1GL4

Nidogen-1 G2/Perlecan IG3 Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1GL4

  • 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 the 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 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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NIDOGEN-1 A285Mus musculusMutation(s): 0 
Gene Names: Nid1, Ent
Find proteins for P10493 (Mus musculus)
Explore P10493 
Go to UniProtKB:  P10493
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BASEMENT MEMBRANE-SPECIFIC HEPARAN SULFATE PROTEOGLYCAN CORE PROTEIN B98Mus musculusMutation(s): 0 
Gene Names: Hspg2
Find proteins for Q05793 (Mus musculus)
Explore Q05793 
Go to UniProtKB:  Q05793
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download Ideal Coordinates CCD File 
B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.92α = 90
b = 72.3β = 90
c = 103.93γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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