2025-03-05 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 INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update RCSB RCSB 2024-06-06 2024-12-18 2024-12-18 2025-03-05 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35 GM150960 United States Structure of Human Adaptor Protein Complex AP-3 in the Apo State Begley MC Baker RW Adaptor Protein complex, AP-3, Lysosomal transport, Endosomal transport, Protein trafficking, TRANSPORT PROTEIN Begley M Aragon M Baker RW A structure-based mechanism for initiation of AP-3 coated vesicle formation. Proc.Natl.Acad.Sci.USA US 121 e2411974121 e2411974121 2024 39705307 doi:10.1073/pnas.2411974121 1091-6490 0040 PNASA6 EMD-45207 other EM volume EMD-45208 other EM volume EMD-45209 other EM volume EMD-45210 other EM volume EMD-45211 other EM volume EMD-45212 other EM volume EMD-45213 other EM volume 9c5c FULLOVERLAP Human Adaptor Protein Complex AP-3 in the Apo state Human Adaptor Protein Complex AP-3 in the Apo state 0 1 2 3 4 Homo sapiens 0.215 AP-3 complex subunit delta-1 Homo sapiens 0.06616495299999998 1 Escherichia coli LEVO LQDLVRGIRNHKEDEAKYISQCIDEIKQELKQDNIAVKANAVCKLTYLQMLGYDISWAAFNIIEVMSASKFTFKRIGYLA ASQSFHEGTDVIMLTTNQIRKDLSSPSQYDTGVALTGLSCFVTPDLARDLANDIMTLMSHTKPYIRKKAVLIMYKVFLKY PESLRPAFPRLKEKLEDPDPGVQSAAVNVICELARRNPKNYLSLAPLFFKLMTSSTNNWVLIKIIKLFGALTPLEPRLGK KLIEPLTNLIHSTSAMSLLYECVNTVIAVLISLSSGMPNHSASIQLCVQKLRILIEDSDQNLKYLGLLAMSKILKTHPKS VQSHKDLILQCLDDKDESIRLRALDLLYGMVSKKNLMEIVKKLMTHVDKAEGTTYRDELLTKIIDICSQSNYQYITNFEW YISILVELTRLEGTRHGHLIAAQMLDVAIRVKAIRKFAVSQMSALLDSAHLLASSTQRNGICEVLYAAAWICGEFSEHLQ EPHHTLEAMLRPRVTTLPGHIQAVYVQNVVKLYASILQQKEQAGEAEGAQAVTQLMVDRLPQFVQSADLEVQERASCILQ LVKHIQKLQAKDVPVAEEVSALFAGELN O14617 AP-3 complex subunit beta-1 Homo sapiens 0.065602797 1 Escherichia coli LEVO DLKKNEDLKQMLESNKDSAKLDAMKRIVGMIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQDLALLSIST FQRALKDPNQLIRASALRVLSSIRVPIIVPIMMLAIKEASADLSPYVRKNAAHAIQKLYSLDPEQKEMLIEVIEKLLKDK STLVAGSVVMAFEEVCPDRIDLIHKNYRKLCNLLVDVEEWGQVVIIHMLTRYARTQFVSPWDPDHRLLIRNTKPLLQSRN AAVVMAVAQLYWHISPKSEAGIISKSLVRLLRSNREVQYIVLQNIATMSIQRKGMFEPYLKSFYVRSTDPTMIKTLKLEI LTNLANEANISTLLREFQTYVKSQDKQFAAATIQTIGRCATNILEVTDTCLNGLVCLLSNRDEIVVAESVVVIKKLLQMQ PAQHGEIIKHMAKLLDSITVPVARASILWLIGENCERVPKIAPDVLRKMAKSFTSEDDLVKLQILNLGAKLYLTNSKQTK LLTQYILNLGKYDQNYDIRDRTRFIRQLIVPNVKSGALSKYAKKIFLAQKPAPLLESPFKDRDHFQLGTLSHTLNIKATG YLELSNWPEVAPDPSVRN O00203 AP-3 complex subunit mu-1 Homo sapiens 0.014274275 1 Escherichia coli LEVO MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIYRDKLFFVSVIQTEVPPLFVI EFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLA Q9Y2T2 AP-3 complex subunit sigma-1 Homo sapiens 0.017412949 1 Escherichia coli LEVO MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSDNKLIYRHYATLYFVFCVDSS ESELGILDLIQVFVETLDKCFENVCELDLIFHVDKVHNILAEMVMGGMVLETNMNEIVTQIDAQNKLEKSE Q92572 singleParticle particle 1.5 7.4 2.7 KCl Potassium Chloride 10.0 Na2HPO4 Sodium Phosphate (Dibasic) 1.8 KH2PO4 Potassium Phosphate (Monobasic) 300.0 NaCl Sodium Chloride 1.0 C9H15O6P TCEP
