8WG4

mouse TMEM63b in DDM-CHS micelle with YN9303-24 Fab

• PDB DOI: https://doi.org/10.2210/pdb8WG4/pdb
• EM Map EMD-37502: 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: 3.50 Å
• Aggregation State: 2D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Mechanosensitive channel TMEM63B functions as a plasma membrane lipid scramblase

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.

To be published.

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: 130.93 kDa 
• Atom Count: 5,887 
• Modelled Residue Count: 688 
• 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	B [auth A]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C42 H82 N O8 P WTJKGGKOPKCXLL-VYOBOKEXSA-N
Y01	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [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: 3.50 Å
• Aggregation State: 2D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Servalcat	0.2.24
RECONSTRUCTION	cryoSPARC	4.2.1

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