5pal: Difference between revisions

Line 3:

== Structural highlights ==

<table><tr><td colspan='2'>[[5pal]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Leopard_shark Leopard shark~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PAL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5PAL FirstGlance]. <br>

<table><tr><td colspan='2'>[[5pal]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Triakis_semifasciata Triakis semifasciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PAL FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.54Å</td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5pal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pal OCA], [~~http~~://pdbe.org/5pal PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5pal RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5pal PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5pal ProSAT]</span></td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=5pal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pal OCA], [https://pdbe.org/5pal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pal RCSB], [https://www.ebi.ac.uk/pdbsum/5pal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pal ProSAT]</span></td></tr>

</table>

== Function ==

[~~[http~~://www.uniprot.org/uniprot/PRVA_TRISE PRVA_TRISE]] In muscle, parvalbumin is thought to be involved in relaxation after contraction. It binds two calcium ions.

[https://www.uniprot.org/uniprot/PRVA_TRISE PRVA_TRISE] In muscle, parvalbumin is thought to be involved in relaxation after contraction. It binds two calcium ions.

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Line 19:

Line 20:

</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=5pal ConSurf].

~~<div style="background-color:#fffaf0;">~~

~~== Publication Abstract from PubMed ==~~

The three-dimensional structure of parvalbumin from leopard shark (Triakis semifasciata) with 109 amino acid residues (alpha-series) is described at 1.54 A resolution. Crystals were grown at 20 degrees C from 2.9 M-potassium/sodium phosphate solutions at pH 5.6. The space group is P3(1)21 and unit cell dimensions are a = b = 32.12 A and c = 149.0 A. The structure has been solved by the molecular replacement method using pike 4.10 parvalbumin as a model. The final structure refinement resulted in an R-factor of 17.3% for 11,363 independent reflections at 1.54 A resolution. The shark parvalbumin shows the main features of all parvalbumins: the folding of the chain including six alpha-helices, the salt bridge between Arg75 and Glu81, and the hydrophobic core. Compared to the structure of beta-parvalbumins from pike and carp, one main difference is observed: the chain is one residue longer and this additional residue, which extends the F helix, is involved through its C-terminal carboxylate group in a network of electrostatic contacts with two basic residues, His31 in the B helix and Lys36 in the BC segment. Furthermore, hydrogen bonds exist between the side-chains of Gln108 (F helix) and Tyr26 (B helix). There is therefore a "locking" of the tertiary structure through contacts between two sequentially distant regions in the protein and this is likely to contribute to making the stability of an alpha-parvalbumin higher in comparison to that of a beta-parvalbumin. The lengthening of the C-terminal F helix by one residue appears to be a major feature of alpha-parvalbumins in general, owing to the homologies of the amino acid sequences. Besides the lengthening of the C-terminal helix, the classification of the leopard shark parvalbumin in the alpha-series rests upon the observation of Lys13, Leu32, Glu61 and Val66. As this is the first crystal structure description of a parvalbumin from the alpha-phylogenetic lineage, it was hoped that it would clearly determine the presence or absence of a third cation binding site in parvalbumins belonging to the alpha-lineage. In beta-pike pI 4.10 parvalbumin, Asp61 participates as a direct ligand of a third site, the satellite of the CD site. In shark parvalbumin, as in nearly all alpha-parvalbumins, one finds Glu at position 61. Unfortunately, the conformation of the polar head of Glu61 cannot be inferred from the X-ray data.(ABSTRACT TRUNCATED AT 400 WORDS)

Crystal structure of the unique parvalbumin component from muscle of the leopard shark (Triakis semifasciata). The first X-ray study of an alpha-parvalbumin.,Roquet F, Declercq JP, Tinant B, Rambaud J, Parello J J Mol Biol. 1992 Feb 5;223(3):705-20. PMID:1542115<ref>PMID:1542115</ref>

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

~~</div>~~

~~<div class="pdbe-citations 5pal" style="background-color:#fffaf0;"></div>~~

==See Also==

*[[Parvalbumin|Parvalbumin]]

~~== References ==~~

~~<references/>~~

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: ~~Leopard shark~~]]

[[Category: Triakis semifasciata]]

[[Category: Declercq, J P]]

[[Category: Declercq J-P]]

[[Category: Parello, J]]

[[Category: Parello J]]

[[Category: Rambaud, J]]