1x PBS (pH 7.4), 300mM NaCl, 1mM TCEP
 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY PLASMA CLEANING AIR
Used Quantifoil Active grids- Backside gold coated before plasma cleaned. 12 mA used for plasma cleaning
 ETHANE 100 296 SPOTITON
Commercialized version - Chameleon.
Specimen appeared as a monodisperse peak via size exclusion chromatography (SEC)
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.4 1.4000000000000001 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris 20 FEI FALCON IV (4k x 4k) 49.97
4 datasets collected, processed independently, and merged.
 1
Mixture of blob picker, template picker, crYOLO, and Topaz
 C1 FOURIER SPACE 3.6 FSC 0.143 CUT-OFF cryoSPARC 4.4.1 1205158 MAXIMUM LIKELIHOOD cryoSPARC 4.4.1 OTHER cryoSPARC 4.4.1 cryoSPARC 4.4.1 emd_45214.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.36 297.36 297.36 90.0 90.0 90.0 X Y Z -0.0016801807 2.1645036 0.0011362912 0.025303898 0.826 0.826 0.826 0.1 AUTHOR deepEMHancer map of human AP-3 in the Apo state AlphaFold in silico model RIGID BODY FIT REAL emd_45214_msk_2.map emd_45214_msk_1.map emd_45214_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.36 297.36 297.36 90.0 90.0 90.0 X Y Z -0.110499926 0.29232532 -0.000049977585 0.007946951 0.826 0.826 0.826 AUTHOR Filtered map of human AP-3 in the Apo state emd_45214_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.36 297.36 297.36 90.0 90.0 90.0 X Y Z -0.7679289 1.0092269 -0.00004997758 0.016403746 0.826 0.826 0.826 AUTHOR B-factor sharpened map of human AP-3 in the Apo state emd_45214_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.36 297.36 297.36 90.0 90.0 90.0 X Y Z -0.0017574867 2.1529896 0.000999713 0.023167556 0.826 0.826 0.826 AUTHOR B-factor sharpened map of human AP-3 in the Apo state emd_45214_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.36 297.36 297.36 90.0 90.0 90.0 X Y Z 0.0 49.831738000000001 0.13849504 0.95302206 0.826 0.826 0.826 AUTHOR Map for coloring by local resolution emd_45214_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.36 297.36 297.36 90.0 90.0 90.0 X Y Z -0.97203207 1.2388226 0.0005692495 0.016735477 0.826 0.826 0.826 AUTHOR Map filter by local resolution for human AP-3 in the Apo state emd_45214_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.36 297.36 297.36 90.0 90.0 90.0 X Y Z -0.1363996 0.31285527 0.000207166 0.00997648 0.826 0.826 0.826 AUTHOR Unfiltered half map of human AP-3 in the Apo state emd_45214_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.36 297.36 297.36 90.0 90.0 90.0 X Y Z -0.14179547 0.32855797 0.00020617965 0.009981803 0.826 0.826 0.826 AUTHOR Unfiltered half map of human AP-3 in the Apo state