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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

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 
• DOI: https://doi.org/10.1007/s13238-017-0439-x
• Primary Citation of Related Structures:  
  5X83

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Organizational Affiliation: 
• State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China.
Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084, China.
The Francis Crick Institute, London, NW1 2BE, UK.
European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany.
State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China. [e-mail].
PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China. [e-mail].
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China. [e-mail].
Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

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

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 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Finci, F.I., Xiao, J., Wang, J.

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

Revision History  

• 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