5X83 | pdb_00005x83

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 (Depositor), 0.276 (DCC)
R-Value Work:
0.221 (Depositor), 0.224 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5X83

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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1007/s13238-017-0439-x
Primary Citation 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
Modeled Residue Count: 586
Deposited Residue Count: 646
Unique protein chains: 2

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43146
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.276 (DCC)
R-Value Work: 0.221 (Depositor), 0.224 (DCC)
R-Value Observed: 0.224 (Depositor)

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

View more in-depth experimental data

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

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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.