6tc7 - Revision history

OCA at 13:08, 6 November 2024

2024-11-06T13:08:48Z

← Older revision		Revision as of 13:08, 6 November 2024
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	<StructureSection load='6tc7' size='340' side='right'caption='[[6tc7]], [[Resolution\|resolution]] 2.13Å' scene=''>		<StructureSection load='6tc7' size='340' side='right'caption='[[6tc7]], [[Resolution\|resolution]] 2.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[6tc7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TC7 FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TC7 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]] 2.13Å</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]] 2.13Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6tc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tc7 OCA], [https://pdbe.org/6tc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tc7 RCSB], [https://www.ebi.ac.uk/pdbsum/6tc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tc7 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=6tc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tc7 OCA], [https://pdbe.org/6tc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tc7 RCSB], [https://www.ebi.ac.uk/pdbsum/6tc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tc7 ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[https://www.uniprot.org/uniprot/PHYA2_SOYBN PHYA2_SOYBN] Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region. Photoconversion of Pr to Pfr induces an array of morphogenic responses, whereas reconversion of Pfr to Pr cancels the induction of those responses. Pfr controls the expression of a number of nuclear genes including those encoding the small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B binding protein, protochlorophyllide reductase, rRNA, etc. It also controls the expression of its own gene(s) in a negative feedback fashion.[UniProtKB:P14713]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Plant phytochromes are red/far-red photochromic photoreceptors that act as master regulators of development, controlling the expression of thousands of genes. Here, we describe the crystal structures of four plant phytochrome sensory modules, three at about 2 A resolution or better, including the first of an A-type phytochrome. Together with extensive spectral data, these structures provide detailed insight into the structure and function of plant phytochromes. In the Pr state, the substitution of phycocyanobilin and phytochromobilin cofactors has no structural effect, nor does the amino-terminal extension play a significant functional role. Our data suggest that the chromophore propionates and especially the phytochrome-specific domain tongue act differently in plant and prokaryotic phytochromes. We find that the photoproduct in period-ARNT-single-minded (PAS)-cGMP-specific phosphodiesterase-adenylyl cyclase-FhlA (GAF) bidomains might represent a novel intermediate between MetaRc and Pfr. We also discuss the possible role of a likely nuclear localization signal specific to and conserved in the phytochrome A lineage.

	Structural insights into photoactivation and signalling in plant phytochromes.,Nagano S, Guan K, Shenkutie SM, Feiler C, Weiss M, Kraskov A, Buhrke D, Hildebrandt P, Hughes J Nat Plants. 2020 May 4. pii: 10.1038/s41477-020-0638-y. doi:, 10.1038/s41477-020-0638-y. PMID:32366982<ref>PMID:32366982</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 6tc7" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Glycine max]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Guan K]]		[[Category: Guan K]]

OCA at 12:59, 24 January 2024

2024-01-24T12:59:27Z

← Older revision		Revision as of 12:59, 24 January 2024
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	<StructureSection load='6tc7' size='340' side='right'caption='[[6tc7]], [[Resolution\|resolution]] 2.13Å' scene=''>		<StructureSection load='6tc7' size='340' side='right'caption='[[6tc7]], [[Resolution\|resolution]] 2.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6tc7]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Glycine_hispida~~ Glycine ~~hispida~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TC7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6TC7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6tc7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TC7 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene>~~, ~~<scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.13Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~phyA, 100790763, GmphyA2, PhyA2, GLYMA_20G090000 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=3847 Glycine hispida]~~)</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6tc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tc7 OCA], [~~http~~://pdbe.org/6tc7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tc7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tc7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tc7 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=6tc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tc7 OCA], [https://pdbe.org/6tc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tc7 RCSB], [https://www.ebi.ac.uk/pdbsum/6tc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tc7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/~~B4YB07_SOYBN B4YB07_SOYBN]~~] Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region.[~~PIRNR~~:~~PIRNR000084~~]		[https://www.uniprot.org/uniprot/PHYA2_SOYBN PHYA2_SOYBN] Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region. Photoconversion of Pr to Pfr induces an array of morphogenic responses, whereas reconversion of Pfr to Pr cancels the induction of those responses. Pfr controls the expression of a number of nuclear genes including those encoding the small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B binding protein, protochlorophyllide reductase, rRNA, etc. It also controls the expression of its own gene(s) in a negative feedback fashion.[UniProtKB:P14713]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Glycine ~~hispida~~]]		[[Category: Glycine max]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Guan, K]]		[[Category: Guan K]]
	[[Category: Hughes~~, J E~~]]		[[Category: Hughes JE]]
	[[Category: Nagano, S]]		[[Category: Nagano S]]
	[[Category: Shenkutie~~, S M]]~~		[[Category: Shenkutie SM]]
	~~[[Category: Phytochrome]]~~
	~~[[Category: Plant protein~~]]

