7ord - Revision history

OCA at 12:55, 1 February 2024

OCA — Thu, 01 Feb 2024 12:55:07 GMT

←Older revision		Revision as of 12:55, 1 February 2024
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	<StructureSection load='7ord' size='340' side='right'caption='[[7ord]], [[Resolution\|resolution]] 2.14Å' scene=''>		<StructureSection load='7ord' size='340' side='right'caption='[[7ord]], [[Resolution\|resolution]] 2.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7ord]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ORD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ORD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ord]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lithobates_pipiens Lithobates pipiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ORD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ORD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.14Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ord FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ord OCA], [https://pdbe.org/7ord PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ord RCSB], [https://www.ebi.ac.uk/pdbsum/7ord PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ord 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=7ord FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ord OCA], [https://pdbe.org/7ord PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ord RCSB], [https://www.ebi.ac.uk/pdbsum/7ord PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ord ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RNP30_LITPI RNP30_LITPI]] Basic protein with antiproliferative/cytotoxic activity against several tumor cell lines in vitro, as well as antitumor in vivo. It exhibits a ribonuclease-like activity against high molecular weight ribosomal RNA.	+	[https://www.uniprot.org/uniprot/RNP30_LITPI RNP30_LITPI] Basic protein with antiproliferative/cytotoxic activity against several tumor cell lines in vitro, as well as antitumor in vivo. It exhibits a ribonuclease-like activity against high molecular weight ribosomal RNA.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Loreto, D~~]]	+	[[Category: Lithobates pipiens]]
-	[[Category: ~~Merlino, A~~]]	+	[[Category: Loreto D]]
-	[[Category: ~~3d domain swapping]]~~	+	[[Category: Merlino A]]
-	~~[[Category: Antitumor activity]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Onconase]]~~	+
-	~~[[Category: Onconase dimer]]~~	+
-	~~[[Category: Ribonuclease~~]]	+

OCA at 12:58, 13 October 2021

OCA — Wed, 13 Oct 2021 12:58:16 GMT

←Older revision		Revision as of 12:58, 13 October 2021
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	==The crystal structure of the domain-swapped dimer of onconase (2)==		==The crystal structure of the domain-swapped dimer of onconase (2)==
-	<StructureSection load='7ord' size='340' side='right'caption='[[7ord]]' scene=''>	+	<StructureSection load='7ord' size='340' side='right'caption='[[7ord]], [[Resolution\|resolution]] 2.14Å' 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=7ORD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ORD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ord]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ORD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ORD FirstGlance]. <br>
-	</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=7ord FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ord OCA], [https://pdbe.org/7ord PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ord RCSB], [https://www.ebi.ac.uk/pdbsum/7ord PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ord 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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=7ord FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ord OCA], [https://pdbe.org/7ord PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ord RCSB], [https://www.ebi.ac.uk/pdbsum/7ord PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ord ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/RNP30_LITPI RNP30_LITPI]] Basic protein with antiproliferative/cytotoxic activity against several tumor cell lines in vitro, as well as antitumor in vivo. It exhibits a ribonuclease-like activity against high molecular weight ribosomal RNA.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Onconase (ONC) is a monomeric amphibian "pancreatic-type" RNase endowed with remarkable anticancer activity. ONC spontaneously forms traces of a dimer (ONC-D) in solution, while larger amounts can be formed when ONC is lyophilized from mildly acidic solutions. Here, we report the crystal structure of ONC-D and analyze its catalytic and antitumor activities in comparison to ONC. ONC-D forms via the three-dimensional swapping of the N-terminal alpha-helix between two monomers, but it displays a significantly different quaternary structure from that previously modeled [Fagagnini A et al., 2017, Biochem J 474, 3767-81], and based on the crystal structure of the RNase A N-terminal swapped dimer. ONC-D presents a variable quaternary assembly deriving from a variable open interface, while it retains a catalytic activity that is similar to that of ONC. Notably, ONC-D displays antitumor activity against two human melanoma cell lines, although it exerts a slightly lower cytostatic effect than the monomer. The inhibition of melanoma cell proliferation by ONC or ONC-D is associated with the reduction of the expression of the anti-apoptotic B cell lymphoma 2 (Bcl2), as well as of the total expression and phosphorylation of the Signal Transducer and Activator of Transcription (STAT)-3. Phosphorylation is inhibited in both STAT3 Tyr705 and Ser727 key-residues, as well as in its upstream tyrosine-kinase Src. Consequently, both ONC species should exert their anti-cancer action by inhibiting the pro-tumor pleiotropic STAT3 effects deriving either by its phospho-tyrosine activation or by its non-canonical signaling pathways. Both ONC species, indeed, increase the portion of A375 cells undergoing apoptotic cell death. This study expands the variety of RNase domain-swapped dimeric structures, underlining the unpredictability of the open interface arrangement upon domain swapping. Structural data also offer valuable insights to analyze the differences in the measured ONC or ONC-D biological activities.
		+
		+	The crystal structure of the domain-swapped dimer of onconase highlights some catalytic and antitumor activity features of the enzyme.,Gotte G, Campagnari R, Loreto D, Bettin I, Calzetti F, Menegazzi M, Merlino A Int J Biol Macromol. 2021 Sep 24;191:560-571. doi:, 10.1016/j.ijbiomac.2021.09.095. PMID:34563576<ref>PMID:34563576</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ord" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Loreto D]]	+	[[Category: Loreto, D]]
-	[[Category: Merlino A]]	+	[[Category: Merlino, A]]
		+	[[Category: 3d domain swapping]]
		+	[[Category: Antitumor activity]]
		+	[[Category: Hydrolase]]
		+	[[Category: Onconase]]
		+	[[Category: Onconase dimer]]
		+	[[Category: Ribonuclease]]

