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- | [[Image:3bp9.jpg|left|200px]] | |
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- | {{Structure
| + | ==Structure of B-tropic MLV capsid N-terminal domain== |
- | |PDB= 3bp9 |SIZE=350|CAPTION= <scene name='initialview01'>3bp9</scene>, resolution 2.600Å
| + | <StructureSection load='3bp9' size='340' side='right'caption='[[3bp9]], [[Resolution|resolution]] 2.60Å' scene=''> |
- | |SITE=
| + | == Structural highlights == |
- | |LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> and <scene name='pdbligand=IPA:ISOPROPYL ALCOHOL'>IPA</scene> | + | <table><tr><td colspan='2'>[[3bp9]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Murine_leukemia_virus Murine leukemia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BP9 FirstGlance]. <br> |
- | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> |
- | |GENE= Gag ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11786 Murine leukemia virus])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</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=3bp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bp9 OCA], [https://pdbe.org/3bp9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bp9 RCSB], [https://www.ebi.ac.uk/pdbsum/3bp9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bp9 ProSAT]</span></td></tr> |
| + | </table> |
| + | == Function == |
| + | [https://www.uniprot.org/uniprot/GAG_MLVAV GAG_MLVAV] Gag polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release (By similarity). Matrix protein p15 targets Gag and gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex (By similarity). Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization (By similarity). |
| + | == Evolutionary Conservation == |
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| + | Check<jmol> |
| + | <jmolCheckbox> |
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bp/3bp9_consurf.spt"</scriptWhenChecked> |
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| + | <text>to colour the structure by Evolutionary Conservation</text> |
| + | </jmolCheckbox> |
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3bp9 ConSurf]. |
| + | <div style="clear:both"></div> |
| + | <div style="background-color:#fffaf0;"> |
| + | == Publication Abstract from PubMed == |
| + | The Gag polyprotein is the major structural protein found in all classes of retroviruses. Interactions between Gag molecules control key events at several stages in the cycle of infection. In particular, the capsid (CA) domain of Gag mediates many of the protein-protein interactions that drive retrovirus assembly, maturation and disassembly. Moreover, in murine leukaemia virus (MLV), sequence variation in CA confers N and B tropism that determines susceptibility to the intracellular restriction factors Fv1n and Fv1b. We have determined the structure of the N-terminal domain (NtD) of CA from B-tropic MLV. A comparison of this structure with that of the NtD of CA from N-tropic MLV reveals that although the crystals belong to different space groups, CA monomers are packed with the same P6 hexagonal arrangement. Moreover, interhexamer crystal contacts between residues located at the periphery of the discs are conserved, indicating that switching of tropism does not result in large differences in the backbone conformation, nor does it alter the quaternary arrangement of the disc. We have also examined crystals of the N-tropic MLV CA containing both N- and C-terminal domains. In this case, the NtD hexamer is still present; however, the interhexamer spacing is increased and the conserved interhexamer contacts are absent. Investigation into the effects of mutation of residues that mediate interhexamer contacts reveals that amino acid substitutions at these positions cause severe defects in viral assembly, budding and Gag processing. Based on our crystal structures and mutational analysis, we propose that in MLV, interactions between the NtDs of CA are required for packing of Gag molecules in the early part of immature particle assembly. Moreover, we present a model where proteolytic cleavage at maturation results in migration of CA C-terminal domains into interstitial spaces between NtD hexamers. As a result, NtD-mediated interhexamer contacts present in the immature particle are displaced and the less densely packed lattice with increased hexamer-hexamer spacing characteristic of the viral core is produced. |
| | | |
- | '''Structure of B-tropic MLV capsid N-terminal domain'''
| + | Structure of B-MLV capsid amino-terminal domain reveals key features of viral tropism, gag assembly and core formation.,Mortuza GB, Dodding MP, Goldstone DC, Haire LF, Stoye JP, Taylor IA J Mol Biol. 2008 Mar 7;376(5):1493-508. Epub 2007 Dec 28. PMID:18222469<ref>PMID:18222469</ref> |
| | | |
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| + | </div> |
| + | <div class="pdbe-citations 3bp9" style="background-color:#fffaf0;"></div> |
| | | |
- | ==Overview== | + | ==See Also== |
- | The Gag polyprotein is the major structural protein found in all classes of retroviruses. Interactions between Gag molecules control key events at several stages in the cycle of infection. In particular, the capsid (CA) domain of Gag mediates many of the protein-protein interactions that drive retrovirus assembly, maturation and disassembly. Moreover, in murine leukaemia virus (MLV), sequence variation in CA confers N and B tropism that determines susceptibility to the intracellular restriction factors Fv1n and Fv1b. We have determined the structure of the N-terminal domain (NtD) of CA from B-tropic MLV. A comparison of this structure with that of the NtD of CA from N-tropic MLV reveals that although the crystals belong to different space groups, CA monomers are packed with the same P6 hexagonal arrangement. Moreover, interhexamer crystal contacts between residues located at the periphery of the discs are conserved, indicating that switching of tropism does not result in large differences in the backbone conformation, nor does it alter the quaternary arrangement of the disc. We have also examined crystals of the N-tropic MLV CA containing both N- and C-terminal domains. In this case, the NtD hexamer is still present; however, the interhexamer spacing is increased and the conserved interhexamer contacts are absent. Investigation into the effects of mutation of residues that mediate interhexamer contacts reveals that amino acid substitutions at these positions cause severe defects in viral assembly, budding and Gag processing. Based on our crystal structures and mutational analysis, we propose that in MLV, interactions between the NtDs of CA are required for packing of Gag molecules in the early part of immature particle assembly. Moreover, we present a model where proteolytic cleavage at maturation results in migration of CA C-terminal domains into interstitial spaces between NtD hexamers. As a result, NtD-mediated interhexamer contacts present in the immature particle are displaced and the less densely packed lattice with increased hexamer-hexamer spacing characteristic of the viral core is produced.
