6g1y - Revision history

OCA at 07:49, 7 February 2024

2024-02-07T07:49:01Z

←Older revision		Revision as of 07:49, 7 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6g1y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6G1Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[6g1y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6G1Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EL5:3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic+acid'>EL5</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EL5:3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic+acid'>EL5</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</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=6g1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g1y OCA], [https://pdbe.org/6g1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6g1y RCSB], [https://www.ebi.ac.uk/pdbsum/6g1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6g1y 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=6g1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g1y OCA], [https://pdbe.org/6g1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6g1y RCSB], [https://www.ebi.ac.uk/pdbsum/6g1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6g1y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A9CI81_AGRFC A9CI81_AGRFC]		[https://www.uniprot.org/uniprot/A9CI81_AGRFC A9CI81_AGRFC]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Phytochromes are modular photoreceptors of plants, bacteria and fungi that use light as a source of information to regulate fundamental physiological processes. Interconversion between the active and inactive states is accomplished by a photoinduced reaction sequence which couples the sensor with the output module. However, the underlying molecular mechanism is yet not fully understood due to the lack of structural data of functionally relevant intermediate states. Here we report the crystal structure of a Meta-F intermediate state of an Agp2 variant from Agrobacterium fabrum. This intermediate, the identity of which was verified by resonance Raman spectroscopy, was formed by irradiation of the parent Pfr state and displays significant reorientations of almost all amino acids surrounding the chromophore. Structural comparisons allow identifying structural motifs that might serve as conformational switch for initiating the functional secondary structure change that is linked to the (de-)activation of these photoreceptors.
-
-	Structural snapshot of a bacterial phytochrome in its functional intermediate state.,Schmidt A, Sauthof L, Szczepek M, Lopez MF, Escobar FV, Qureshi BM, Michael N, Buhrke D, Stevens T, Kwiatkowski D, von Stetten D, Mroginski MA, Krauss N, Lamparter T, Hildebrandt P, Scheerer P Nat Commun. 2018 Nov 21;9(1):4912. doi: 10.1038/s41467-018-07392-7. PMID:30464203<ref>PMID:30464203</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6g1y" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 04:10, 25 May 2023

2023-05-25T04:10:31Z

←Older revision		Revision as of 04:10, 25 May 2023
Line 1:		Line 1:

	==Crystal structure of the photosensory core module (PCM) of a bathy phytochrome from Agrobacterium fabrum in the Pfr state.==		==Crystal structure of the photosensory core module (PCM) of a bathy phytochrome from Agrobacterium fabrum in the Pfr state.==
-	<StructureSection load='6g1y' size='340' side='right' caption='[[6g1y]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='6g1y' size='340' side='right'caption='[[6g1y]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6g1y]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Agrfc Agrfc~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G1Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6G1Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6g1y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6G1Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EL5:~~Biliverdin'>EL5</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EL5:3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic+acid'>EL5</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>~~[[~~Non~~-~~Standard_Residue\|NonStd Res:~~]]~~</b~~></~~td><td class="sblockDat"~~><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</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=6g1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g1y OCA], [https://pdbe.org/6g1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6g1y RCSB], [https://www.ebi.ac.uk/pdbsum/6g1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6g1y ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6g1z\|6g1z]], [[6g20\|6g20]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Atu2165 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRFC])~~</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=6g1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g1y OCA], [~~http~~://pdbe.org/6g1y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6g1y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6g1y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6g1y ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A9CI81_AGRFC A9CI81_AGRFC]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Agrfc~~]]	+	[[Category: Agrobacterium fabrum str. C58]]
-	[[Category: ~~Qureshi, B M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Scheerer, P~~]]	+	[[Category: Qureshi BM]]
-	[[Category: ~~Schmidt, A~~]]	+	[[Category: Scheerer P]]
-	[[Category: ~~Bacteriophytochrome]]~~	+	[[Category: Schmidt A]]
-	~~[[Category: Bathy phytochrome]]~~	+
-	~~[[Category: Bilin chromophore]]~~	+
-	~~[[Category: Light adaptation]]~~	+
-	~~[[Category: Methylation]]~~	+
-	~~[[Category: Pfr state]]~~	+
-	~~[[Category: Photoisomerization]]~~	+
-	~~[[Category: Photosensory core module]]~~	+
-	~~[[Category: Phytochrome]]~~	+
-	~~[[Category: Signal transduction]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 07:04, 5 December 2018

2018-12-05T07:04:58Z

←Older revision		Revision as of 07:04, 5 December 2018
Line 10:		Line 10:
	<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=6g1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g1y OCA], [http://pdbe.org/6g1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g1y RCSB], [http://www.ebi.ac.uk/pdbsum/6g1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g1y ProSAT]</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=6g1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g1y OCA], [http://pdbe.org/6g1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g1y RCSB], [http://www.ebi.ac.uk/pdbsum/6g1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g1y ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phytochromes are modular photoreceptors of plants, bacteria and fungi that use light as a source of information to regulate fundamental physiological processes. Interconversion between the active and inactive states is accomplished by a photoinduced reaction sequence which couples the sensor with the output module. However, the underlying molecular mechanism is yet not fully understood due to the lack of structural data of functionally relevant intermediate states. Here we report the crystal structure of a Meta-F intermediate state of an Agp2 variant from Agrobacterium fabrum. This intermediate, the identity of which was verified by resonance Raman spectroscopy, was formed by irradiation of the parent Pfr state and displays significant reorientations of almost all amino acids surrounding the chromophore. Structural comparisons allow identifying structural motifs that might serve as conformational switch for initiating the functional secondary structure change that is linked to the (de-)activation of these photoreceptors.
		+
		+	Structural snapshot of a bacterial phytochrome in its functional intermediate state.,Schmidt A, Sauthof L, Szczepek M, Lopez MF, Escobar FV, Qureshi BM, Michael N, Buhrke D, Stevens T, Kwiatkowski D, von Stetten D, Mroginski MA, Krauss N, Lamparter T, Hildebrandt P, Scheerer P Nat Commun. 2018 Nov 21;9(1):4912. doi: 10.1038/s41467-018-07392-7. PMID:30464203<ref>PMID:30464203</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6g1y" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 20:31, 2 December 2018

2018-12-02T20:31:28Z

←Older revision		Revision as of 20:31, 2 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6g1y is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the photosensory core module (PCM) of a bathy phytochrome from Agrobacterium fabrum in the Pfr state.==
-		+	<StructureSection load='6g1y' size='340' side='right' caption='[[6g1y]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6g1y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrfc Agrfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G1Y FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EL5:Biliverdin'>EL5</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6g1z\|6g1z]], [[6g20\|6g20]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Atu2165 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRFC])</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=6g1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g1y OCA], [http://pdbe.org/6g1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g1y RCSB], [http://www.ebi.ac.uk/pdbsum/6g1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g1y ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Agrfc]]
		+	[[Category: Qureshi, B M]]
		+	[[Category: Scheerer, P]]
		+	[[Category: Schmidt, A]]
		+	[[Category: Bacteriophytochrome]]
		+	[[Category: Bathy phytochrome]]
		+	[[Category: Bilin chromophore]]
		+	[[Category: Light adaptation]]
		+	[[Category: Methylation]]
		+	[[Category: Pfr state]]
		+	[[Category: Photoisomerization]]
		+	[[Category: Photosensory core module]]
		+	[[Category: Phytochrome]]
		+	[[Category: Signal transduction]]
		+	[[Category: Signaling protein]]

OCA at 12:36, 11 April 2018

2018-04-11T12:36:31Z

←Older revision		Revision as of 12:36, 11 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6g1y is ON HOLD	+	The entry 6g1y is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6g1y" [edit=sysop:move=sysop]

2018-03-28T05:31:08Z

Protected "6g1y" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:31, 28 March 2018

OCA: New page: '''Unreleased structure''' The entry 6g1y is ON HOLD Authors: Description: Category: Unreleased Structures

2018-03-28T05:31:07Z

New page: '''Unreleased structure''' The entry 6g1y is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6g1y is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]