PDBsum entry 1h4u

Extracellular matrix protein

PDB id: 1h4u

Contents

Protein chain

245 a.a. *

Waters ×75

* Residue conservation analysis

PDB id:

1h4u

Name:

Extracellular matrix protein

Title:

Domain g2 of mouse nidogen-1

Structure:

Nidogen-1. Chain: a. Fragment: g2 fragment, residues 395-659. Engineered: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: 293-ebna.

Resolution:

2.20Å R-factor: 0.241 R-free: 0.280

Authors:

M.Hopf,W.Gohring,A.Ries,R.Timpl,E.Hohenester

Key ref:

M.Hopf et al. (2001). Crystal structure and mutational analysis of a perlecan-binding fragment of nidogen-1. Nat Struct Biol, 8, 634-640. PubMed id: 11427896 DOI: 10.1038/89683

Date:

14-May-01 Release date: 28-Jun-01

Protein chain

P10493  (NID1_MOUSE) -  Nidogen-1 from Mus musculus

Seq: 1245 a.a.

Struc: 245 a.a.

DOI no: 10.1038/89683

Nat Struct Biol 8:634-640 (2001)

PubMed id: 11427896

Crystal structure and mutational analysis of a perlecan-binding fragment of nidogen-1.

M.Hopf, W.Göhring, A.Ries, R.Timpl, E.Hohenester.

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.

Selected figure(s)

Figure 1.
Figure 1. The nidogen G2 structure. a, Stereo view of the structure with the EGF-like domain in green and the -barrel domain in cyan. -strands are labeled a -b in the EGF-like domain and A -K in the -barrel domain. The -helices 1 -3 are in red and disulfide bridges in yellow. To facilitate the tracing of the polypeptide chain disordered segments (residues 357 -366, 374 -380, 565 -570 and 588 -595) have been included in arbitrary but stereochemically sensible conformations and are shown in light gray. b, Topology diagram of the -barrel domain. The barrel is closed by the parallel interaction of strands A and F. c, Stereo view of a portion of the experimental electron density map after solvent flattening at 2.8 Å resolution. The final model is superimposed on the map. Shown are -strands D, E and F. Figs 1a,c, 2 and 4 were made with BOBSCRIPT35 and RASTER3D^36.

Figure 2.
Figure 2. Comparison of the -barrels of nidogen G2 and Aequora victoria GFP22. Nidogen G2 is in magenta and GFP in green. A total of 195 C atoms were superimposed with an r.m.s. deviation of 2.5 Å. In the nidogen G2 trace every 20^th C atom is shown as a small, labeled sphere. The chromophore in GFP is shown as a ball-and-stick model.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 634-640) copyright 2001.

Figures were selected by an automated process.