2w9u

From Proteopedia

(Difference between revisions)

Current revision

Solution structure of jerdostatin mutant R24K from Trimeresurus jerdonii

Structural highlights

2w9u is a 1 chain structure with sequence from Protobothrops jerdonii. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR, 42 models
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DIS_PROJR Recombinant protein inhibits the adhesion of alpha-1/beta-1-K562 (ITGA1/ITGB1) cells to collagen IV with an IC(50) of 80 nM.^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

NMR analysis of four recombinant jerdostatin molecules was assessed to define the structural basis of two naturally occurring gain-of-function events: C-terminal dipeptide processing and mutation of the active residue K21 to arginine. Removal of the highly mobile and a bulky C-terminal dipeptide produced pronounced chemical shift changes in the sequentially unconnected but spatially nearby alpha(1)beta(1) inhibitory loop. Analysis of chemical shift divergence and (15)N backbone relaxation dynamics indicated differences in motions in the picosecond to nanosecond time scale, and the higher T(2) rate of S25, S26, and H27 of rJerK21 point to a slowdown in the microsecond to millisecond motions of these residues when compared with rJerR21. The evidence presented in this article converges on the hypothesis that dynamic differences between the alpha(1)beta(1) recognition loops of rJerR21 and rJerK21 may influence the thermodynamics of their receptor recognition and binding. A decrease in the mus-ms time scale may impair the binding affinity by reducing the rate of possible conformations that the rJerK21 can adopt in this time scale.

NMR structure and dynamics of recombinant wild type and mutated jerdostatin, a selective inhibitor of integrin alpha1beta1.,Carbajo RJ, Sanz L, Mosulen S, Perez A, Marcinkiewicz C, Pineda-Lucena A, Calvete JJ Proteins. 2011 Aug;79(8):2530-42. doi: 10.1002/prot.23076. Epub 2011 Jun, 7. PMID:21656569^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sanz L, Chen RQ, Pérez A, Hilario R, Juárez P, Marcinkiewicz C, Monleón D, Celda B, Xiong YL, Pérez-Payá E, Calvete JJ. 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. 2005 Dec 9;280(49):40714-22. PMID:16215260 doi:10.1074/jbc.M509738200
↑ Carbajo RJ, Sanz L, Mosulen S, Perez A, Marcinkiewicz C, Pineda-Lucena A, Calvete JJ. NMR structure and dynamics of recombinant wild type and mutated jerdostatin, a selective inhibitor of integrin alpha1beta1. Proteins. 2011 Aug;79(8):2530-42. doi: 10.1002/prot.23076. Epub 2011 Jun, 7. PMID:21656569 doi:10.1002/prot.23076
↑ Carbajo RJ, Sanz L, Mosulen S, Perez A, Marcinkiewicz C, Pineda-Lucena A, Calvete JJ. NMR structure and dynamics of recombinant wild type and mutated jerdostatin, a selective inhibitor of integrin alpha1beta1. Proteins. 2011 Aug;79(8):2530-42. doi: 10.1002/prot.23076. Epub 2011 Jun, 7. PMID:21656569 doi:10.1002/prot.23076

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2w9u"

@@ Line 1: / Line 1: @@
 ==Solution structure of jerdostatin mutant R24K from Trimeresurus jerdonii==
-<StructureSection load='2w9u' size='340' side='right'caption='[[2w9u]], [[NMR_Ensembles_of_Models | 42 NMR models]]' scene=''>
+<StructureSection load='2w9u' size='340' side='right'caption='[[2w9u]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2w9u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W9U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2w9u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Protobothrops_jerdonii Protobothrops jerdonii]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W9U FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2w9o|2w9o]], [[2w9v|2w9v]], [[2w9w|2w9w]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 42 models</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2w9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w9u OCA], [https://pdbe.org/2w9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w9u RCSB], [https://www.ebi.ac.uk/pdbsum/2w9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w9u ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DIS_PROJR DIS_PROJR] Recombinant protein inhibits the adhesion of alpha-1/beta-1-K562 (ITGA1/ITGB1) cells to collagen IV with an IC(50) of 80 nM.<ref>PMID:16215260</ref> <ref>PMID:21656569</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 12: / Line 14: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w9/2w9u_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 34: / Line 36: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Calvete, J J]]
+[[Category: Protobothrops jerdonii]]
-[[Category: Carbajo, R J]]
+[[Category: Calvete JJ]]
-[[Category: Mosulen, S]]
+[[Category: Carbajo RJ]]
-[[Category: Pineda-Lucena, A]]
+[[Category: Mosulen S]]
-[[Category: Sanz, L]]
+[[Category: Pineda-Lucena A]]
-[[Category: Blood coagulation]]
+[[Category: Sanz L]]
-[[Category: Cell adhesion]]
-[[Category: Toxin]]
-[[Category: Venom]]

2w9u

From Proteopedia

Current revision

Solution structure of jerdostatin mutant R24K from Trimeresurus jerdonii

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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