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dc.contributor.authorKim, Walter Minsub
dc.contributor.authorSigalov, Alexander B.
dc.contributor.authorStern, Lawrence J.
dc.date2022-08-11T08:08:47.000
dc.date.accessioned2022-08-23T16:08:17Z
dc.date.available2022-08-23T16:08:17Z
dc.date.issued2010-02-01
dc.date.submitted2010-05-09
dc.identifier.issn1399-0047
dc.identifier.pmid20124696
dc.identifier.urihttp://hdl.handle.net/20.500.14038/32413
dc.description.abstractHIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling zeta subunit of the T-cell receptor (TCRzeta). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nef(core)) in complex with two different TCRzeta fragments are described. The structure of SIVmac239 Nef(core) bound to the longer TCRzeta polypeptide (Leu51-Asp93) was determined to 3.7 A resolution (R(work) = 28.7%) in the tetragonal space group P4(3)2(1)2. The structure of SIVmac239 Nef(core) in complex with the shorter TCRzeta polypeptide (Ala63-Arg80) was determined to 2.05 A resolution (R(work) = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P2(1)2(1)2(1). The reduction in crystal space-group symmetry induced by the truncated TCRzeta polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, -l) and a and b unit-cell parameters that were nearly identical predisposed the P2(1)2(1)2(1) crystal form to pseudo-merohedral twinning.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=20124696&dopt=Abstract">Link to article in PubMed</a>
dc.rightsCitation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):163-75. Epub 2010 Jan 22. <a href="http://dx.doi.org/10.1107/S090744490904880X">Link to article on publisher's website</a>
dc.subjectAmino Acid Sequence
dc.subjectCrystallography, X-Ray
dc.subjectGene Products, nef
dc.subjectHydrogen Bonding
dc.subjectLigands
dc.subjectModels, Molecular
dc.subjectMolecular Sequence Data
dc.subjectPeptide Fragments
dc.subjectProtein Binding
dc.subjectProtein Interaction Domains and Motifs
dc.subjectProtein Structure, Quaternary
dc.subjectReceptors, Antigen, T-Cell
dc.subjectSimian immunodeficiency virus
dc.subjectLaboratory and Basic Science Research
dc.subjectMedicine and Health Sciences
dc.titlePseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.
dc.typeJournal Article
dc.source.journaltitleActa crystallographica. Section D, Biological crystallography
dc.source.volume66
dc.source.issuePt 2
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1013&amp;context=gsbs_mdphd&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/gsbs_mdphd/13
dc.identifier.contextkey1303276
refterms.dateFOA2022-08-23T16:08:18Z
html.description.abstract<p>HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling zeta subunit of the T-cell receptor (TCRzeta). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nef(core)) in complex with two different TCRzeta fragments are described. The structure of SIVmac239 Nef(core) bound to the longer TCRzeta polypeptide (Leu51-Asp93) was determined to 3.7 A resolution (R(work) = 28.7%) in the tetragonal space group P4(3)2(1)2. The structure of SIVmac239 Nef(core) in complex with the shorter TCRzeta polypeptide (Ala63-Arg80) was determined to 2.05 A resolution (R(work) = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P2(1)2(1)2(1). The reduction in crystal space-group symmetry induced by the truncated TCRzeta polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, -l) and a and b unit-cell parameters that were nearly identical predisposed the P2(1)2(1)2(1) crystal form to pseudo-merohedral twinning.</p>
dc.identifier.submissionpathgsbs_mdphd/13
dc.contributor.departmentDepartment of Pathology
dc.contributor.departmentGraduate School of Biomedical Sciences, MD/PhD Program
dc.contributor.studentWalter M. Kim


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