2023-03-08 REL RCSB RCSB RCSB 2021-08-04 2021-08-25 2021-08-25 2023-03-08 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) UM1-AI144371 United States Edwards RJ Mansouri K Saunders KO Edwards RJ Tilahun K Manne K Lu X Cain DW Wiehe K Williams WB Mansouri K Hernandez GE Sutherland L Scearce R Parks R Barr M DeMarco T Eater CM Eaton A Morton G Mildenberg B Wang Y Rountree RW Tomai MA Fox CB Moody MA Alam SM Santra S Lewis MG Denny TN Shaw GM Montefiori DC Acharya P Haynes BF Sci Transl Med US 14 eabo5598 eabo5598 2022 36070369 doi:10.1126/scitranslmed.abo5598 1946-6242 EMD-24619 associated EM volume Complex of HIV Env CH505TFchim.6R.SOSIP.664.v4.1 with DH1024 antibody Fab Complex of HIV Env CH505TFchim.6R.SOSIP.664.v4.1 with DH1024 antibody Fab 0 1 2 3 Human immunodeficiency virus 2 0.023 HIV Env CH505TFchim.6R.SOSIP.664.v4.1 trimer 1 1 Human immunodeficiency virus 2 DH1024 Antibody Fab 1 2 3 Macaca mulatta DH1024 Antibody Fab Heavy Chain 3 2 Macaca mulatta DH1024 Antibody Fab Light Chain 3 3 Macaca mulatta HIV Env CH505TFchim.6R.SOSIP.664.v4.1 Human immunodeficiency virus 2 Homo sapiens LEVO AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLKNVTENFNMWKNDMVDQMHEDVISLWDQSLKPCVKLTPLCVTLNCTNATASNSSIIEGMKNCSFNITTELRDKREKKNALFYKLDIVQLDGNSSQYRLINCNTSVITQACPKVSFDPIPIHYCAPAGYAILKCNNKTFTGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEGEIIIRSENITNNVKTIIVHLNESVKIECTRPNNKTRTSIRIGPGQAFYATGQVIGDIREAYCNINESKWNETLQRVSKKLKEYFPHKNITFQPSSGGDLEITTHSFNCGGEFFYCNTSSLFNRTYMANSTDMANSTETNSTRTITIHCRIKQIINMWQEVGRAMYAPPIAGNITCISNITGLLLTRDGGKNNTETFRPGGGNMKDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD DH1024 Antibody Fab Heavy Chain Macaca mulatta

Antibody Fab heavy chain

Homo sapiens LEVO QVQLQESGPGLVKPSETLSLTCGVSGGSVSYFNWWSWIRQPPGKGLEWIGSISGSSGSTHYNPSLKSRVTISTDTSKNQFSLKLSSVTAADTAVYHCASALKFLDWVLHSLRENNWFEVWGPGVLVTVSS astkg psvfplapss rstsestaal gclvkdyfpe pvtvswnsgs ltsgvhtfpa vlqssglysl ssvvtvpsss lgtqtyvcnv nhkpsntkvd krveiktcgg DH1024 Antibody Fab Light Chain Macaca mulatta Homo sapiens LEVO EIVMTQSPATLSLSPGERATLSCRASQSVSSYVAWYQQKPEQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISSLEPEDVGVYYCQQYNNWNSFGQGTKVEIK gqpkasptvt lfppsseelq ankatlvcli sdfypgvvkv awkadgsavn agvetttpsk qsnnkyaass ylsltsdqwk shksyscqvt hegstvektv apaecs singleParticle particle 0.8 7.4 20.0 HEPES N-2-Hydroxyethyl-piperazine-N-2-ethanesulfonic acid 150.0 NaCl sodium chloride 5.0 glycerol glycerol NEGATIVE uranyl formate

For negative staining, 5 microliter of the diluted filter retentate was applied to a freshly glow-discharged, 300 mesh, carbon-coated EM grid and incubated 10-12 s, then rinsed with 70 microliter of 2% uranyl formate delivered in one smooth ejection from a pipet. The drop of uranyl formate remaining on the grid was allowed to incubate for 60 s, then the grid was blotted with filter paper and allowed to air dry.

Homemade COPPER 300 CARBON CONTINUOUS 5.0 GLOW DISCHARGE 30

Frozen aliquots of SOSIP and Fab were thawed in an Aluminum block at room temperature for 2-3 minutes, then 10 microgram of SOSIP were mixed with 36 microgram Fab (~1:15 molar ratio) and diluted to 100 microliter final volume with HEPES-buffered saline (HBS), containing 20 mM HEPES buffer and 150 mM NaCl, pH 7.4, augmented with 5% glycerol. Mixture was incubated at 22 degrees C overnight. The following day, a 0.08% glutaraldehyde fixative was prepared by diluting an 8% stock 1/100 with HBS. Then 400 microliter of fixative was added to the SOSIP-Fab mixture and incubated 5 min at room temperature to crosslink the complex, followed by addition of 40 microliter of a 1 M Tris solution, pH 7.4 to quench any unreacted glutaraldehyde. The reaction mixture was then transferred to a 0.5-ml Amicon Ultra centrifugal filter device with a 100-kDa cutoff filter (Millipore, #UFC510096) and spun 10 min at 14,000 g in a benchtop centrifuge held at 20 degrees C to remove excess Fab. The filter retentate, usually ~25 microliter, was collected and diluted 1:1 with HBS augmented with 5% glycerol.