OCA at 05:33, 6 October 2021

OCA — Wed, 06 Oct 2021 05:33:05 GMT

←Older revision		Revision as of 05:33, 6 October 2021
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-	'''Unreleased structure'''

-	~~The entry 7ord is ON HOLD until Paper Publication~~	+	==The crystal structure of the domain-swapped dimer of onconase (2)==
-		+	<StructureSection load='7ord' size='340' side='right'caption='[[7ord]]' scene=''>
-	~~Authors: Merlino, A., Loreto, D.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ORD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ORD FirstGlance]. <br>
-	~~Description:~~ The crystal structure of the domain-swapped dimer of onconase (2)	+	</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=7ord FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ord OCA], [https://pdbe.org/7ord PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ord RCSB], [https://www.ebi.ac.uk/pdbsum/7ord PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ord ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Merlino~~, A]]	+	__TOC__
-	[[Category: Loreto, D]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Loreto D]]
		+	[[Category: Merlino A]]

OCA at 08:49, 7 July 2021

OCA — Wed, 07 Jul 2021 08:49:19 GMT

←Older revision		Revision as of 08:49, 7 July 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ord is ON HOLD	+	The entry 7ord is ON HOLD until Paper Publication

	Authors: Merlino, A., Loreto, D.		Authors: Merlino, A., Loreto, D.
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	Description: The crystal structure of the domain-swapped dimer of onconase (2)		Description: The crystal structure of the domain-swapped dimer of onconase (2)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Loreto, D]]
	[[Category: Merlino, A]]		[[Category: Merlino, A]]
		+	[[Category: Loreto, D]]

OCA: Protected "7ord" [edit=sysop:move=sysop]

OCA — Thu, 17 Jun 2021 13:50:00 GMT

Protected "7ord" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:50, 17 June 2021

OCA: New page: '''Unreleased structure''' The entry 7ord is ON HOLD Authors: Merlino, A., Loreto, D. Description: The crystal structure of the domain-swapped dimer of onconase (2) [[Category: Unrelea...

OCA — Thu, 17 Jun 2021 13:49:59 GMT

New page: '''Unreleased structure''' The entry 7ord is ON HOLD Authors: Merlino, A., Loreto, D. Description: The crystal structure of the domain-swapped dimer of onconase (2) [[Category: Unrelea...

New page

'''Unreleased structure'''

The entry 7ord is ON HOLD

Authors: Merlino, A., Loreto, D.

Description: The crystal structure of the domain-swapped dimer of onconase (2)
[[Category: Unreleased Structures]]
[[Category: Loreto, D]]
[[Category: Merlino, A]]