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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: 2D ARRAY
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q3TWI9P42212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LBN Query on LBN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] 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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]