1H4U

Domain G2 of mouse nidogen-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

  • DOI: https://doi.org/10.1038/89683
  • Primary Citation of Related Structures:  
    1H4U

  • PubMed Abstract: 

    Nidogen, an invariant component of basement membranes, is a multifunctional protein that interacts with most other major basement membrane proteins. Here, we report the crystal structure of the mouse nidogen-1 G2 fragment, which contains binding sites for collagen IV and perlecan. The structure is composed of an EGF-like domain and an 11-stranded beta-barrel with a central helix. The beta-barrel domain has unexpected similarity to green fluorescent protein. A large surface patch on the beta-barrel is strikingly conserved in all metazoan nidogens. Site-directed mutagenesis demonstrates that the conserved residues are involved in perlecan binding.


  • Organizational Affiliation

    Abteilung Proteinchemie, Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NIDOGEN-1265Mus musculusMutation(s): 0 
UniProt
Find proteins for P10493 (Mus musculus)
Explore P10493 
Go to UniProtKB:  P10493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10493
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.18α = 90
b = 95.18β = 90
c = 65.39γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Other, Structure summary