[[Category: Rambaud J]]

[[Category: Roquet, F]]

[[Category: Roquet F]]

[[Category: Tinant, B]]

[[Category: Tinant B]]

~~[[Category: Calcium-binding protein~~]]

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 3: / Line 3: @@
 <StructureSection load='5pal' size='340' side='right'caption='[[5pal]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5pal]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Leopard_shark Leopard shark]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PAL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5PAL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5pal]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Triakis_semifasciata Triakis semifasciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PAL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.54&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5pal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pal OCA], [http://pdbe.org/5pal PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pal RCSB], [http://www.ebi.ac.uk/pdbsum/5pal PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pal ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=5pal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pal OCA], [https://pdbe.org/5pal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pal RCSB], [https://www.ebi.ac.uk/pdbsum/5pal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pal ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PRVA_TRISE PRVA_TRISE]] In muscle, parvalbumin is thought to be involved in relaxation after contraction. It binds two calcium ions.
+[https://www.uniprot.org/uniprot/PRVA_TRISE PRVA_TRISE] In muscle, parvalbumin is thought to be involved in relaxation after contraction. It binds two calcium ions.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 19: / Line 20: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=5pal ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The three-dimensional structure of parvalbumin from leopard shark (Triakis semifasciata) with 109 amino acid residues (alpha-series) is described at 1.54 A resolution. Crystals were grown at 20 degrees C from 2.9 M-potassium/sodium phosphate solutions at pH 5.6. The space group is P3(1)21 and unit cell dimensions are a = b = 32.12 A and c = 149.0 A. The structure has been solved by the molecular replacement method using pike 4.10 parvalbumin as a model. The final structure refinement resulted in an R-factor of 17.3% for 11,363 independent reflections at 1.54 A resolution. The shark parvalbumin shows the main features of all parvalbumins: the folding of the chain including six alpha-helices, the salt bridge between Arg75 and Glu81, and the hydrophobic core. Compared to the structure of beta-parvalbumins from pike and carp, one main difference is observed: the chain is one residue longer and this additional residue, which extends the F helix, is involved through its C-terminal carboxylate group in a network of electrostatic contacts with two basic residues, His31 in the B helix and Lys36 in the BC segment. Furthermore, hydrogen bonds exist between the side-chains of Gln108 (F helix) and Tyr26 (B helix). There is therefore a "locking" of the tertiary structure through contacts between two sequentially distant regions in the protein and this is likely to contribute to making the stability of an alpha-parvalbumin higher in comparison to that of a beta-parvalbumin. The lengthening of the C-terminal F helix by one residue appears to be a major feature of alpha-parvalbumins in general, owing to the homologies of the amino acid sequences. Besides the lengthening of the C-terminal helix, the classification of the leopard shark parvalbumin in the alpha-series rests upon the observation of Lys13, Leu32, Glu61 and Val66. As this is the first crystal structure description of a parvalbumin from the alpha-phylogenetic lineage, it was hoped that it would clearly determine the presence or absence of a third cation binding site in parvalbumins belonging to the alpha-lineage. In beta-pike pI 4.10 parvalbumin, Asp61 participates as a direct ligand of a third site, the satellite of the CD site. In shark parvalbumin, as in nearly all alpha-parvalbumins, one finds Glu at position 61. Unfortunately, the conformation of the polar head of Glu61 cannot be inferred from the X-ray data.(ABSTRACT TRUNCATED AT 400 WORDS)
-Crystal structure of the unique parvalbumin component from muscle of the leopard shark (Triakis semifasciata). The first X-ray study of an alpha-parvalbumin.,Roquet F, Declercq JP, Tinant B, Rambaud J, Parello J J Mol Biol. 1992 Feb 5;223(3):705-20. PMID:1542115<ref>PMID:1542115</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5pal" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Parvalbumin|Parvalbumin]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Leopard shark]]
+[[Category: Triakis semifasciata]]
-[[Category: Declercq, J P]]
+[[Category: Declercq J-P]]
-[[Category: Parello, J]]
+[[Category: Parello J]]
-[[Category: Rambaud, J]]
+[[Category: Rambaud J]]
-[[Category: Roquet, F]]
+[[Category: Roquet F]]
-[[Category: Tinant, B]]
+[[Category: Tinant B]]
-[[Category: Calcium-binding protein]]