5KF4

Crystal structure of FN3 domain (Residues P368-P466) of Human collagen XX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the second fibronectin type III (FN3) domain from human collagen alpha 1 type XX

Zhao, J.Ren, J.Wang, N.Cheng, Z.Yang, R.Lin, G.Guo, Y.Cai, D.Xie, Y.Zhao, X.

(2017) Acta Crystallogr F Struct Biol Commun 73: 695-700

  • DOI: 10.1107/S2053230X1701648X

  • PubMed Abstract: 
  • Collagen α1 type XX, which contains fibronectin type III (FN3) repeats involving six FN3 domains (referred to as the FN#1-FN#6 domains), is an unusual member of the fibril-associated collagens with interrupted triple helices (FACIT) subfamily of coll ...

    Collagen α1 type XX, which contains fibronectin type III (FN3) repeats involving six FN3 domains (referred to as the FN#1-FN#6 domains), is an unusual member of the fibril-associated collagens with interrupted triple helices (FACIT) subfamily of collagens. The results of standard protein BLAST suggest that the FN3 repeats might contribute to collagen α1 type XX acting as a cytokine receptor. To date, solution NMR structures of the FN#3, FN#4 and FN#6 domains have been determined. To obtain further structural evidence to understand the relationship between the structure and function of the FN3 repeats from collagen α1 type XX, the crystal structure of the FN#2 domain from human collagen α1 type XX (residues Pro386-Pro466; referred to as FN2-HCXX) was solved at 2.5 Å resolution. The crystal structure of FN2-HCXX shows an immunoglobulin-like fold containing a β-sandwich structure, which is formed by a three-stranded β-sheet (β1, β2 and β5) packed onto a four-stranded β-sheet (β3, β4, β6 and β7). Two consensus domains, tencon and fibcon, are structural analogues of FN2-HCXX. Fn8, an FN3 domain from human oncofoetal fibronectin, is the closest structural analogue of FN2-HCXX derived from a naturally occurring sequence. Based solely on the structural similarity of FN2-HCXX to other FN3 domains, the detailed functions of FN2-HCXX and the FN3 repeats in collagen α1 type XX cannot be identified.


    Related Citations: 
    • Design of novel FN3 domains with high stability by a consensus sequence approach
      Jacobs, S.A.,Diem, M.D.,Luo, J.,Teplyakov, A.,Obmolova, G.,Malia, T.,Gilliland, G.L.,ONeil, K.T.
      (2012) Protein Engineering, Design & Selection 25: 107


    Organizational Affiliation

    Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, People's Republic of China.,College of Life Science, Liaocheng University, Liaocheng, Shandong 252059, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagen alpha-1(XX) chain
A, B, C, D
100Homo sapiensMutation(s): 0 
Gene Names: COL20A1 (KIAA1510)
Find proteins for Q9P218 (Homo sapiens)
Go to Gene View: COL20A1
Go to UniProtKB:  Q9P218
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.476α = 90.00
b = 78.597β = 90.00
c = 81.989γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHASERphasing
PHASERphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81473114

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2017-12-27
    Type: Database references, Derived calculations