2024-12-25 REL RCSB RCSB RCSB 2018-08-11 2018-10-17 2018-10-17 2024-12-25 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P50 GM082545-06 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) P01 AI100148 United States B41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-receptor mimicking antibody 21c and the broadly neutralizing antibody 8ANC195 Barnes CO Bjorkman PJ HIV-1 Env, broadly neutralizing antibodies, cryo-EM, single particle analysis, VIRAL PROTEIN-IMMUNE SYSTEM complex, IMMUNE SYSTEM Wang H Barnes CO Yang Z Nussenzweig MC Bjorkman PJ Partially Open HIV-1 Envelope Structures Exhibit Conformational Changes Relevant for Coreceptor Binding and Fusion. Cell Host Microbe US 24 579 592.e4 2018 30308160 doi:10.1016/j.chom.2018.09.003 1934-6069 EMD-7516 other EM volume
Map contains BG505 Env bound by sCD4, 8ANC195, and 17b Fabs.
 6edu FULLOVERLAP B41 SOSIP-sCD4-21c-8ANC195 complex B41 SOSIP-sCD4-21c-8ANC195 complex 0 1 2 3 4 5 6 7 Homo sapiens 0.7 Envelope glycoprotein gp160 Human immunodeficiency virus 1 0.017357824 3 Cricetulus griseus LEVO AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVWGIKQLQARVLAVERYLRDQQ LLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQWEKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD B3UEZ6 Envelope glycoprotein gp160 Human immunodeficiency virus 1 0.05770246899999999 3 Cricetulus griseus 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 21c Fab VH domain Homo sapiens 0.02461959 3 Homo sapiens LEVO QVQVVQSGAEVRKPGASVKVSCKVSGFTLTGLSIHWVRQAPGKGLEWMGGFGPEENEIIYAQKFQGRVSMTEDTSTNTAY MELSSLRSEDTAVYYCATGGNYYNLWTGYYPLAYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPE PVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKT 21c Fab VL domain Homo sapiens 0.022815264 3 Homo sapiens LEVO QSVLTQPPSVSAAPGQKVTISCSGSSSNIGKNYVSWYQQLPGAAPKLLIFDDTQRPSGIPDRFSGSKSGTSATLAITGLQ TGDEADYYCGTWDSSLSTGQLFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPV KAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTMAHAECS 8ANC195 G52K5 Fab VH domain Homo sapiens 0.02612527 3 Homo sapiens LEVO QIHLVQSGTEVKKPGSSVTVSCKAYGVNTFGLYAVNWVRQAPGQSLEYIGQIWRWKSSASHHFRGRVLISAVDLTGSSPP ISSLEIKNLTSDDTAVYFCTTTSTYDKWSGLHHDGVMAFSSWGQGTLISVSAASTKGPSVFPLAPSSKSTSGGTAALGCL VKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHH HHHH 8ANC195 G52K5 Fab VL domain Homo sapiens 0.023401984 3 Homo sapiens LEVO DIQMTQSPSTLSASIGDTVRISCRASQSITGNWVAWYQQRPGKAPRLLIYRGAALLGGVPSRFSGSAAGTDFTLTIGNLQ AEDFGTFYCQQYDTYPGTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 27 NAG singleParticle particle 0.35 8.0 20.0 Tris Tris 125.0 NaCl Sodium Chloride Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY ARRAY GLOW DISCHARGE AIR
0.26 mA
 ETHANE 95 293 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.7 3.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1 2531 10.0 60.0 1 5THR
A model structure of the Env-sCD4-21c-8ANC195 complex was generated by replacing 17b Fab with 21c Fab in the partially-open BG505-sCD4-17b-8ANC195 structure (PDB 5THR). The 21c Fab binding angle was determined by aligning gp120s from the gp120-sCD4-21c crystal structure (PDB 3LQA) and the BG505-sCD4-17b-8ANC195 structure. The modeled structure was low-pass filtered to 60 Angstroms to serve as the initial 3D reference.
 4 C3 4.06 FSC 0.143 CUT-OFF RELION 2.1 305469 NOT APPLICABLE NOT APPLICABLE 4 RELION 2.1 emd_9038.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 377.27997 377.27997 377.27997 90.0 90.0 90.0 X Y Z -0.10165401 0.19407721 0.000012395091 0.0050455267 1.31 1.31 1.31 0.041 AUTHOR Sharpened map of complex used for model building and refinement. RIGID BODY FIT Correlation coefficient REAL emd_9038_msk_2.map emd_9038_msk_1.map emd_9038_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 377.27997 377.27997 377.27997 90.0 90.0 90.0 X Y Z -0.13950668 0.2453407 0.0000070199203 0.0057889447 1.31 1.31 1.31 AUTHOR Sharpened map of focused refinement of 21c, gp120, and sCD4. Used for model building and refinement of V1V2 region, 21c-gp120 interface, and 21c-sCD4 interface.