This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6r23

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

The structure of a Ty3 retrotransposon capsid C-terminal domain dimer

6r23, resolution 4.90Å

Structural highlights

6r23 is a 2 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	TY3B-I, YILWTy3-1 POL, YIL082W-A (Baker's yeast)
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[YI31B_YEAST] Capsid protein (CA) is the structural component of the virus-like particle (VLP), forming the shell that encapsulates the genomic RNA-nucleocapsid complex. Nucleocapsid protein p11 (NC) forms the nucleocore that coats the retro-elements dimeric RNA. Binds these RNAs through its zinc fingers (By similarity). Promotes primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty3 RNA and initiation of reverse transcription (By similarity). The aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP. Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that catalyzes the conversion of the retro-elements RNA genome into dsDNA within the VLP. The enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes during plus-strand synthesis and hydrolyzes RNA primers. The conversion leads to a linear dsDNA copy of the retrotransposon that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase (IN) targets the VLP to the nucleus, where a subparticle preintegration complex (PIC) containing at least integrase and the newly synthesized dsDNA copy of the retrotransposon must transit the nuclear membrane. Once in the nucleus, integrase performs the integration of the dsDNA into the host genome (By similarity).

Publication Abstract from PubMed

Retroviruses evolved from long terminal repeat (LTR) retrotransposons by acquisition of envelope functions, and subsequently reinvaded host genomes. Together, endogenous retroviruses and LTR retrotransposons represent major components of animal, plant, and fungal genomes. Sequences from these elements have been exapted to perform essential host functions, including placental development, synaptic communication, and transcriptional regulation. They encode a Gag polypeptide, the capsid domains of which can oligomerize to form a virus-like particle. The structures of retroviral capsids have been extensively described. They assemble an immature viral particle through oligomerization of full-length Gag. Proteolytic cleavage of Gag results in a mature, infectious particle. In contrast, the absence of structural data on LTR retrotransposon capsids hinders our understanding of their function and evolutionary relationships. Here, we report the capsid morphology and structure of the archetypal Gypsy retrotransposon Ty3. We performed electron tomography (ET) of immature and mature Ty3 particles within cells. We found that, in contrast to retroviruses, these do not change size or shape upon maturation. Cryo-ET and cryo-electron microscopy of purified, immature Ty3 particles revealed an irregular fullerene geometry previously described for mature retrovirus core particles and a tertiary and quaternary arrangement of the capsid (CA) C-terminal domain within the assembled capsid that is conserved with mature HIV-1. These findings provide a structural basis for studying retrotransposon capsids, including those domesticated in higher organisms. They suggest that assembly via a structurally distinct immature capsid is a later retroviral adaptation, while the structure of mature assembled capsids is conserved between LTR retrotransposons and retroviruses.

Structure of the Ty3/Gypsy retrotransposon capsid and the evolution of retroviruses.,Dodonova SO, Prinz S, Bilanchone V, Sandmeyer S, Briggs JAG Proc Natl Acad Sci U S A. 2019 Apr 29. pii: 1900931116. doi:, 10.1073/pnas.1900931116. PMID:31036670^[1]

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

References

↑ Dodonova SO, Prinz S, Bilanchone V, Sandmeyer S, Briggs JAG. Structure of the Ty3/Gypsy retrotransposon capsid and the evolution of retroviruses. Proc Natl Acad Sci U S A. 2019 Apr 29. pii: 1900931116. doi:, 10.1073/pnas.1900931116. PMID:31036670 doi:http://dx.doi.org/10.1073/pnas.1900931116

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6r23"

@@ Line 1: / Line 1: @@
 ==The structure of a Ty3 retrotransposon capsid C-terminal domain dimer==
-<StructureSection load='6r23' size='340' side='right'caption='[[6r23]], [[Resolution|resolution]] 4.90&Aring;' scene=''>
+<SX load='6r23' size='340' side='right' viewer='molstar' caption='[[6r23]], [[Resolution|resolution]] 4.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6r23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R23 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6r23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R23 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6R23 FirstGlance]. <br>
 </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TY3B-I, YILWTy3-1 POL, YIL082W-A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=6r23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r23 OCA], [http://pdbe.org/6r23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r23 RCSB], [http://www.ebi.ac.uk/pdbsum/6r23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r23 ProSAT]</span></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=6r23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r23 OCA], [http://pdbe.org/6r23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r23 RCSB], [http://www.ebi.ac.uk/pdbsum/6r23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r23 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 21: / Line 21: @@
 <references/>
 __TOC__
-</StructureSection>
+</SX>
 [[Category: Baker's yeast]]
 [[Category: Large Structures]]

6r23

From Proteopedia

Current revision

The structure of a Ty3 retrotransposon capsid C-terminal domain dimer

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox