Computational protocol: Structures of CD6 and Its Ligand CD166 Give Insight into Their Interaction

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Protocol publication

[…] Native datasets were collected for CD6 and CD166, to 3.15 Å and 1.86 Å, respectively. The data were integrated and scaled using XDS () and aimless () as implemented in XIA2 (). Molecular replacement search models were generated using CHAINSAW (), and large loops removed. The structure of human CD6 was solved by searching for three copies of a search model derived from the Mac2 binding protein, a single SRCR domain (PDB: 1BY2; ) using PHASER (), part of the CCP4 software suite (). The human CD166 structure was solved by searching with a search model derived from the second immunoglobulin domain in the ligand binding domain of human RAGE (PDB: 3CJJ; ). Model building and refinement were carried out using Coot () and AUTOBUSTER (). The CD6 and CD166 structures were refined to Rwork/Rfree of 0.25/0.28 and 0.22/0.24, respectively. Coordinates were deposited in the PDB (PDB: 5a2e for CD6 and PDB: 5a2f for CD166). […]

Pipeline specifications

Software tools XDS, CCP4, xia2, Coot
Applications Small-angle scattering, Protein structure analysis
Organisms Dipturus trachyderma
Chemicals Cysteine