIRHNIE DGSVQLADHY QQNTPIGD G PVLLPDNHYL STQSKLSKDP NEKRDHMVLL EFVTAAGITL GMDELYKSGL RSWSHPQFEK GGGSGGGSGG SAWSHPQFE K

UniProtKB: Mechanosensitive cation channel TMEM63B, Green fluorescent protein

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 3 / Number of copies: 1 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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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 / Mesh: 300 / 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) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 110878
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
Output model

PDB-8wg3:
mouse TMEM63b in LMNG-CHS micelle

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