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PDBsum entry 1rmr

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protein links
Protein binding PDB id
1rmr
Jmol
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P83658  (DISS_ECHCA) -  Disintegrin schistatin
Seq:
Struc:
64 a.a.
64 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 

 

 
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19495561 R.Doley, and R.M.Kini (2009).
Protein complexes in snake venom.
  Cell Mol Life Sci, 66, 2851-2871.  
18381281 A.V.Osipov, I.E.Kasheverov, Y.V.Makarova, V.G.Starkov, O.V.Vorontsova, R.K.h.Ziganshin, T.V.Andreeva, M.V.Serebryakova, A.Benoit, R.C.Hogg, D.Bertrand, V.I.Tsetlin, and Y.N.Utkin (2008).
Naturally occurring disulfide-bound dimers of three-fingered toxins: a paradigm for biological activity diversification.
  J Biol Chem, 283, 14571-14580.  
18391413 N.Moiseeva, R.Bau, S.D.Swenson, F.S.Markland, J.Y.Choe, Z.J.Liu, and M.Allaire (2008).
Structure of acostatin, a dimeric disintegrin from Southern copperhead (Agkistrodon contortrix contortrix), at 1.7 A resolution.
  Acta Crystallogr D Biol Crystallogr, 64, 466-470.
PDB code: 3c05
17177090 A.Bazaa, P.Juárez, N.Marrakchi, Z.Bel Lasfer, M.El Ayeb, R.A.Harrison, J.J.Calvete, and L.Sanz (2007).
Loss of introns along the evolutionary diversification pathway of snake venom disintegrins evidenced by sequence analysis of genomic DNA from Macrovipera lebetina transmediterranea and Echis ocellatus.
  J Mol Evol, 64, 261-271.  
16786436 P.Juárez, S.C.Wagstaff, J.Oliver, L.Sanz, R.A.Harrison, and J.J.Calvete (2006).
Molecular cloning of disintegrin-like transcript BA-5A from a Bitis arietans venom gland cDNA library: a putative intermediate in the evolution of the long-chain disintegrin bitistatin.
  J Mol Evol, 63, 142-152.  
16830094 P.Juárez, S.C.Wagstaff, L.Sanz, R.A.Harrison, and J.J.Calvete (2006).
Molecular cloning of Echis ocellatus disintegrins reveals non-venom-secreted proteins and a pathway for the evolution of ocellatusin.
  J Mol Evol, 63, 183-193.  
16215260 L.Sanz, R.Q.Chen, A.Pérez, R.Hilario, P.Juárez, C.Marcinkiewicz, D.Monleón, B.Celda, Y.L.Xiong, E.Pérez-Payá, and J.J.Calvete (2005).
cDNA cloning and functional expression of jerdostatin, a novel RTS-disintegrin from Trimeresurus jerdonii and a specific antagonist of the alpha1beta1 integrin.
  J Biol Chem, 280, 40714-40722.  
16102046 Q.Lu, J.M.Clemetson, and K.J.Clemetson (2005).
Snake venoms and hemostasis.
  J Thromb Haemost, 3, 1791-1799.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.