2025-04-16 REL PDBe 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 DATABASE_REFERENCES citation citation_author em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin em_virus_natural_host _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID _em_admin.last_update _em_virus_natural_host.ncbi_tax_id _em_virus_natural_host.organism SOURCE_AND_TAXONOMY citation citation_author em_admin em_virus_natural_host _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID _em_admin.last_update _em_virus_natural_host.ncbi_tax_id _em_virus_natural_host.organism DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _citation.page_last _em_admin.last_update PDBe PDBe 2024-10-10 2024-12-04 2024-12-04 2025-04-16 German Research Foundation (DFG) 240245660 - SFB 1129 (project 5 HGK, project 6 BM, project 931 21 JAGB) Germany German Research Foundation (DFG) DFG KR 906/7-1 (HGK) Germany National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) T32 AI055403 United States Max Planck Society Germany Mature HIV-1 matrix from MA-SP1 cleavage mutant Stacey JCV Hrebik D Briggs JAG HIV-1, HIV, matrix, mature, spacer peptide 2, SP2, VIRAL PROTEIN Stacey JCV Hrebik D Nand E Shetty SD Qu K Boicu M Anders-Osswein M Uchil PD Dick RA Mothes W Krausslich HG Muller B Briggs JAG The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation. Nature UK 640 258 264 2025 40011770 doi:10.1038/s41586-025-08624-9 1476-4687 0006 NATUAS Stacey JCV Hrebik D Nand E Shetty SD Qu K Boicu M Anders-Osswein M Dick RA Mothes W Krausslich HG Muller B Briggs JAG The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation. Biorxiv US 2024 39574591 doi:10.1101/2024.11.06.622200 2692-8205 9h1p FULLOVERLAP HIV-1 vector pNL4-3 HIV-1 vector pNL4-3 0 1 2
HEK293T cells were transfected with pcHIV which was expressed and purified.
HIV-1 vector pNL4-3 Homo sapiens 82 Gag 1200.0 VIRUS-LIKE PARTICLE STRAIN true false HIV-1 mature matrix 1 1 2
HIV-1 mature matrix as a part of the MA-SP1 polypeptide, in a complex with SP2
HIV-1 vector pNL4-3 Gag polyprotein Human immunodeficiency virus type 1 group M subtype B (isolate NY5) 0.014734615999999999 12 Homo sapiens LEVO GARASVLSGGELDKWEKIRLRPGGKKQYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNT IAVLYCVHQRIDVKDTKEALDKIEEEQNKSKKKAQQAAADTGNNSQVSQNY P12493 Gag polyprotein Human immunodeficiency virus type 1 group M subtype B (isolate NY5) 0.0018451539999999999
spacer peptide 2
12 Homo sapiens LEVO FLGKIWPSHKGRPGNF P12493 singleParticle particle 7.4 8.1 Na2HPO4 disodium hydrogen phosphate 1.5 KH2PO4 potassium dihydrogen phosphate 137.0 NaCl sodium chloride 2.7 KCl potassium chloride
PBS
 Quantifoil R2/2 COPPER 300 CARBON HOLEY 50.0 GLOW DISCHARGE AIR ETHANE-PROPANE 100 293 LEICA EM GP
purified HIV-1 MA-SP1 particles in PBS
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.6 0.45 3.6 4.5 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 88.0 93.0 TFS Selectris 15 FEI FALCON IV (4k x 4k) 4096 4096 1 14222 4.0 40.0
EER mode
 1 5704512
A new model was trained in crYOLO using a training dataset annotated in a randomly selected set of 50-100 micrographs. Annotation was performed in the crYOLO boxmanager GUI placing positions all over the visible surface of an HIV virus particle. The picks did not distinguish individual proteins or membranes.
 EMD-13088 C3 BACK PROJECTION 3.1 FSC 0.143 CUT-OFF cryoSPARC 4.3 5486693 MAXIMUM LIKELIHOOD cryoSPARC 4.3 MAXIMUM LIKELIHOOD cryoSPARC 4.3 6 210000.0 cryoSPARC 4.3
particle stack after 2D classification was split into 4 independent subsets and each subset was classified independently
 emd_51769.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 486.4 486.4 486.4 90.0 90.0 90.0 X Y Z -1.3631687 2.2647994 -0.00377327 0.03979854 0.95 0.95 0.95 0.25 AUTHOR Sharpened map of the mature HIV matrix solved from the virion of the HIV-1 MA-SP1 cleavage mutant. 2H3I A PDB experimental model FLEXIBLE FIT cross-correlation REAL 52.490000000000002 emd_51769_msk_1.map emd_51769_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 486.4 486.4 486.4 90.0 90.0 90.0 X Y Z -0.1860875 0.41787973 -0.0037732697 0.023160411 0.95 0.95 0.95 AUTHOR Unsharpened map of the mature HIV matrix solved from the virion of the HIV-1 MA-SP1 cleavage mutant. emd_51769_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 486.4 486.4 486.4 90.0 90.0 90.0 X Y Z -0.19499336 0.415638 -0.0011163803 0.028495409 0.95 0.95 0.95 AUTHOR Half map 2 of the mature HIV matrix solved from the virion of the HIV-1 MA-SP1 cleavage mutant. emd_51769_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 486.4 486.4 486.4 90.0 90.0 90.0 X Y Z -0.19695349 0.43188018 -0.0011064699 0.028537335 0.95 0.95 0.95 AUTHOR Half map 1 of the mature HIV matrix solved from the virion of the HIV-1 MA-SP1 cleavage mutant.