OCA at 05:56, 13 May 2020

2020-05-13T05:56:09Z

← Older revision		Revision as of 05:56, 13 May 2020
Line 1:		Line 1:

	==PAS-GAF bidomain of Glycine max phytochromeA==		==PAS-GAF bidomain of Glycine max phytochromeA==
	<StructureSection load='6tc7' size='340' side='right'caption='[[6tc7]]' scene=''>		<StructureSection load='6tc7' size='340' side='right'caption='[[6tc7]], [[Resolution\|resolution]] 2.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TC7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TC7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6tc7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TC7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TC7 FirstGlance]. <br>
	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6tc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tc7 OCA], [http://pdbe.org/6tc7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tc7 RCSB], [http://www.ebi.ac.uk/pdbsum/6tc7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tc7 ProSAT]</span></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phyA, 100790763, GmphyA2, PhyA2, GLYMA_20G090000 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>
			<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6tc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tc7 OCA], [http://pdbe.org/6tc7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tc7 RCSB], [http://www.ebi.ac.uk/pdbsum/6tc7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tc7 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/B4YB07_SOYBN B4YB07_SOYBN]] Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region.[PIRNR:PIRNR000084]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Plant phytochromes are red/far-red photochromic photoreceptors that act as master regulators of development, controlling the expression of thousands of genes. Here, we describe the crystal structures of four plant phytochrome sensory modules, three at about 2 A resolution or better, including the first of an A-type phytochrome. Together with extensive spectral data, these structures provide detailed insight into the structure and function of plant phytochromes. In the Pr state, the substitution of phycocyanobilin and phytochromobilin cofactors has no structural effect, nor does the amino-terminal extension play a significant functional role. Our data suggest that the chromophore propionates and especially the phytochrome-specific domain tongue act differently in plant and prokaryotic phytochromes. We find that the photoproduct in period-ARNT-single-minded (PAS)-cGMP-specific phosphodiesterase-adenylyl cyclase-FhlA (GAF) bidomains might represent a novel intermediate between MetaRc and Pfr. We also discuss the possible role of a likely nuclear localization signal specific to and conserved in the phytochrome A lineage.

			Structural insights into photoactivation and signalling in plant phytochromes.,Nagano S, Guan K, Shenkutie SM, Feiler C, Weiss M, Kraskov A, Buhrke D, Hildebrandt P, Hughes J Nat Plants. 2020 May 4. pii: 10.1038/s41477-020-0638-y. doi:, 10.1038/s41477-020-0638-y. PMID:32366982<ref>PMID:32366982</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6tc7" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Glycine hispida]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Guan K]]		[[Category: Guan, K]]
	[[Category: Hughes JE]]		[[Category: Hughes, J E]]
	[[Category: Nagano S]]		[[Category: Nagano, S]]
	[[Category: Shenkutie SM]]		[[Category: Shenkutie, S M]]
			[[Category: Phytochrome]]
			[[Category: Plant protein]]

OCA at 06:03, 6 May 2020

2020-05-06T06:03:16Z

← Older revision		Revision as of 06:03, 6 May 2020
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6tc7 is ~~ON HOLD~~		==PAS-GAF bidomain of Glycine max phytochromeA==
			<StructureSection load='6tc7' size='340' side='right'caption='[[6tc7]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TC7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TC7 FirstGlance]. <br>
	~~Description~~:		</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6tc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tc7 OCA], [http://pdbe.org/6tc7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tc7 RCSB], [http://www.ebi.ac.uk/pdbsum/6tc7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tc7 ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Guan K]]
			[[Category: Hughes JE]]
			[[Category: Nagano S]]
			[[Category: Shenkutie SM]]

OCA: Protected "6tc7" [edit=sysop:move=sysop]

2019-11-13T09:27:56Z

Protected "6tc7" [edit=sysop:move=sysop]

← Older revision	Revision as of 09:27, 13 November 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6tc7 is ON HOLD Authors: Description: Category: Unreleased Structures

2019-11-13T09:27:55Z

New page: '''Unreleased structure''' The entry 6tc7 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6tc7 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]