8sxu - Revision history

OCA at 09:44, 14 February 2024

OCA — Wed, 14 Feb 2024 09:44:00 GMT

←Older revision		Revision as of 09:44, 14 February 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/LORF2_HUMAN LORF2_HUMAN] Has a reverse transcriptase activity required for target-primed reverse transcription of the LINE-1 element mRNA, a crucial step in LINE-1 retrotransposition. Has also an endonuclease activity that allows the introduction of nicks in the chromosomal target DNA. Cleaves DNA in AT-rich regions between a 5' stretch of purines and a 3' stretch of pyrimidines, corresponding to sites of LINE-1 integration in the genome.<ref>PMID:7516468</ref> <ref>PMID:8945517</ref> <ref>PMID:9140393</ref>		[https://www.uniprot.org/uniprot/LORF2_HUMAN LORF2_HUMAN] Has a reverse transcriptase activity required for target-primed reverse transcription of the LINE-1 element mRNA, a crucial step in LINE-1 retrotransposition. Has also an endonuclease activity that allows the introduction of nicks in the chromosomal target DNA. Cleaves DNA in AT-rich regions between a 5' stretch of purines and a 3' stretch of pyrimidines, corresponding to sites of LINE-1 integration in the genome.<ref>PMID:7516468</ref> <ref>PMID:8945517</ref> <ref>PMID:9140393</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The LINE-1 (L1) retrotransposon is an ancient genetic parasite that has written around one third of the human genome through a "copy-and-paste" mechanism catalyzed by its multifunctional enzyme, open reading frame 2 protein (ORF2p)(1). ORF2p reverse transcriptase (RT) and endonuclease activities have been implicated in the pathophysiology of cancer(2,3), autoimmunity(4,5), and aging(6,7), making ORF2p a potential therapeutic target. However, a lack of structural and mechanistic knowledge has hampered efforts to rationally exploit it. We report structures of the human ORF2p 'core' (residues 238-1061, including the RT domain) by X-ray crystallography and cryo-EM in multiple conformational states. Our analyses reveal two novel folded domains, extensive contacts to RNA templates, and associated adaptations that contribute to unique aspects of the L1 replication cycle. Computed integrative structural models of full-length ORF2p show a dynamic closed ring conformation that appears to open during retrotransposition. We characterize ORF2p RT inhibition and reveal its underlying structural basis. Imaging and biochemistry reveal that non-canonical cytosolic ORF2p RT activity can produce RNA:DNA hybrids, activating innate immune signaling via cGAS/STING and resulting in interferon production(6-8). In contrast to retroviral RTs, L1 RT is efficiently primed by short RNAs and hairpins, which likely explains cytosolic priming. Additional biochemical activities including processivity, DNA-directed polymerization, non-templated base addition, and template switching together allow us to propose an updated L1 insertion model. Finally, our evolutionary analysis reveals structural conservation between ORF2p and other RNA- and DNA-dependent polymerases. We therefore provide key mechanistic insights into L1 polymerization and insertion, shed light on L1 evolutionary history, and enable rational drug development targeting L1.
-
-	Structures, functions, and adaptations of the human LINE-1 ORF2 protein.,Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS Nature. 2023 Dec 14. doi: 10.1038/s41586-023-06947-z. PMID:38096902<ref>PMID:38096902</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8sxu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:27, 10 January 2024

OCA — Wed, 10 Jan 2024 10:27:18 GMT

←Older revision		Revision as of 10:27, 10 January 2024
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8sxu is ~~ON HOLD until Paper~~ Publication	+	==Structure of LINE-1 ORF2p with an oligo(A) template==
		+	<StructureSection load='8sxu' size='340' side='right'caption='[[8sxu]], [[Resolution\|resolution]] 3.66Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8sxu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8SXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8SXU FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.66Å</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=8sxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8sxu OCA], [https://pdbe.org/8sxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8sxu RCSB], [https://www.ebi.ac.uk/pdbsum/8sxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8sxu ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/LORF2_HUMAN LORF2_HUMAN] Has a reverse transcriptase activity required for target-primed reverse transcription of the LINE-1 element mRNA, a crucial step in LINE-1 retrotransposition. Has also an endonuclease activity that allows the introduction of nicks in the chromosomal target DNA. Cleaves DNA in AT-rich regions between a 5' stretch of purines and a 3' stretch of pyrimidines, corresponding to sites of LINE-1 integration in the genome.<ref>PMID:7516468</ref> <ref>PMID:8945517</ref> <ref>PMID:9140393</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The LINE-1 (L1) retrotransposon is an ancient genetic parasite that has written around one third of the human genome through a "copy-and-paste" mechanism catalyzed by its multifunctional enzyme, open reading frame 2 protein (ORF2p)(1). ORF2p reverse transcriptase (RT) and endonuclease activities have been implicated in the pathophysiology of cancer(2,3), autoimmunity(4,5), and aging(6,7), making ORF2p a potential therapeutic target. However, a lack of structural and mechanistic knowledge has hampered efforts to rationally exploit it. We report structures of the human ORF2p 'core' (residues 238-1061, including the RT domain) by X-ray crystallography and cryo-EM in multiple conformational states. Our analyses reveal two novel folded domains, extensive contacts to RNA templates, and associated adaptations that contribute to unique aspects of the L1 replication cycle. Computed integrative structural models of full-length ORF2p show a dynamic closed ring conformation that appears to open during retrotransposition. We characterize ORF2p RT inhibition and reveal its underlying structural basis. Imaging and biochemistry reveal that non-canonical cytosolic ORF2p RT activity can produce RNA:DNA hybrids, activating innate immune signaling via cGAS/STING and resulting in interferon production(6-8). In contrast to retroviral RTs, L1 RT is efficiently primed by short RNAs and hairpins, which likely explains cytosolic priming. Additional biochemical activities including processivity, DNA-directed polymerization, non-templated base addition, and template switching together allow us to propose an updated L1 insertion model. Finally, our evolutionary analysis reveals structural conservation between ORF2p and other RNA- and DNA-dependent polymerases. We therefore provide key mechanistic insights into L1 polymerization and insertion, shed light on L1 evolutionary history, and enable rational drug development targeting L1.

-	~~Authors~~:	+	Structures, functions, and adaptations of the human LINE-1 ORF2 protein.,Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS Nature. 2023 Dec 14. doi: 10.1038/s41586-023-06947-z. PMID:38096902<ref>PMID:38096902</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8sxu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Rout MP]]
		+	[[Category: Taylor MS]]
		+	[[Category: Van Eeuwen T]]

OCA at 20:00, 28 June 2023

OCA — Wed, 28 Jun 2023 20:00:35 GMT

←Older revision		Revision as of 20:00, 28 June 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8sxu is ON HOLD	+	The entry 8sxu is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8sxu" [edit=sysop:move=sysop]

OCA — Wed, 31 May 2023 04:16:20 GMT

Protected "8sxu" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:16, 31 May 2023

OCA: New page: '''Unreleased structure''' The entry 8sxu is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 31 May 2023 04:16:19 GMT

New page: '''Unreleased structure''' The entry 8sxu is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8sxu is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]