SPA of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly.

2026-08-05 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY citation citation_author em_admin em_entity_assembly em_entity_assembly_naturalsource em_specimen em_support_film em_vitrification entity entity_src_gen pdbx_database_related struct _citation.title _em_admin.last_update _em_admin.title _em_entity_assembly.details _em_entity_assembly_naturalsource.strain _em_specimen.details _em_support_film.thickness _em_vitrification.chamber_temperature _em_vitrification.humidity _entity.pdbx_description _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_strain _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_scientific_name _struct.title STRUCTURE_SUMMARY citation citation_author em_admin em_entity_assembly em_entity_assembly_naturalsource em_specimen em_support_film em_vitrification entity entity_src_gen pdbx_database_related _citation.title _em_admin.last_update _em_admin.title _em_entity_assembly.details _em_entity_assembly_naturalsource.strain _em_specimen.details _em_support_film.thickness _em_vitrification.chamber_temperature _em_vitrification.humidity _entity.pdbx_description _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_strain _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_scientific_name DATABASE_REFERENCES citation em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update COORDINATE_REPLACEMENT AUTHOR Model completeness STRUCTURE_SUMMARY atom_site em_admin entity entity_src_gen pdbx_contact_author pdbx_entity_instance_feature pdbx_struct_assembly pdbx_struct_assembly_gen pdbx_struct_oper_list pdbx_unobs_or_zero_occ_atoms pdbx_validate_planes pdbx_validate_rmsd_angle pdbx_validate_rmsd_bond _em_admin.last_update _entity.pdbx_description _entity_src_gen.pdbx_gene_src_gene _pdbx_struct_oper_list.id _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.type _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] STRUCTURE_SUMMARY em_admin entity entity_src_gen _em_admin.last_update _entity.pdbx_description _entity_src_gen.pdbx_gene_src_gene RCSB RCSB 2024-12-22 2026-01-14 2026-01-14 2026-08-05 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01AI147890 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) U54AI170855 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) U24GM129547 United States National Science Foundation (NSF, United States) DMR-1719875 United States SPA of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly. Ricana CL Dick RA HIV, Mature, VLP, Lenacapavir, VIRUS LIKE PARTICLE Ricana CL Brancato SG Highland CM Ekbataniamiri F Ambrus K Rey JS Faerch M Torbett BE Perilla JR Dick RA Lenacapavir prevents production of infectious HIV-1 by abrogating immature virus assembly. Biorxiv US 2026 41867786 doi:10.64898/2026.03.02.709178 2692-8205 9mnm FULLOVERLAP EMDB EMD-48430 associated EM volume

SPA of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology) in the presence of 500 uM LEN.

HIV-1 HIV-1 0 1

Purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly.

HIV-1 BH10 Homo sapiens Capsid 1000.0 VIRUS-LIKE PARTICLE STRAIN false true Capsid protein p24 Human immunodeficiency virus type 1 BH10 BH10 0.025630425999999998 4 Escherichia coli LEVO PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEW DRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEP FRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL P12493 Lenacapavir 0.000968282 3 QNG INOSITOL HEXAKISPHOSPHATE 0.0006600349999999999 2 IHP singleParticle particle 13 6.2 25.0 C6H13NO4S MES 2.0 C9H15O6P TCEP 500.0 C39H32ClF10N7O5S2 Lenacapavir

25 mM MES, 2mM TCEP, 500 uM LEN

Quantifoil R2/2 GOLD 300 CARBON HOLEY 120.0 GLOW DISCHARGE 45 AIR 0.027

Vacuum held for 30 sec before 20 mA were applied for 45 sec.

ETHANE 90 279 LEICA EM GP

Purified HIV-1 CASPNC protein in vitro assembled with IP6 (immature morphology). 500 uM LEN was added post assembly.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.4 2.4 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 93.15 103.15 GIF Bioquantum 20

Preliminary grid screening was performed manually.

GATAN K3 BIOCONTINUUM (6k x 4k) 11520 8184 1 7510 1.731 50.0

Images were collected in movie-mode with 50 frames per image at a total dose of 50 e-/A2.

1 25118581 CTFFIND 4.1.14 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab-initio

C6 BACK PROJECTION 3.5 FSC 0.143 CUT-OFF RELION 5.0 594567 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 MAXIMUM LIKELIHOOD RELION 5.0

Iterative Bayesian sampling approach via RELION 5.0

RELION 5.0 emd_48430.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 295.92 295.92 295.92 90.0 90.0 90.0 X Y Z -0.003998664 0.008762086 0.000007525749 0.00041589414 0.822 0.822 0.822 0.0018 AUTHOR ::::EMDATABANK.org::::EMD-48430:::: Refine 3D map of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly. Determined via SPA. 8G6M PDB experimental model FLEXIBLE FIT

Molecular dynamics flexible fitting was done using NAMD targeting cross-correlation coefficients.

Cross-correlation coefficient REAL emd_48430_msk_1.map emd_48430_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 295.92 295.92 295.92 90.0 90.0 90.0 X Y Z -0.025189776 0.044449132 0.000038499435 0.00094308547 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-48430:::: Postprocess map of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly. Determined via SPA. emd_48430_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 295.92 295.92 295.92 90.0 90.0 90.0 X Y Z -0.0049176016 0.009096146 0.000009214262 0.00048790956 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-48430:::: Refine 3D half1 map of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly. Determined via SPA. emd_48430_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 295.92 295.92 295.92 90.0 90.0 90.0 X Y Z -0.004784919 0.010203128 0.000008762202 0.0005146198 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-48430:::: Refine 3D half2 map of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly. Determined via SPA.