3IK5

SIVmac239 Nef in complex with TCR zeta ITAM 1 polypeptide (A63-R80)

Summary for 3IK5

• Entry DOI: 10.2210/pdb3ik5/pdb
• Descriptor: Protein Nef, T-cell surface glycoprotein CD3 zeta chain (3 entities in total)
• Functional Keywords: protein-protein complex, cell membrane, lipoprotein, membrane, myristate, viral immunoevasion, virulence, disulfide bond, host-virus interaction, phosphoprotein, receptor, transmembrane, viral protein-antiviral protein complex, viral protein-signaling protein complex, viral protein/signaling protein
• Biological source: Simian immunodeficiency virus (SIV-cpz); More
• Cellular location: Membrane; Single-pass type I membrane protein: P20963
• Total number of polymer chains: 4
• Total formula weight: 37732.04

Authors

Kim, W.M.,Sigalov, A.B.,Stern, L.J. (deposition date: 2009-08-05, release date: 2010-02-02, Last modification date: 2024-02-21)

Primary citation

Kim, W.M.,Sigalov, A.B.,Stern, L.J.
Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.
Acta Crystallogr.,Sect.D, 66:163-175, 2010

PubMed Abstract: 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.

PubMed: 20124696
DOI: 10.1107/S090744490904880X

Experimental method

X-RAY DIFFRACTION (2.05 Å)