2024-12-25 REL RCSB RCSB RCSB 2017-04-28 2017-07-12 2017-07-12 2024-12-25 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) UM1 AI100663 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) P01 AI110657 United States Cryo-EM reconstruction of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding of 17b Pallesen J Ozorowski G de Val N Ward AB Viral fusion, HIV-1, envelope glycoprotein, CD4 receptor binding, IMMUNE SYSTEM Ozorowski G Pallesen J de Val N Lyumkis D Cottrell CA Torres JL Copps J Stanfield RL Cupo A Pugach P Moore JP Wilson IA Ward AB Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. Nature UK 547 360 363 2017 28700571 doi:10.1038/nature23010 1476-4687 0006 NATUAS EMD-8714 other EM volume EMD-8715 other EM volume EMD-8716 other EM volume EMD-8717 other EM volume 5vn3 FULLOVERLAP HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) and 17b fragment antigen binding HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) and 17b fragment antigen binding 0 1 2 3 4 5 0.63 HIV-1 Env B41 SOSIP.664 1 1 5 Human immunodeficiency virus 1 CD4 (2-domain) 1 4 Homo sapiens 17b fragment antigen 1 2 3 Homo sapiens 17b Fab light chain Homo sapiens 0.023425869 3 Homo sapiens LEVO ELELTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQS EDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG Envelope glycoprotein gp160 Human immunodeficiency virus 1 0.017357824 3 Homo sapiens LEVO AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVWGIKQLQARVLAVERYLRDQQ LLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQWEKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD B3UEZ6 Envelope glycoprotein gp160 Human immunodeficiency virus 1 0.05770246899999999 3 Homo sapiens LEVO MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACV PTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMET GEMKNCSFNVTTSIRDKIKKEYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTR KSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCN TTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV B3UES2 T-cell surface glycoprotein CD4 Homo sapiens 0.02050326 3 Homo sapiens LEVO KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSD TYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCT VLQNQKKVEFKIDIVVLAFQKASNT P01730 17b Fab heavy chain Homo sapiens 0.024484455000000002 3 Homo sapiens LEVO QVQLLESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVY LELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQGTLVTVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDY FPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 24 NAG singleParticle particle 4 7.4 150.0 NaCl sodium chloride 50.0 Tris 0.06 DDM
DDM was added to a final concentration of 0.06 mM prior to vitrification
 C-flat-2/2 COPPER 300 CARBON HOLEY PLASMA CLEANING OTHER ETHANE 277 HOMEMADE PLUNGER
3 uL of sample applied to a holey carbon grid on glow discharged face and blotted manually on sample side until filter paper detached from grid, followed by immediate plunging.
B41 SOSIP.664 was incubated with a 6X molar excess of soluble CD4 and 17b Fab overnight at room temperature, purified by size exclusion chromatography, and concentrated prior to grid application
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.0 4.0 22500.0 38168.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 4096 4096 1-50 1169 10.0 58.0 1 C3 3.7 FSC 0.143 CUT-OFF RELION 2.0 46855 PROJECTION MATCHING 7.5 RELION 2.0 PROJECTION MATCHING 0.94 RELION 2.0 RELION 2.0 emd_8713.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.17061247 0.3141209 0.000080461716 0.010144891 1.31 1.31 1.31 0.07 AUTHOR B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b FLEXIBLE FIT
Homology model of B41 SOSIP.664 created using PDB 5CEZ as initial model. sCD4 and 17b coordinates taken from PDB 1GC1. Performed fragment based refinement using Rosetta, followed by relaxed refinement in Rosetta. Modeled glycans using Chimera and performed final refinements using Phenix.
EMRinger REAL emd_8713_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.04315671 0.14083263 0.000080461716 0.0070226653 1.31 1.31 1.31 AUTHOR B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b, additional map emd_8713_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.018524056 0.064431004 0.000038337614 0.0034691156 1.31 1.31 1.31 AUTHOR B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b, half map emd_8713_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.017225277 0.06670444 0.000042124106 0.00347816 1.31 1.31 1.31 AUTHOR B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b, half-map