2024-11-20 REL RCSB RCSB RCSB 2021-11-30 2022-01-12 2022-01-12 2024-11-20 Other private United States cryoEM reconstruction of the HIV gp140 in complex with the extracellular domains of CD4 and the adnectin domain of Combinectin. The gp140 and CD4 coordinates from entry 6EDU were rigid body fitted to the EM map along withe the crystal structure of CD4+adnectin Concha NO William SP Inhibitor, HIV gp140, CD4, adnectin, ANTIVIRAL PROTEIN Wensel D Williams S Dixon DP Ward P McCormick P Concha N Stewart E Hong X Mazzucco C Pal S Ding B Fellinger C Krystal M Novel Bent Conformation of CD4 Induced by HIV-1 Inhibitor Indirectly Prevents Productive Viral Attachment. J.Mol.Biol. UK 434 167395 167395 2021 34896364 doi:10.1016/j.jmb.2021.167395 1089-8638 0070 JMOBAK 7t0o FULLOVERLAP Ternary complex of the HIV-1 gp140 trimer in complex with the extracellular domains (domains 1-4) of CD4 and an adnectin domain of Combinectin Ternary complex of the HIV-1 gp140 trimer in complex with the extracellular domains (domains 1-4) of CD4 and an adnectin domain of Combinectin 0 1 2 3 4 5 6
the gp140 trimer at 0.67 mg/ml was mixed with soluble CD4 first, and then with Combinection in a 1.25:1 ratio. The sample was incubated overnight at 4 degC. The sample was concentrated to 35ul before injecting into a Phenomenex 4.6 x 300 mm 3um bead 500Angstroms pore Yara SEC column equilibrated with 20mM Hepes pH7.5, 200 mM KCl, 5mM MgCl2. The complexes were eluted with a flow rate of 0.2 ml/min and fractions collected every 20 seconds into a Thermo-Fisher UV transparent 96-well plates. The absorbance at 280nm was measured for each fraction using a Spectramax plate scanner. The high-molecular weight complex appeared to be comprised of gp140:CD4:Combinectin in a 1:1:1 ratio. The sample used for cryo-EM studies was the single peak fraction of gp140/CD4/Combinectin (0.076 mg/ml)
 BG505 SOSIP.664 gp140 HIV-1 06TG.HT008 0.072830398 3 Homo sapiens LEVO AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIIS LWDQSLKPCVKLTPLCVTLNCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKE YRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRK HFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQ AMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR RAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQ QLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALDGSGSGG SGHHHHHHHH BG505 SOSIP.664 gp140 HIV-1 06TG.HT008 0.003337105 1 Homo sapiens LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) BG505 SOSIP.664 gp140 HIV-1 06TG.HT008 0.0032519999999999997 2 Homo sapiens LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) T-cell surface glycoprotein CD4 Homo sapiens 0.041385449 3 Spodoptera frugiperda LEVO KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSD TYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCT VLQNQKKVEFKIDIVVLAFQKASSIVYKKEGEQVEFSFPLAFTVEKLTGSGELWWQAERASSSKSWITFDLKNKEVSVKR VTQDPKLQMGKKLPLHLTLPQALPQYAGSGNLTLALEAKTGKLHQEVNLVVMRATQLQKNLTCEVWGPTSPKLMLSLKLE NKEAKVSKREKAVWVLNPEAGMWQCLLSDSGQVLLESNIKVLPTHHHHHH P01730 Adnectin Homo sapiens 0.011959172
The native 10th fibronectin type III (10Fn3) domain from human fibronectin was used as the template for construction of novel libraries of Adnectin variants (Wenzel, D., et al. (2017) Antimicrobial Agents and Chemotherapy, Vol 61(8), e00508-17, pp 1-19)
3 Escherichia coli LEVO GVSDVPRDLEVVAATPTSLLISWDAPAVTVHSYHIQYWPLGSYQRYQVFSVPGSKSTATISGLKPGVEYQIRVYAETGGA DSDQSMGWIQIGYRTEGDKPSQHHHHHH BG505 SOSIP.664 gp140 HIV-1 06TG.HT008 0.002996685 3 Homo sapiens LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) singleParticle particle 0.08 7.5 20.0 HEPES 200.0 KCl 5.0 MgCl Quantifoil R1.2/1.3 COPPER 400 GLOW DISCHARGE AIR 30.0
glow discharged for 20 sec using a EasyGlo (20mA, 0.3 mBar)
 ETHANE 100 277 FEI VITROBOT MARK IV
the gp140/CD4/Combinectin (0.076 mg/ml), 3.5uL were applied to Quantifoil 1.2/1.3 Cu 400 mesh grids that had previously been glow discharged for 20 sec using a EasyGlo (20mA, 0.3 mBar). The grids were plunged into liquid ethane using a Vitrobot plunger (chamber set to 4 degC and 80% RH) immediately after blotting from 2.5 to 4 sec
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.4000000000000001 3.4 OTHER Cs corrector FEI FALCON III (4k x 4k) COUNTING 4096 4096 1078 75.7 1.022 1
initial model generated with cisTEM
 3 C3 8.7 FSC 0.143 CUT-OFF RELION 208485 MAXIMUM LIKELIHOOD RELION MAXIMUM LIKELIHOOD RELION 4 RELION emd_25581.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 50 93 99 41 38 25 99 93 50 243.7776 229.00319 123.119995 90.0 90.0 90.0 Z Y X -5.1388183 28.004534 0.624528 2.529406 2.4624 2.4624 2.4624 4.42 EMDB RIGID BODY FIT emd_25581_msk_1.map