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5upw

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Revision as of 03:53, 16 November 2017

CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations

Structural highlights

5upw is a 6 chain structure with sequence from Hiv-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	gag (HIV-1)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[GAG_HV1N5] Matrix protein p17 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. Implicated in the release from host cell mediated by Vpu. Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex. Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1 (By similarity).

Publication Abstract from PubMed

Single particle cryoEM has emerged as a powerful method for structure determination of proteins and complexes, complementing X-ray crystallography and NMR spectroscopy. Yet, for many systems, the resolution of cryoEM density map has been limited to 4-6 A, which only allows for resolving bulky amino acids side chains, thus hindering accurate model building from the density map. On the other hand, experimental chemical shifts (CS) from solution and solid state MAS NMR spectra provide atomic level data for each amino acid within a molecule or a complex; however, structure determination of large complexes and assemblies based on NMR data alone remains challenging. Here, we present a novel integrated strategy to combine the highly complementary experimental data from cryoEM and NMR computationally by molecular dynamics simulations to derive an atomistic model, which is not attainable by either approach alone. We use the HIV-1 capsid protein (CA) C-terminal domain as well as the large capsid assembly to demonstrate the feasibility of this approach, termed NMR CS-biased cryoEM structure refinement.

CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.,Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P J Phys Chem B. 2017 Feb 22. doi: 10.1021/acs.jpcb.6b13105. PMID:28181439^[1]

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

References

↑ Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P. CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. J Phys Chem B. 2017 Feb 22. doi: 10.1021/acs.jpcb.6b13105. PMID:28181439 doi:http://dx.doi.org/10.1021/acs.jpcb.6b13105

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/5upw"

@@ Line 3: / Line 3: @@
 <StructureSection load='5upw' size='340' side='right' caption='[[5upw]], [[Resolution|resolution]] 5.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5upw]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UPW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5upw]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Hiv-1 Hiv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UPW FirstGlance]. <br>
-</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=5upw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5upw OCA], [http://pdbe.org/5upw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5upw RCSB], [http://www.ebi.ac.uk/pdbsum/5upw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5upw ProSAT]</span></td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gag ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11698 HIV-1])</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=5upw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5upw OCA], [http://pdbe.org/5upw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5upw RCSB], [http://www.ebi.ac.uk/pdbsum/5upw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5upw ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
+[[Category: Hiv-1]]
 [[Category: Perilla, J R]]
 [[Category: Chemical shift]]

5upw

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Revision as of 03:53, 16 November 2017

CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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