8WG3 | pdb_00008wg3

mouse TMEM63b in LMNG-CHS micelle

• PDB DOI: https://doi.org/10.2210/pdb8WG3/pdb
• EM Map EMD-37501: EMDB EMDataResource

• Classification: LIPID TRANSPORT
• Organism(s): Mus musculus, Aequorea victoria
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-09-20 Released: 2024-09-25 
• Deposition Author(s): Miyata, Y., Takahashi, K., Lee, Y., Sultan, C.S., 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 Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: 2D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Membrane structure-responsive lipid scrambling by TMEM63B to control plasma membrane lipid distribution.

Miyata, Y., Takahashi, K., Lee, Y., Sultan, C.S., Kuribayashi, R., Takahashi, M., Hata, K., Bamba, T., Izumi, Y., Liu, K., Uemura, T., Nomura, N., Iwata, S., Nagata, S., Nishizawa, T., Segawa, K.

(2025) Nat Struct Mol Biol 32: 185-198

• PubMed: 39424995 
• DOI: https://doi.org/10.1038/s41594-024-01411-6
• Primary Citation of Related Structures:  
  8WG3, 8WG4


• PubMed 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 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.

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Organizational Affiliation: 
• Department of Medical Chemistry, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.
Division of Metabolomics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Biochemistry and Immunology, World Premier International Research Center, Immunology Frontier Research Center, Osaka University, Osaka, Japan.
Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan. [e-mail].
Department of Medical Chemistry, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan. [e-mail].
Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 128.98 kDa 
• Atom Count: 4,585 
• Modeled Residue Count: 548 
• Deposited Residue Count: 1,117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CSC1-like protein 2,Green fluorescent protein	A	1,117	Mus musculus, Aequorea victoria This entity is chimeric	Mutation(s): 4  Gene Names: Tmem63b, GFP Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212
Find proteins for Q3TWI9 (Mus musculus) Explore Q3TWI9  Go to UniProtKB:  Q3TWI9
IMPC:  MGI:2387609
UniProt Groups	Q3TWI9P42212

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LBN	E [auth A]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C42 H82 N O8 P WTJKGGKOPKCXLL-VYOBOKEXSA-N
Y01	B [auth A], C [auth A], D [auth A]	CHOLESTEROL HEMISUCCINATE C31 H50 O4 WLNARFZDISHUGS-MIXBDBMTSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
P1L	A	L-PEPTIDE LINKING	C19 H37 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: 2D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.2.1
MODEL REFINEMENT	Servalcat	0.2.24

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Miyata, Y., Takahashi, K., Lee, Y., Sultan, C.S., Kuribayashi, R., Takahashi, M., Hata, K., Bamba, T., Izumi, Y., Liu, K., Uemura, T., Nomura, N., Iwata, S., Nagata, S., Nishizawa, T., Segawa, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release
  
• Version 1.1: 2025-10-22
  Changes: Data collection, Database references, Structure summary