6h01: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 6h01 is ~~ON HOLD~~

==Crystal structure of a domain-swapped dark-state sfGFP containing the unnatural amino acid ortho-nitrobenzyl-tyrosine (ONBY) at residue 66==

== Structural highlights ==

<table><tr><td colspan='2'>[[6h01]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6H01 FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.776Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FHE:2-[(4~{Z})-2-[(1~{R})-1-azanyl-2-oxidanylidene-propyl]-4-[[4-[(2-nitrophenyl)methoxy]phenyl]methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic+acid'>FHE</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=6h01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h01 OCA], [https://pdbe.org/6h01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6h01 RCSB], [https://www.ebi.ac.uk/pdbsum/6h01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6h01 ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/A0A059PIQ0_AEQVI A0A059PIQ0_AEQVI]

== Publication Abstract from PubMed ==

Photoactivatable fluorescent proteins (PA-FPs) are a powerful non-invasive tool in high-resolution live-cell imaging. They can be converted from an inactive to an active form by light, enabling the spatial and temporal trafficking of proteins and cell dynamics. PA-FPs have been previously generated by mutating selected residues in the chromophore or in its close proximity. A new strategy to generate PA-FPs is the genetic incorporation of unnatural amino acids (UAAs) containing photocaged groups using unique suppressor tRNA/aminoacyl-tRNA synthetase pairs. We set out to develop a photoactivatable GFP variant suitable for time-resolved structural studies. Here, we report the crystal structure of superfolder GFP (sfGFP) containing the UAA ortho-nitrobenzyl-tyrosine (ONBY) at position 66 and its spectroscopic characterization. Surprisingly, the crystal structure (to 2.7 A resolution) reveals a dimeric domain-swapped arrangement of sfGFP66ONBY with residues 1-142 of one molecule associating with residues 148-234 from another molecule. This unusual domain-swapped structure supports a previously postulated GFP folding pathway that proceeds via an equilibrium intermediate.

~~Authors:~~ Kesgin-Schaefer, S., Tidow, H.

Crystal structure of a domain-swapped photoactivatable sfGFP variant provides evidence for GFP folding pathway.,Kesgin-Schaefer S, Heidemann J, Puchert A, Koelbel K, Yorke BA, Huse N, Pearson AR, Uetrecht C, Tidow H FEBS J. 2019 Feb 28. doi: 10.1111/febs.14797. PMID:30817081<ref>PMID:30817081</ref>

~~Description: Crystal structure~~ of ~~a domain-swapped dark-state sfGFP containing~~ the ~~unnatural amino acid ortho~~-~~nitrobenzyl~~-~~tyrosine (ONBY) at residue 66~~

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

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: Kesgin-Schaefer, S]]

[[Category: Tidow, H]]

==See Also==

*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]

== References ==

__TOC__

</StructureSection>

[[Category: Aequorea victoria]]

[[Category: Large Structures]]

[[Category: Kesgin-Schaefer S]]

[[Category: Tidow H]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6h01 is ON HOLD
+==Crystal structure of a domain-swapped dark-state sfGFP containing the unnatural amino acid ortho-nitrobenzyl-tyrosine (ONBY) at residue 66==
+<StructureSection load='6h01' size='340' side='right'caption='[[6h01]], [[Resolution|resolution]] 2.78&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6h01]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6H01 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.776&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FHE:2-[(4~{Z})-2-[(1~{R})-1-azanyl-2-oxidanylidene-propyl]-4-[[4-[(2-nitrophenyl)methoxy]phenyl]methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic+acid'>FHE</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=6h01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h01 OCA], [https://pdbe.org/6h01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6h01 RCSB], [https://www.ebi.ac.uk/pdbsum/6h01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6h01 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A059PIQ0_AEQVI A0A059PIQ0_AEQVI]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Photoactivatable fluorescent proteins (PA-FPs) are a powerful non-invasive tool in high-resolution live-cell imaging. They can be converted from an inactive to an active form by light, enabling the spatial and temporal trafficking of proteins and cell dynamics. PA-FPs have been previously generated by mutating selected residues in the chromophore or in its close proximity. A new strategy to generate PA-FPs is the genetic incorporation of unnatural amino acids (UAAs) containing photocaged groups using unique suppressor tRNA/aminoacyl-tRNA synthetase pairs. We set out to develop a photoactivatable GFP variant suitable for time-resolved structural studies. Here, we report the crystal structure of superfolder GFP (sfGFP) containing the UAA ortho-nitrobenzyl-tyrosine (ONBY) at position 66 and its spectroscopic characterization. Surprisingly, the crystal structure (to 2.7 A resolution) reveals a dimeric domain-swapped arrangement of sfGFP66ONBY with residues 1-142 of one molecule associating with residues 148-234 from another molecule. This unusual domain-swapped structure supports a previously postulated GFP folding pathway that proceeds via an equilibrium intermediate.
-Authors: Kesgin-Schaefer, S., Tidow, H.
+Crystal structure of a domain-swapped photoactivatable sfGFP variant provides evidence for GFP folding pathway.,Kesgin-Schaefer S, Heidemann J, Puchert A, Koelbel K, Yorke BA, Huse N, Pearson AR, Uetrecht C, Tidow H FEBS J. 2019 Feb 28. doi: 10.1111/febs.14797. PMID:30817081<ref>PMID:30817081</ref>
-Description: Crystal structure of a domain-swapped dark-state sfGFP containing the unnatural amino acid ortho-nitrobenzyl-tyrosine (ONBY) at residue 66
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Kesgin-Schaefer, S]]
+<div class="pdbe-citations 6h01" style="background-color:#fffaf0;"></div>
-[[Category: Tidow, H]]
+==See Also==
+*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Aequorea victoria]]
+[[Category: Large Structures]]
+[[Category: Kesgin-Schaefer S]]
+[[Category: Tidow H]]