Computational protocol: Structure of a Novel Shoulder-to-Shoulder p24 Dimer in Complex with the Broad-Spectrum Antibody A10F9 and Its Implication in Capsid Assembly

Similar protocols

Protocol publication

[…] Crystals were cryo-protected in the reservoir solution, which was supplemented with 25–30% glycerol, and flash cooled at 100 K. The diffraction data from the p24:A10F9 crystals were collected at the Shanghai Synchrotron Radiation Facility (SSRF) beamline BL17U using a Quantum-315r CCD Area Detector. All of the datasets were processed using the HKL-2000 program package (www.hkl-xray.com). The structures of the BMJ4 p24 dimer in complex with the A10F9 Fab fragment were determined by molecular replacement using Fab 13B5 as the search model (PDBID: 1E6J). The A10F9 Fab fragment part was built and refined first, and the p24 dimer model was subsequently built after several rounds of refinement on the A10F9 Fab model only. The model was built using the O program (http://xray.bmc.uu.se/alwyn) and refined using REFMAC/CCP4 (www.ccp4.ac.uk) with the crystallographic statistics listed in . Our current complex model includes two A10F9 Fab fragment copies and one p24 CTD dimer (residues 149–221), and the p24 NTD is not included in our final model due to the low quality of its density map. […]

Pipeline specifications

Software tools HKL-2000, CCP4
Application Protein structure analysis
Organisms Human immunodeficiency virus 1, Dipturus trachyderma, Human immunodeficiency virus 2
Chemicals Cysteine, Fullerenes