4ZG0

Crystal structure of Mouse Syndesmos protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.006 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of syndesmos and its interaction with Syndecan-4 proteoglycan

Kim, H.Yoo, J.Lee, I.Kang, Y.J.Cho, H.S.Lee, W.

(2015) Biochem.Biophys.Res.Commun. 463: 762-767

  • DOI: 10.1016/j.bbrc.2015.06.010

  • PubMed Abstract: 
  • Syndesmos, nucleoside diphosphate linked moiety X (nudix)-type motif 16-like 1 (Nudt16l1), is evolutionarily divergent from the Nudt16 family. Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain (Syn4(cyto)) in focal contacts, interac ...

    Syndesmos, nucleoside diphosphate linked moiety X (nudix)-type motif 16-like 1 (Nudt16l1), is evolutionarily divergent from the Nudt16 family. Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain (Syn4(cyto)) in focal contacts, interacts with various cell adhesion adaptor proteins to control cell signaling. We determined the X-ray crystal structure of syndesmos; it is composed of seven α-helices and seven β-strands. Although syndesmos has a molecular topology similar to that of nudix hydrolase proteins, the structure of the nudix motif differs from that of X29. The dimeric interface of syndesmos is composed of α-helix 4, 7 and β-strand 2, 7, which primarily form hydrophobic interactions. The binding interaction between syndesmos and syn4(cyto) was characterized as a low-affinity interaction (Kd = 62 μM) by surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR). The NMR resonances of Lys (177, 178, 179), Gly182, and Ser183 in the C1 region and Lys193 and Lys194 in the V region of syndecan-4 are perturbed upon syndesmos binding. Our results provide structural insight into the molecular function of syndesmos in the regulation of cell signaling via binding to syndecan-4.


    Organizational Affiliation

    Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, South Korea. Electronic address: wlee@spin.yonsei.ac.kr.,Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, South Korea.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, South Korea.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, South Korea. Electronic address: hscho8@yonsei.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein syndesmos
A, B
212Mus musculusMutation(s): 0 
Gene Names: Nudt16l1 (Sdos, Tirr)
Find proteins for Q8VHN8 (Mus musculus)
Go to UniProtKB:  Q8VHN8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.006 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.318α = 90.00
b = 68.701β = 103.93
c = 66.191γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data processing
PHENIXrefinement
HKL-2000data reduction
Cootmodel building
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references