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.

2xi1

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 06:13, 5 August 2020

Crystal structure of the HIV-1 Nef sequenced from a patient's sample

Structural highlights

2xi1 is a 2 chain structure with sequence from Hiv-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

HIV-1 Nef modulates disease progression through interactions with over 30 host proteins. Individual chains fold into membrane-interacting N-terminal and C-terminal core (Nef(core)) domains respectively. Nef exists as small oligomers near membranes and associates into higher oligomers such as tetramers or hexadecamers in the cytoplasm. Earlier structures of the Nef(core) in apo and complexed forms with the Fyn-kinase SH3 domain revealed dimeric association details and the role of the conserved PXXP recognition motif (residues 72-78) of Nef in SH3-domain interactions. The crystal structure of the tetrameric Nef reported here corresponds to the elusive cytoplasmic stage. Comparative analyses show that subunits of Nef(core) dimers (open conformation) swing out with a relative displacement of approximately 22 A and rotation of approximately 174 degrees to form the 'closed' tetrameric structure. The changes to the association are around Asp125, a conserved residue important for viral replication and the important XR motif (residues 107-108). The tetramer associates through C4 symmetry instead of the 222 symmetry expected when two dimers associate together. This novel dimer-tetramer transition agrees with earlier solution studies including small angle X-ray scattering, analytical ultracentrifugation, dynamic laser light scattering and our glutaraldehyde cross-linking experiments. Comparisons with the Nef(core)-Fyn-SH3 domain complexes reveal that the PXXP motif that interacts with the SH3-domain in the dimeric form is sterically occluded in the tetramer. However the 151-180 loop that is distal to the PXXP motif and contains several protein interaction motifs remains accessible. The results suggest how changes to the oligomeric state of Nef can help it distinguish between protein partners.

A Novel Dimer-Tetramer Transition Captured by the Crystal Structure of the HIV-1 Nef.,Singh P, Yadav GP, Gupta S, Tripathi AK, Ramachandran R, Tripathi RK PLoS One. 2011;6(11):e26629. Epub 2011 Nov 2. PMID:22073177^[1]

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

References

↑ Singh P, Yadav GP, Gupta S, Tripathi AK, Ramachandran R, Tripathi RK. A Novel Dimer-Tetramer Transition Captured by the Crystal Structure of the HIV-1 Nef. PLoS One. 2011;6(11):e26629. Epub 2011 Nov 2. PMID:22073177 doi:10.1371/journal.pone.0026629

1 Structural highlights
2 Publication Abstract from PubMed
3 See Also
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2xi1"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the HIV-1 Nef sequenced from a patient's sample==
-<StructureSection load='2xi1' size='340' side='right' caption='[[2xi1]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+<StructureSection load='2xi1' size='340' side='right'caption='[[2xi1]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xi1]] is a 2 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=2XI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XI1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xi1]] is a 2 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=2XI1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2XI1 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=2xi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xi1 OCA], [http://pdbe.org/2xi1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xi1 RCSB], [http://www.ebi.ac.uk/pdbsum/2xi1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xi1 ProSAT]</span></td></tr>
+</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=2xi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xi1 OCA], [http://pdbe.org/2xi1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xi1 RCSB], [http://www.ebi.ac.uk/pdbsum/2xi1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xi1 ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 17: / Line 17: @@
 ==See Also==
-*[[HIV-1 NEF|HIV-1 NEF]]
 *[[Protein Nef|Protein Nef]]
 == References ==
@@ Line 24: / Line 23: @@
 </StructureSection>
 [[Category: Hiv-1]]
+[[Category: Large Structures]]
 [[Category: Gupta, S]]
 [[Category: Ramachandran, R]]

2xi1

From Proteopedia

Revision as of 06:13, 5 August 2020

Crystal structure of the HIV-1 Nef sequenced from a patient's sample

Structural highlights

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox