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PDBsum entry 3ioz

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protein Protein-protein interface(s) links
Viral protein/signaling protein PDB id
3ioz
Jmol
Contents
Protein chains
109 a.a. *
16 a.a. *
* Residue conservation analysis
PDB id:
3ioz
Name: Viral protein/signaling protein
Title: Sivmac239 nef in complex with a tcr zeta polypeptide dp1 (l5
Structure: Protein nef. Chain: a. Engineered: yes. T-cell surface glycoprotein cd3 zeta chain. Chain: b. Synonym: t-cell receptor t3 zeta chain. Engineered: yes
Source: Simian immunodeficiency virus. Organism_taxid: 388909. Expressed in: escherichia coli. Expression_system_taxid: 469008. Homo sapiens. Human. Organism_taxid: 9606.
Resolution:
3.70Å     R-factor:   0.302     R-free:   0.329
Authors: W.M.Kim,A.B.Sigalov,L.J.Stern
Key ref: W.M.Kim et al. (2010). Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments. Acta Crystallogr D Biol Crystallogr, 66, 163-175. PubMed id: 20124696
Date:
15-Aug-09     Release date:   02-Feb-10    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5QGG3  (Q5QGG3_SIV) -  Protein Nef
Seq:
Struc:
263 a.a.
109 a.a.
Protein chain
Pfam   ArchSchema ?
P20963  (CD3Z_HUMAN) -  T-cell surface glycoprotein CD3 zeta chain
Seq:
Struc:
164 a.a.
16 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     cell surface receptor signaling pathway   1 term 
  Biochemical function     transmembrane signaling receptor activity     2 terms  

 

 
Acta Crystallogr D Biol Crystallogr 66:163-175 (2010)
PubMed id: 20124696  
 
 
Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.
W.M.Kim, A.B.Sigalov, L.J.Stern.
 
  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.