1GL4

Nidogen-1 G2/Perlecan IG3 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the High-Affinity Interaction of Nidogen-1 with Immunoglobulin-Like Domain 3 of Perlecan

Kvansakul, M.Hopf, M.Ries, A.Timpl, R.Hohenester, E.

(2001) Embo J. 20: 5342

  • DOI: 10.1093/emboj/20.19.5342

  • PubMed Abstract: 
  • Nidogen and perlecan are large multifunctional basement membrane (BM) proteins conserved in all metazoa. Their high-affinity interaction, which is likely to contribute to BM assembly and function, is mediated by the central G2 domain in nidogen and t ...

    Nidogen and perlecan are large multifunctional basement membrane (BM) proteins conserved in all metazoa. Their high-affinity interaction, which is likely to contribute to BM assembly and function, is mediated by the central G2 domain in nidogen and the third immunoglobulin (IG)-like domain in perlecan, IG3. We have solved the crystal structure at 2.0 A resolution of the mouse nidogen-1 G2-perlecan IG3 complex. Perlecan IG3 belongs to the I-set of the IG superfamily and binds to the wall of the nidogen-1 G2 beta-barrel using beta-strands C, D and F. Nidogen-1 residues participating in the extensive interface are highly conserved, whereas the corresponding binding site on perlecan is more variable. We hypothesize that a second, as yet unidentified, activity of nidogen overlaps with perlecan binding and accounts for the unusually high degree of surface conservation in the G2 domain.


    Related Citations: 
    • Crystal Structure and Mutational Analysis of a Perlecan-Binding Fragment of Nidogen-1
      Hopf, M.,Gohring, W.,Ries, A.,Timpl, R.,Hohenester, E.
      (2001) Nat.Struct.Mol.Biol. 8: 634
    • Mapping of Binding Sites for Nidogens, Fibulin-2, Fibronectin and Heparin to Different Ig Modules of Perlecan
      Hopf, M.,Gohring, W.,Mann, K.,Timpl, R.
      (2001) J.Mol.Biol. 311: 529


    Organizational Affiliation

    Biophysics Section, Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2BW, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NIDOGEN-1
A
285Mus musculusMutation(s): 0 
Gene Names: Nid1 (Ent)
Find proteins for P10493 (Mus musculus)
Go to UniProtKB:  P10493
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BASEMENT MEMBRANE-SPECIFIC HEPARAN SULFATE PROTEOGLYCAN CORE PROTEIN
B
98Mus musculusMutation(s): 0 
Gene Names: Hspg2
Find proteins for Q05793 (Mus musculus)
Go to UniProtKB:  Q05793
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.920α = 90.00
b = 72.300β = 90.00
c = 103.930γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance