8K9C | pdb_00008k9c

Structure of human Caprin-2 HR1 domain

PDB DOI: https://doi.org/10.2210/pdb8K9C/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-31 Released: 2024-08-21
Deposition Author(s): Song, X.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural insights into the Caprin-2 HR1 domain in canonical Wnt signaling

Song, X.M.

To be published.

Macromolecule Content

Total Structure Weight: 58.82 kDa
Atom Count: 3,400
Modeled Residue Count: 409
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caprin-2	A, B	254	Homo sapiens	Mutation(s): 0 Gene Names: CAPRIN2, C1QDC1, EEG1, KIAA1873, RNG140
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IMN6 (Homo sapiens) Explore Q6IMN6 Go to UniProtKB: Q6IMN6
PHAROS: Q6IMN6 GTEx: ENSG00000110888
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6IMN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.721	α = 90
b = 65.322	β = 113.75
c = 112.203	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31530094
National Natural Science Foundation of China (NSFC)	China	31100532

Revision History (Full details and data files)

Version 1.0: 2024-08-21
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary

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.