2024-11-13 REL RCSB RCSB RCSB 2019-04-25 2019-06-12 2020-10-21 2024-11-13 Other private 109718-63-RKNT United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM069832 United States CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35 Ozorowski G Torres JL HIV-1, Env, CD4, receptor-bound state, small molecule, fusion inhibitor, VIRAL PROTEIN, VIRAL PROTEIN-Immune System complex Ozorowski G Torres JL Santos-Martins D Forli S Ward AB A Strain-Specific Inhibitor of Receptor-Bound HIV-1 Targets a Pocket near the Fusion Peptide. Cell Rep US 33 108428 108428 2020 33238117 doi:10.1016/j.celrep.2020.108428 2211-1247 Ozorowski G Torres JL Santos-Martins D Forli S Ward AB A strain-specific inhibitor of receptor-bound HIV-1 targets a pocket near the fusion peptide and offers a template for drug design Biorxiv US 2020 doi:10.1101/2020.06.11.146654v1 2692-8205 6opn FULLOVERLAP CD4- and 17b-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35 CD4- and 17b-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35 0 1 2 3 Human immunodeficiency virus 1 0.05 17b fragment antigen binding 1
17b Fab added to aid in particle tumbling and initial alignments. Most of the Fab was masked out during final refinements to increase resolution of particle core and small molecule binding pocket.
 Envelope glycoprotein gp160 Human immunodeficiency virus 1 0.058872902 3 Homo sapiens LEVO MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACV PTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMET GEMKNCSFNVTTSIRDKIKKEYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTR KSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCN TTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRVVQRRRRRR B3UES2 Envelope glycoprotein gp41 Human immunodeficiency virus 1 B41 0.017357824 3 Homo sapiens LEVO AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVWGIKQLQARVLAVERYLRDQQ LLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQWEKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD B3UEZ6 T-cell surface glycoprotein CD4 Homo sapiens 0.023039171999999997 3 Homo sapiens LEVO METDTLLLWVLLLWVPGSTGKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQG GKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAGGSGHHHHHH P01730 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 27 NAG [3'-(5-methyl-1,3,4-oxadiazol-2-yl)[1,1'-biphenyl]-3-yl](piperidin-1-yl)methanone 0.00034741 3 N07 singleParticle particle 6 7.4 50.0 Tris 150.0 NaCl 1.0 dimethyl sulfoxide 0.005 lauryl maltose neopentyl glycol
Detergent (LMNG) added shortly (<5 minutes) prior to grid freezing using an 8X concentrated stock.
 C-flat-2/2 COPPER 400 CARBON HOLEY PLASMA CLEANING ETHANE 100 283 FEI VITROBOT MARK IV
Complex of CD4- and 17b-bound B41 SOSIP was SEC purified and GO35 was diluted 1:100 into the complex and incubated for 1 hr prior to grid freezing.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.6 2.2 29000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1285 12.5 60.0 1 EMD-8715 1 C3 3.5 FSC 0.143 CUT-OFF cryoSPARC 2 Non-uniform refinement
FSC resolution estimation calculated using CryoSparc 2 and Relion 3.0
30415 MAXIMUM LIKELIHOOD cryoSPARC 2 MAXIMUM LIKELIHOOD cryoSPARC 2 3 33000.0 cryoSPARC 2 emd_20150.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 296.63998 296.63998 296.63998 90.0 90.0 90.0 X Y Z -0.7688051 1.6918817 -0.00014661852 0.063546844 1.03 1.03 1.03 0.4 AUTHOR Sharpened map 5VN3 PDB experimental model FLEXIBLE FIT REAL emd_20150_msk_1.map emd_20150_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 296.63998 296.63998 296.63998 90.0 90.0 90.0 X Y Z -1.4415941 1.9370573 0.0025670235 0.18212047 1.03 1.03 1.03 AUTHOR Half map B emd_20150_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 296.63998 296.63998 296.63998 90.0 90.0 90.0 X Y Z -1.434098 1.8240539 0.0025274812 0.18690741 1.03 1.03 1.03 AUTHOR Half map A