FEI/PHILIPS EM420 FLOOD BEAM BRIGHT FIELD LAB6 120 50.0 2.0 0.2 1.5 82000.0 SIDE ENTRY, EUCENTRIC NITROGEN OTHER 2048 2048 1 341 0.25 32.0

Images were collected with a minimal dose approach using a manually controlled low dose unit to keep the beam blanked except during initial grid orientation and image collection. To create an initial atlas, the entire grid was imaged once at 49x magnification at very low beam intensity by decreasing the emission current, strongly focusing C1 (Spot Size 6) and defocusing C2 (Intensity knob fully clockwise). The stage was then quickly translated to center the desired gridsquare, with an estimated exposure of < 2 s at this very low illumination level, at which point the beam was blanked. A 3,300x magnification was then selected so that a single gridsquare approximately fills the scintillator screen. The beam was then unblanked and the stage manually tilted and the eucentric height quickly adjusted by noting the movement of the gridbars, and then the stage was translated to center on the lower-left corner of the gridsquare, with an estimated exposure of < 2 s at this very low illumination level, at which point the beam was blanked. A magnfication of 82,000x was then selected and C2 focused by a known number of clicks of the Intensity knob so that the beam would approximately fill the scintillator screen. The beam was then unblanked, the objective lens focused by eye and then adjusted to approximately 0.5 micron underfocused, and C2 adjusted so the beam just filled the scintillator screen. Because this focusing step involved a long exposure to the focused beam, no data was collected in this area. For data collection, the stage was translated blindly, with the beam blanked, by noting the micrometer markings on the left-hand stage control, to move to an un-irradiated area that was approximately two screen-widths vertically away from the initial position. The beam was then unblanked, an image captured with 0.25 s exposure to the focused beam without any adjustment of the objective lens focus, and the beam then re-blanked. The FFT of the collected image was examined and the position of the first Thon ring noted and the objective lens focus adjusted if needed for subsequent images. The stage was then moved blindly in the same direction to an un-irradiated area and a new image collected. In this way images were collected until the gridbar was encountered, at which point the beam was unblanked and the stage moved so that the gridbar occluded all of the beam except a small sliver of the gridsquare at the bottom or top of the screen, and the right hand stage control was used to translate the specimen to a new location at least two screen widths away horizontally. In this way the entire gridsquare could be imaged in a rastered fashion with each area only irradiated with the full strength beam during the 0.25 s image capture.

1 231985 An unliganded (no Fab) Env trimer homology model was built with SwissModel using the CH505 sequence and PDB 5UM8 as template, then converted to a map using UCSF Chimera's molmap function with 15 angstrom resolution and 4.02 angstrom gridspacing

The starting model was further low-pass filtered to 60 angstroms for use in 3D classification. Resulting 3D classification map was used for as starting model for final 3d refinements.

1 C1 BACK PROJECTION 15.0 FSC 0.143 CUT-OFF RELION 3.0 6501 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 2 6083.0 RELION 3.0 emd_24619_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 96 96 96 0 0 0 96 96 96 385.91998 385.91998 385.91998 90.0 90.0 90.0 X Y Z -0.07413285 0.18593495 -0.00011054517 0.010002281 4.02 4.02 4.02 AUTHOR ::::EMDATABANK.org::::EMD-24619:::: Raw, unsharpened map of negative stain electron microscopy single particle reconstruction of monoclonal antibody DH1024 Fab in complex with HIV Env CH505 SOSIP trimer emd_24619_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 96 96 96 0 0 0 96 96 96 385.91998 385.91998 385.91998 90.0 90.0 90.0 X Y Z -0.08755163 0.18837924 -4.4964396e-05 0.010353076 4.02 4.02 4.02 AUTHOR ::::EMDATABANK.org::::EMD-24619:::: Half-map A of negative stain electron microscopy single particle reconstruction of monoclonal antibody DH1024 Fab in complex with HIV Env CH505 SOSIP trimer emd_24619_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 96 96 96 0 0 0 96 96 96 385.91998 385.91998 385.91998 90.0 90.0 90.0 X Y Z -0.0816794 0.18813622 -5.8439902e-05 0.01037685 4.02 4.02 4.02 AUTHOR ::::EMDATABANK.org::::EMD-24619:::: Half-map B of negative stain electron microscopy single particle reconstruction of monoclonal antibody DH1024 Fab in complex with HIV Env CH505 SOSIP trimer