5X83

Structure of DCC FN456 domains

PDB DOI: https://doi.org/10.2210/pdb5X83/pdb

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

Deposited: 2017-02-28 Released: 2017-09-06
Deposition Author(s): Finci, F.I., Xiao, J., Wang, J.
Funding Organization(s): National Science Foundation of China (NSFC), NIH grant

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.278
R-Value Work: 0.221
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of unliganded membrane-proximal domains FN4-FN5-FN6 of DCC

Finci, L.I., Zhang, J., Sun, X., Smock, R.G., Meijers, R., Zhang, Y., Xiao, J., Wang, J.H.

(2017) Protein Cell 8: 701-705

PubMed: 28664251 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s13238-017-0439-x
Primary Citation of Related Structures:
5X83

Organizational Affiliation

State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China.

Macromolecule Content

Total Structure Weight: 70.76 kDa
Atom Count: 4,627
Modelled Residue Count: 586
Deposited Residue Count: 646
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin receptor DCC	A, C	116	Homo sapiens	Mutation(s): 0 Gene Names: DCC, IGDCC1
UniProt & NIH Common Fund Data Resources
Find proteins for P43146 (Homo sapiens) Explore P43146 Go to UniProtKB: P43146
PHAROS: P43146 GTEx: ENSG00000187323
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43146
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin receptor DCC	B, D	207	Homo sapiens	Mutation(s): 0 Gene Names: DCC, IGDCC1
UniProt & NIH Common Fund Data Resources
Find proteins for P43146 (Homo sapiens) Explore P43146 Go to UniProtKB: P43146
PHAROS: P43146 GTEx: ENSG00000187323
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43146
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.278
R-Value Work: 0.221
R-Value Observed: 0.224
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.459	α = 90
b = 126.971	β = 99.68
c = 57.162	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-09-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation of China (NSFC)	China	81425009
NIH grant	China	HL48675

Revision History (Full details and data files)

Version 1.0: 2017-09-06
Type: Initial release
Version 1.1: 2017-12-13
Changes: Database references
Version 1.2: 2024-03-27
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.