PDBsum entry 1rmr

Protein binding

PDB id: 1rmr

Contents

Protein chain

64 a.a. *

Waters ×22

* Residue conservation analysis

PDB id:

1rmr

Name:

Protein binding

Title:

Crystal structure of schistatin, a disintegrin homodimer from saw- scaled viper (echis carinatus) at 2.5 a resolution

Structure:

Disintegrin schistatin. Chain: a

Source:

Echis carinatus. Saw-scaled viper. Organism_taxid: 40353. Secretion: venom

Biol. unit:

Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.192 R-free: 0.230

Authors:

S.Bilgrami,S.Tomar,S.Yadav,P.Kaur,J.Kumar,T.Jabeen,S.Sharma,T.P.Singh

Key ref:

S.Bilgrami et al. (2004). Crystal structure of schistatin, a disintegrin homodimer from saw-scaled viper (Echis carinatus) at 2.5 A resolution. J Mol Biol, 341, 829-837. PubMed id: 15317139 DOI: 10.1016/j.jmb.2004.06.048

Date:

28-Nov-03 Release date: 16-Jun-04

Protein chain

P83658  (DIDS_ECHCA) -  Disintegrin schistatin from Echis carinatus

Seq: 64 a.a.

Struc: 64 a.a.

DOI no: 10.1016/j.jmb.2004.06.048

J Mol Biol 341:829-837 (2004)

PubMed id: 15317139

Crystal structure of schistatin, a disintegrin homodimer from saw-scaled viper (Echis carinatus) at 2.5 A resolution.

S.Bilgrami, S.Tomar, S.Yadav, P.Kaur, J.Kumar, T.Jabeen, S.Sharma, T.P.Singh.

ABSTRACT

This is the first structure of a biological homodimer of disintegrin. Disintegrins are a class of small (4-14 kDa) proteins that bind to transmembrane integrins selectively. The present molecule is the first homodimer that has been isolated from the venom of Echis carinatus. The monomeric chain contains 64 amino acid residues. The three-dimensional structure of schistatin has been determined by the multiple isomorphous replacement method. It has been refined to an R-factor of 0.190 using all the data to 2.5 A resolution. The two subunits of the disintegrin homodimer are related by a 2-fold crystallographic symmetry. Thus, the crystallographic asymmetric unit contains a monomer of disintegrin. The monomer folds into an up-down topology with three sets of antiparallel beta-strands. The structure is well ordered with four intramolecular disulfide bonds. the two monomers are firmly linked to each other through two intermolecular disulfide bridges at their N termini together with several other interactions. This structure has corrected the error in the disulfide bond pattern of the two intermolecular disulfide bridges that was reported earlier using chemical methods. Unique sequence and structural features of the schistatin monomers suggest that they have the ability to bind well with both alphaIIb beta3 and alphav beta3 integrins. The N termini anchored two chains of the dimer diverge away at their C termini exposing the Arg-Gly-Asp motif into opposite directions thus enhancing their binding efficiency to integrins. This is one of the unique features of the present disintegrin homodimer and seems to be responsible for the clustering of integrin molecules. The homodimer binds to integrins apparently with a higher affinity than the monomers and also plays a role in the signaling pathway.

Selected figure(s)

Figure 2.
Figure 2. (a) The electron density (2F[o] -F[c]) of a representative region in the structure. (b) The electron density (2F[o] -F[c]) of the Arg-Gly-Asp loop.

Figure 4.
Figure 4. The arrangement of the Arg-Gly-Asp loop and the C-terminal fragment and the interactions between them.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 341, 829-837) copyright 2004.

Figures were selected by an automated process.