9Z0M | pdb_00009z0m

Human CD300c extracellular domain pH 7.5

PDB DOI: https://doi.org/10.2210/pdb9Z0M/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2025-11-02 Released: 2025-11-19
Deposition Author(s): Tennant, L., Littler, D.R., Rossjohn, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Ligand recognition in the CD300c extracellular domain

Tennant, L., Littler, D.R., Rossjohn, J.

To be published.

Macromolecule Content

Total Structure Weight: 12.58 kDa
Atom Count: 904
Modeled Residue Count: 109
Deposited Residue Count: 113
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CMRF35-like molecule 6	A	113	Homo sapiens	Mutation(s): 0 Gene Names: CD300C, CMRF35, CMRF35A, CMRF35A1, IGSF16
UniProt & NIH Common Fund Data Resources
Find proteins for Q08708 (Homo sapiens) Explore Q08708 Go to UniProtKB: Q08708
GTEx: ENSG00000167850
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08708
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.239 (Depositor), 0.239 (DCC)
R-Value Work: 0.202 (Depositor), 0.202 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.329	α = 90
b = 38.207	β = 90
c = 82.366	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-19
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.