Computational protocol: Structure of the human activating natural cytotoxicity receptor NKp30 bound to its tumor cell ligand B7-H6

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Protocol publication

[…] The structure of B7-H6 was solved by molecular replacement with Phaser () using the V-like and C-like domains of human PD-L1 (Protein Data Bank accession no. 3BIK; ) as separate search models. The partially refined B7-H6 structure and the human CTLA-4 structure (1I85; ) were used as search models for solving the structure of the NKp30–B7-H6 complex. All refinements were performed using the program CNS1.1 (), including iterative cycles of simulated annealing, positional refinement, and B factor refinement, interspersed with model rebuilding into σA-weighted Fo − Fc and 2Fo − Fc electron density maps using XtalView (). Refinement statistics are summarized in . Stereochemical parameters were evaluated with PROCHECK (). Atomic coordinates and structure factors for the NKp30–B7-H6 complex and B7-H6 have been deposited in the Protein Data Bank under accession nos. 3PV6 and 3PV7, respectively. […]

Pipeline specifications

Software tools CNS, PROCHECK
Application Protein structure analysis
Organisms Homo sapiens
Diseases Neoplasms, Drug-Related Side Effects and Adverse Reactions