2c9j: Difference between revisions
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==Structure of the fluorescent protein cmFP512 at 1.35A from Cerianthus membranaceus== | |||
<StructureSection load='2c9j' size='340' side='right' caption='[[2c9j]], [[Resolution|resolution]] 1.35Å' scene=''> | <StructureSection load='2c9j' size='340' side='right' caption='[[2c9j]], [[Resolution|resolution]] 1.35Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
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</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> | </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">[[1b9c|1b9c]], [[1bfp|1bfp]], [[1c4f|1c4f]], [[1ema|1ema]], [[1emb|1emb]], [[1emc|1emc]], [[1eme|1eme]], [[1emf|1emf]], [[1emg|1emg]], [[1emk|1emk]], [[1eml|1eml]], [[1emm|1emm]], [[1f09|1f09]], [[1f0b|1f0b]], [[1g7k|1g7k]], [[1gfl|1gfl]], [[1ggx|1ggx]], [[1h6r|1h6r]], [[1hcj|1hcj]], [[1huy|1huy]], [[1jby|1jby]], [[1jbz|1jbz]], [[1jc0|1jc0]], [[1jc1|1jc1]], [[1kp5|1kp5]], [[1kyp|1kyp]], [[1kyr|1kyr]], [[1kys|1kys]], [[1myw|1myw]], [[1oxd|1oxd]], [[1oxe|1oxe]], [[1oxf|1oxf]], [[1q4a|1q4a]], [[1q4b|1q4b]], [[1q4c|1q4c]], [[1q4d|1q4d]], [[1q4e|1q4e]], [[1q73|1q73]], [[1qxt|1qxt]], [[1qy3|1qy3]], [[1qyf|1qyf]], [[1rm9|1rm9]], [[1rmm|1rmm]], [[1rmo|1rmo]], [[1rmp|1rmp]], [[1rrx|1rrx]], [[1s6z|1s6z]], [[1w7s|1w7s]], [[1w7t|1w7t]], [[1w7u|1w7u]], [[1xa9|1xa9]], [[1xae|1xae]], [[1xss|1xss]], [[1yjf|1yjf]], [[1z1p|1z1p]], [[1z1q|1z1q]], [[1zgo|1zgo]], [[1zgp|1zgp]], [[1zgq|1zgq]], [[1zux|1zux]], [[2a46|2a46]], [[2a50|2a50]], [[2a52|2a52]], [[2a53|2a53]], [[2a54|2a54]], [[2a56|2a56]], [[2b3p|2b3p]], [[2b3q|2b3q]], [[2btj|2btj]], [[2emd|2emd]], [[2emn|2emn]], [[2emo|2emo]], [[2c9i|2c9i]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1b9c|1b9c]], [[1bfp|1bfp]], [[1c4f|1c4f]], [[1ema|1ema]], [[1emb|1emb]], [[1emc|1emc]], [[1eme|1eme]], [[1emf|1emf]], [[1emg|1emg]], [[1emk|1emk]], [[1eml|1eml]], [[1emm|1emm]], [[1f09|1f09]], [[1f0b|1f0b]], [[1g7k|1g7k]], [[1gfl|1gfl]], [[1ggx|1ggx]], [[1h6r|1h6r]], [[1hcj|1hcj]], [[1huy|1huy]], [[1jby|1jby]], [[1jbz|1jbz]], [[1jc0|1jc0]], [[1jc1|1jc1]], [[1kp5|1kp5]], [[1kyp|1kyp]], [[1kyr|1kyr]], [[1kys|1kys]], [[1myw|1myw]], [[1oxd|1oxd]], [[1oxe|1oxe]], [[1oxf|1oxf]], [[1q4a|1q4a]], [[1q4b|1q4b]], [[1q4c|1q4c]], [[1q4d|1q4d]], [[1q4e|1q4e]], [[1q73|1q73]], [[1qxt|1qxt]], [[1qy3|1qy3]], [[1qyf|1qyf]], [[1rm9|1rm9]], [[1rmm|1rmm]], [[1rmo|1rmo]], [[1rmp|1rmp]], [[1rrx|1rrx]], [[1s6z|1s6z]], [[1w7s|1w7s]], [[1w7t|1w7t]], [[1w7u|1w7u]], [[1xa9|1xa9]], [[1xae|1xae]], [[1xss|1xss]], [[1yjf|1yjf]], [[1z1p|1z1p]], [[1z1q|1z1q]], [[1zgo|1zgo]], [[1zgp|1zgp]], [[1zgq|1zgq]], [[1zux|1zux]], [[2a46|2a46]], [[2a50|2a50]], [[2a52|2a52]], [[2a53|2a53]], [[2a54|2a54]], [[2a56|2a56]], [[2b3p|2b3p]], [[2b3q|2b3q]], [[2btj|2btj]], [[2emd|2emd]], [[2emn|2emn]], [[2emo|2emo]], [[2c9i|2c9i]]</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=2c9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9j OCA], [http://pdbe.org/2c9j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c9j RCSB], [http://www.ebi.ac.uk/pdbsum/2c9j 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=2c9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9j OCA], [http://pdbe.org/2c9j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c9j RCSB], [http://www.ebi.ac.uk/pdbsum/2c9j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2c9j ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c9/2c9j_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c9/2c9j_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<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/ | </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=2c9j ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
Revision as of 11:37, 23 May 2018
Structure of the fluorescent protein cmFP512 at 1.35A from Cerianthus membranaceusStructure of the fluorescent protein cmFP512 at 1.35A from Cerianthus membranaceus
Structural highlights
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 PubMedAutofluorescent proteins of the GFP family all share the same three-dimensional beta-can fold; yet they exhibit widely different optical properties, arising either from chemical modification of the chromophore itself or from specific interactions of the chromophore with the surrounding protein moiety. Here we present a structural and spectroscopic characterization of the green fluorescent protein cmFP512 from Cerianthus membranaceus, a nonbioluminescent, azooxanthellate cnidarian, which has only approximately 22% sequence identity with Aequorea victoria GFP. The X-ray structure, obtained by molecular replacement at a resolution of 1. 35 A, shows the chromophore, formed from the tripeptide Gln-Tyr-Gly, in a hydrogen-bonded cage in the center of an 11-stranded beta-barrel, tightly restrained by adjacent residues and structural water molecules. It exists in a neutral (A) and an anionic (B) species, with absorption/emission maxima at 392/460 (pH 5) and 503/512 nm (pH 7). Their fractional populations and peak positions depend sensitively on pH, reflecting protonation of groups adjacent to the chromophore. The pH dependence of the spectra is explained by a protonation mechanism involving a hydrogen-bonded cluster of charged/polar groups. Cryospectroscopy at 12 K was also performed to analyze the vibronic coupling of the electronic transitions. Exploring chromophore--protein interactions in fluorescent protein cmFP512 from Cerianthus membranaceus: X-ray structure analysis and optical spectroscopy.,Nienhaus K, Renzi F, Vallone B, Wiedenmann J, Nienhaus GU Biochemistry. 2006 Oct 31;45(43):12942-53. PMID:17059211[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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