2018-02-14 REL RCSB RCSB RCSB 2017-04-28 2017-06-14 2017-07-26 2018-02-14 Cryo-EM reconstruction of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) Pallesen J Ozorowski G de Val N Ward AB 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-8715 associated EM volume
Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b
 EMD-8713 other EM volume EMD-8714 other EM volume EMD-8716 other EM volume EMD-8717 other EM volume HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) 0 1 2 3 0.48 HIV-1 Env B41 SOSIP.664 1 1 2 Human immunodeficiency virus 1 Homo sapiens HEK293F CD4 (2-domain) 1 3 Homo sapiens Homo sapiens HEK293F HIV-1 Env B41 SOSIP.664 gp41 Human immunodeficiency virus 1 9032-08.A1.4685 Homo sapiens LEVO AVGLGA FILGFLGAAG STMGAASMAL TVQARLLLSG IVQQQNNLLR APEAQQHMLQ LTVWGIKQLQ ARVLAVERYL RDQQLLGIWG CSGKIICCTN VPWNDSWSNK TINEIWDNMT WMQWEKEIDN YTQHIYTLLE VSQIQQEKNE QELLELD HIV-1 Env B41 SOSIP.664 gp120 Human immunodeficiency virus 1 9032-08.A1.4685 Homo sapiens LEVO MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV HNVWATHACV PTDPNPQEIV LGNVTENFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCNNVN TNNTNNSTNA TISDWEKMET GEMKNCSFNV TTSIRDKIKK EYALFYKLDV VPLENKNNIN NTNITNYRLI NCNTSVITQA CPKVSFEPIP IHYCAPAGFA ILKCNSKTFN GSGPCTNVST VQCTHGIRPV VSTQLLLNGS LAEEEIVIRS ENITDNAKTI IVQLNEAVEI NCTRPNNNTR KSIHIGPGRA FYATGDIIGN IRQAHCNISK ARWNETLGQI VAKLEEQFPN KTIIFNHSSG GDPEIVTHSF NCGGEFFYCN TTPLFNSTWN NTRTDDYPTG GEQNITLQCR IKQIINMWQG VGKAMYAPPI RGQIRCSSNI TGLLLTRDGG RDQNGTETFR PGGGNMRDNW RSELYKYKVV KIEPLGIAPT ACKRRVVQRRRR Soluble CD4 (2-domain) Homo sapiens Homo sapiens LEVO KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSD TYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCT VLQNQKKVEFKIDIVVLAFQKASNT 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 overnight at room temperature, purified by size exclusion chromatography, and concentrated prior to grid application
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.7 0.8 2.5 36000. 43478. OTHER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 4096 4096 0.000115 1-50 1540 10.0 65.0 1 Gctf 1.06 C3 5.2 FSC 0.143 CUT-OFF RELION 2.0 46567 PROJECTION MATCHING 7.5 RELION 2.0 PROJECTION MATCHING 1.88 RELION 2.0 RELION 2.0 emd_8715.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 309.76 309.76 309.76 90.0 90.0 90.0 X Y Z -0.03765318 0.16243076 0.0006033636 0.007123429 1.21 1.21 1.21 0.05 AUTHOR HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) emd_8715_additional.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 309.76 309.76 309.76 90.0 90.0 90.0 X Y Z -0.009772984 0.109874375 0.0006033636 0.006318402 1.21 1.21 1.21 0.05 AUTHOR HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain), additional map emd_8715_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 309.76 309.76 309.76 90.0 90.0 90.0 X Y Z -0.009187592 0.049810626 0.0002892262 0.0030146257 1.21 1.21 1.21 0.05 AUTHOR emd_8715_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 309.76 309.76 309.76 90.0 90.0 90.0 X Y Z -0.008312324 0.048914015 0.00028187493 0.0030230326 1.21 1.21 1.21 0.05 AUTHOR