2vad: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
No edit summary
No edit summary
Line 1: Line 1:
==MONOMERIC RED FLUORESCENT PROTEIN, DSRED.M1==
==MONOMERIC RED FLUORESCENT PROTEIN, DSRED.M1==
<StructureSection load='2vad' size='340' side='right' caption='[[2vad]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
<StructureSection load='2vad' size='340' side='right' caption='[[2vad]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2vad]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Discosoma_sp. Discosoma sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VAD FirstGlance]. <br>
<table><tr><td colspan='2'>[[2vad]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dissp Dissp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VAD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRQ:[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC+ACID'>CRQ</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRQ:[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC+ACID'>CRQ</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vae|2vae]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vae|2vae]]</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vad OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vad RCSB], [http://www.ebi.ac.uk/pdbsum/2vad PDBsum]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vad OCA], [http://pdbe.org/2vad PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vad RCSB], [http://www.ebi.ac.uk/pdbsum/2vad PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vad ProSAT]</span></td></tr>
</table>
</table>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
Line 16: Line 17:
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</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/chain_selection.php?pdb_ID=2ata 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=2vad ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
Line 26: Line 27:
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 2vad" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
Line 33: Line 35:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Discosoma sp]]
[[Category: Dissp]]
[[Category: Bevis, B]]
[[Category: Bevis, B]]
[[Category: Downing, M E]]
[[Category: Downing, M E]]

Revision as of 16:52, 11 August 2016

MONOMERIC RED FLUORESCENT PROTEIN, DSRED.M1MONOMERIC RED FLUORESCENT PROTEIN, DSRED.M1

Structural highlights

2vad is a 1 chain structure with sequence from Dissp. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, ,
NonStd Res:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

The red fluorescent protein DsRed has been extensively engineered for use as an in vivo research tool. In fast maturing DsRed variants, the chromophore maturation half-time is approximately 40 min, compared to approximately 12 h for wild-type DsRed. Further, DsRed has been converted from a tetramer into a monomer, a task that entailed mutating approximately 20% of the amino acids. These engineered variants of DsRed have proven extremely valuable for biomedical research, but the structural basis for the improved characteristics has not been thoroughly investigated. Here we present a 1.7 A crystal structure of the fast maturing tetrameric variant DsRed.T4. We also present a biochemical characterization and 1.6 A crystal structure of the monomeric variant DsRed.M1, also known as DsRed-Monomer. Analysis of the crystal structures suggests that rearrangements of Ser69 and Glu215 contribute to fast maturation, and that positioning of the Lys70 side chain modulates fluorescence quantum yield. Despite the 45 mutations in DsRed.M1 relative to wild-type DsRed, there is a root-mean-square deviation of only 0.3 A between the two structures. We propose that novel intramolecular interactions in DsRed.M1 partially compensate for the loss of intermolecular interactions found in the tetramer.

Structural rearrangements near the chromophore influence the maturation speed and brightness of DsRed variants.,Strongin DE, Bevis B, Khuong N, Downing ME, Strack RL, Sundaram K, Glick BS, Keenan RJ Protein Eng Des Sel. 2007 Nov;20(11):525-34. Epub 2007 Oct 25. PMID:17962222[1]

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

See Also

References

  1. Strongin DE, Bevis B, Khuong N, Downing ME, Strack RL, Sundaram K, Glick BS, Keenan RJ. Structural rearrangements near the chromophore influence the maturation speed and brightness of DsRed variants. Protein Eng Des Sel. 2007 Nov;20(11):525-34. Epub 2007 Oct 25. PMID:17962222 doi:10.1093/protein/gzm046

2vad, resolution 1.59Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA