2024-03-06 REL RCSB RCSB RCSB 2020-02-20 2020-03-18 2020-10-21 2024-03-06 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01-67167 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01-AI062520 United States Hexamer of Helical HIV capsid by RASTR method Zhao H Iqbal N Helical reconstruction, GS-6207 Hexamer HIV, VIRAL PROTEIN, RASTR Bester SM Wei G Zhao H Adu-Ampratwum D Iqbal N Courouble VV Francis AC Annamalai AS Singh PK Shkriabai N Van Blerkom P Morrison J Poeschla EM Engelman AN Melikyan GB Griffin PR Fuchs JR Asturias FJ Kvaratskhelia M Structural and mechanistic bases for a potent HIV-1 capsid inhibitor. Science US 370 360 364 2020 33060363 doi:10.1126/science.abb4808 1095-9203 0038 SCIEAS 6vws FULLOVERLAP Hexamer of helical HIV capsid protein Hexamer of helical HIV capsid protein 0 1 Human immunodeficiency virus 1 HIV capsid protein Human immunodeficiency virus 1 0.024613173999999998 6 Escherichia coli LEVO PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEW DRLHPVHAGPIEPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEP FRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG B6DRA0 helical helicalArray 3 8.0
1M NaCl, 50mM Tris pH 8.0
 C-flat COPPER 400 PLASMA CLEANING OTHER ETHANE 100 298 FEI VITROBOT MARK IV FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 1.2 0.7000000000000001 2.5 2.0 28000.0 28000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 80.0 GATAN K3 (6k x 4k) 5760 4092 4 4246 47.36 1 96392 7.61 150.32 C1 BACK PROJECTION 6.08 FSC 0.143 CUT-OFF cryoSPARC 2.0
A non-helical approach (RASTR) to calculate a volume from the same subset of data used for helical analysis. The position and rotation to the center of a single hexamer in the final helical volume was determined and used along the final refined helical rise and twist to extract a total of 245050 unique particles from which surrounding tube density was subtracted by reprojection using Relion. The resulting stack of 245050 particles, each extracted into a 192 multiple 192 pixel box centered around the chosen asymmetric unit for each subtracted volume, was imported into Cryosparc. 2D clustering and ab-initio heterogeneous reconstruction with 4 volumes were then used to select a subset of 96392 particle images. These images, along with the cleanest reference from ab-initio volume determination were then used to obtain a volume through 3D Refinement.
245050 146291 RELION 3.0.4
A total of 208,225helical segments were extracted from manually selected, well-ordered helical tubes using Relion
Featureless cylindrical shell as initial model made by Relion.
 NOT APPLICABLE RELION 3.0.4 3D refinement
3D refinement in Relion
 emd_21423.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 268.8 268.8 268.8 90.0 90.0 90.0 X Y Z -12.289834000000001 21.173817 -0.0052193888 0.5280938 1.4 1.4 1.4 3.3 AUTHOR Hexamer of Helical HIV capsid by RASTR 6VKV A 1-220 PDB experimental model RIGID BODY FIT REAL 204.639999999999986 emd_21423_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 560.0 560.0 560.0 90.0 90.0 90.0 X Y Z -0.016149225 0.041853525 0.0011572639 0.0036426543 1.4 1.4 1.4 EMDB Additional map