| + | *[[Gag polyprotein 3D structures|Gag polyprotein 3D structures]] |
- | | + | == References == |
- | ==About this Structure== | + | <references/> |
- | 3BP9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Murine_leukemia_virus Murine leukemia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BP9 OCA].
| + | __TOC__ |
- | | + | </StructureSection> |
- | ==Reference==
| + | [[Category: Large Structures]] |
- | Structure of B-MLV capsid amino-terminal domain reveals key features of viral tropism, gag assembly and core formation., Mortuza GB, Dodding MP, Goldstone DC, Haire LF, Stoye JP, Taylor IA, J Mol Biol. 2008 Mar 7;376(5):1493-508. Epub 2007 Dec 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18222469 18222469]
| + | |
| [[Category: Murine leukemia virus]] | | [[Category: Murine leukemia virus]] |
- | [[Category: Single protein]]
| + | [[Category: Dodding MP]] |
- | [[Category: Dodding, M P.]] | + | [[Category: Goldstone DC]] |
- | [[Category: Goldstone, D C.]] | + | [[Category: Gulnahar MB]] |
- | [[Category: Gulnahar, M B.]] | + | [[Category: Haire LF]] |
- | [[Category: Haire, L F.]] | + | [[Category: Stoye JP]] |
- | [[Category: Stoye, J P.]] | + | [[Category: Taylor IA]] |
- | [[Category: Taylor, I A.]] | + | |
- | [[Category: GOL]]
| + | |
- | [[Category: IPA]]
| + | |
- | [[Category: capsid]]
| + | |
- | [[Category: hexamer]]
| + | |
- | [[Category: metal-binding]]
| + | |
- | [[Category: mlv]]
| + | |
- | [[Category: viral protein]]
| + | |
- | [[Category: zinc]]
| + | |
- | [[Category: zinc-finger]]
| + | |
- | | + | |
- | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:00:26 2008''
| + | |
| Structural highlights
Function
GAG_MLVAV Gag polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release (By similarity). Matrix protein p15 targets Gag and gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex (By similarity). Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization (By similarity).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The Gag polyprotein is the major structural protein found in all classes of retroviruses. Interactions between Gag molecules control key events at several stages in the cycle of infection. In particular, the capsid (CA) domain of Gag mediates many of the protein-protein interactions that drive retrovirus assembly, maturation and disassembly. Moreover, in murine leukaemia virus (MLV), sequence variation in CA confers N and B tropism that determines susceptibility to the intracellular restriction factors Fv1n and Fv1b. We have determined the structure of the N-terminal domain (NtD) of CA from B-tropic MLV. A comparison of this structure with that of the NtD of CA from N-tropic MLV reveals that although the crystals belong to different space groups, CA monomers are packed with the same P6 hexagonal arrangement. Moreover, interhexamer crystal contacts between residues located at the periphery of the discs are conserved, indicating that switching of tropism does not result in large differences in the backbone conformation, nor does it alter the quaternary arrangement of the disc. We have also examined crystals of the N-tropic MLV CA containing both N- and C-terminal domains. In this case, the NtD hexamer is still present; however, the interhexamer spacing is increased and the conserved interhexamer contacts are absent. Investigation into the effects of mutation of residues that mediate interhexamer contacts reveals that amino acid substitutions at these positions cause severe defects in viral assembly, budding and Gag processing. Based on our crystal structures and mutational analysis, we propose that in MLV, interactions between the NtDs of CA are required for packing of Gag molecules in the early part of immature particle assembly. Moreover, we present a model where proteolytic cleavage at maturation results in migration of CA C-terminal domains into interstitial spaces between NtD hexamers. As a result, NtD-mediated interhexamer contacts present in the immature particle are displaced and the less densely packed lattice with increased hexamer-hexamer spacing characteristic of the viral core is produced.
Structure of B-MLV capsid amino-terminal domain reveals key features of viral tropism, gag assembly and core formation.,Mortuza GB, Dodding MP, Goldstone DC, Haire LF, Stoye JP, Taylor IA J Mol Biol. 2008 Mar 7;376(5):1493-508. Epub 2007 Dec 28. PMID:18222469[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Mortuza GB, Dodding MP, Goldstone DC, Haire LF, Stoye JP, Taylor IA. Structure of B-MLV capsid amino-terminal domain reveals key features of viral tropism, gag assembly and core formation. J Mol Biol. 2008 Mar 7;376(5):1493-508. Epub 2007 Dec 28. PMID:18222469 doi:10.1016/j.jmb.2007.12.043
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