1hdf: Difference between revisions

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<StructureSection load='1hdf' size='340' side='right'caption='[[1hdf]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
<StructureSection load='1hdf' size='340' side='right'caption='[[1hdf]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1hdf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phypo Phypo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HDF FirstGlance]. <br>
<table><tr><td colspan='2'>[[1hdf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HDF 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]] 2.35&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ag4|1ag4]]</div></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=1hdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hdf OCA], [https://pdbe.org/1hdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hdf RCSB], [https://www.ebi.ac.uk/pdbsum/1hdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hdf ProSAT]</span></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=1hdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hdf OCA], [https://pdbe.org/1hdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hdf RCSB], [https://www.ebi.ac.uk/pdbsum/1hdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hdf ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/SR3A_PHYPO SR3A_PHYPO]] Structural protein.  
[https://www.uniprot.org/uniprot/SR3A_PHYPO SR3A_PHYPO] Structural protein.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1hdf ConSurf].
</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=1hdf ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: The betagamma-crystallins belong to a superfamily of two-domain proteins found in vertebrate eye lenses, with distant relatives occurring in microorganisms. It has been considered that an eukaryotic stress protein, spherulin 3a, from the slime mold Physarum polycephalum shares a common one-domain ancestor with crystallins, similar to the one-domain 3-D structure determined by NMR. RESULTS: The X-ray structure of spherulin 3a shows it to be a tight homodimer, which is consistent with ultracentrifugation studies. The (two-motif) domain fold contains a pair of calcium binding sites very similar to those found in a two-domain prokaryotic betagamma-crystallin fold family member, Protein S. Domain pairing in the spherulin 3a dimer is two-fold symmetric, but quite different in character from the pseudo-two-fold pairing of domains in betagamma-crystallins. There is no evidence that the spherulin 3a single domain can fold independently of its partner domain, a feature that may be related to the absence of a tyrosine corner. CONCLUSION: Although it is accepted that the vertebrate two-domain betagamma-crystallins evolved from a common one-domain ancestor, the mycetezoan single-domain spherulin 3a, with its unique mode of domain pairing, is likely to be an evolutionary offshoot, perhaps from as far back as the one-motif ancestral stage. The spherulin 3a protomer stability appears to be dependent on domain pairing. Spherulin-like domain sequences that are found within bacterial proteins associated with virulence are likely to bind calcium.
Crystal structure of the calcium-loaded spherulin 3a dimer sheds light on the evolution of the eye lens betagamma-crystallin domain fold.,Clout NJ, Kretschmar M, Jaenicke R, Slingsby C Structure. 2001 Feb 7;9(2):115-24. PMID:11250196<ref>PMID:11250196</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1hdf" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Phypo]]
[[Category: Physarum polycephalum]]
[[Category: Clout, N J]]
[[Category: Clout NJ]]
[[Category: Jaenicke, R]]
[[Category: Jaenicke R]]
[[Category: Kretschmar, M]]
[[Category: Kretschmar M]]
[[Category: Slingsby, C]]
[[Category: Slingsby C]]
[[Category: Crystallin]]
[[Category: Domain interaction]]
[[Category: Eye lens]]
[[Category: Spherulin 3a]]
[[Category: Structural protein]]
[[Category: Tyrosine corner]]

Revision as of 14:30, 27 March 2024

Evolution of the eye lens beta-gamma-crystallin domain foldEvolution of the eye lens beta-gamma-crystallin domain fold

Structural highlights

1hdf is a 2 chain structure with sequence from Physarum polycephalum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.35Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SR3A_PHYPO Structural protein.

Evolutionary Conservation

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

1hdf, resolution 2.35Å

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OCA
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