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 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 AP-3 bound to myristoylated Arf1 and LAMPI on a lipid nanodisc; concensus refinement Baker RW Begley M 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 AP-3 bound to myristoylated Arf1 and LAMPI on a lipid nanodisc; consensus refinement AP-3 bound to myristoylated Arf1 and LAMPI on a lipid nanodisc; consensus refinement 0 1 2 3 4 5 6 0.215 AP-3 1 1 2 3 4 Homo sapiens Arf1 1 5 Homo sapiens LAMPI 1 6 Homo sapiens AP-3 subunit Delta Homo sapiens Escherichia coli LEVO MALKMVKGSIDRMFDKNLQDLVRGIRNHKEDEAKYISQCIDEIKQELKQDNIAVKANAVCKLTYLQMLGYDISWAAFNIIEVMSASKFTFKRIGYLAASQSFHEGTDVIMLTTNQIRKDLSSPSQYDTGVALTGLSCFVTPDLARDLANDIMTLMSHTKPYIRKKAVLIMYKVFLKYPESLRPAFPRLKEKLEDPDPGVQSAAVNVICELARRNPKNYLSLAPLFFKLMTSSTNNWVLIKIIKLFGALTPLEPRLGKKLIEPLTNLIHSTSAMSLLYECVNTVIAVLISLSSGMPNHSASIQLCVQKLRILIEDSDQNLKYLGLLAMSKILKTHPKSVQSHKDLILQCLDDKDESIRLRALDLLYGMVSKKNLMEIVKKLMTHVDKAEGTTYRDELLTKIIDICSQSNYQYITNFEWYISILVELTRLEGTRHGHLIAAQMLDVAIRVKAIRKFAVSQMSALLDSAHLLASSTQRNGICEVLYAAAWICGEFSEHLQEPHHTLEAMLRPRVTTLPGHIQAVYVQNVVKLYASILQQKEQAGEAEGAQAVTQLMVDRLPQFVQSADLEVQERASCILQLVKHIQKLQAKDVPVAEEVSALFAGELNPVAPKAQKKVPV O14617 AP-3 subunit Beta-1 Homo sapiens Escherichia coli LEVO MSSNSFPYNEQSGGGEATELGQEATSTISPSGAFGLFSSDLKKNEDLKQMLESNKDSAKLDAMKRIVGMIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQDLALLSISTFQRALKDPNQLIRASALRVLSSIRVPIIVPIMMLAIKEASADLSPYVRKNAAHAIQKLYSLDPEQKEMLIEVIEKLLKDKSTLVAGSVVMAFEEVCPDRIDLIHKNYRKLCNLLVDVEEWGQVVIIHMLTRYARTQFVSPWKEGDELEDNGKNFYESDDDQKEKTDKKKKPYTMDPDHRLLIRNTKPLLQSRNAAVVMAVAQLYWHISPKSEAGIISKSLVRLLRSNREVQYIVLQNIATMSIQRKGMFEPYLKSFYVRSTDPTMIKTLKLEILTNLANEANISTLLREFQTYVKSQDKQFAAATIQTIGRCATNILEVTDTCLNGLVCLLSNRDEIVVAESVVVIKKLLQMQPAQHGEIIKHMAKLLDSITVPVARASILWLIGENCERVPKIAPDVLRKMAKSFTSEDDLVKLQILNLGAKLYLTNSKQTKLLTQYILNLGKYDQNYDIRDRTRFIRQLIVPNVKSGALSKYAKKIFLAQKPAPLLESPFKDRDHFQLGTLSHTLNIKATGYLELSNWPEVAPDPSVRNVEVIELAKEWTPAGKAKQENSAKKFYS O00203 AP-3 subunit Mu-1 Homo sapiens Escherichia coli LEVO MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIYRDKLFFVSVIQTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLATESNILKELIKPPTILRSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSISFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLTWDVGKITPQKLPSLKGLVNLQSGAPKPEENPSLNIQFKIQQLAISGLKVNRLDMYGEKYKPFKGVKYVTKAGKFQVRT Q9Y2T2 AP-3 subunit Sigma-1 Homo sapiens Escherichia coli LEVO MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSDNKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHVDKVHNILAEMVMGGMVLETNMNEIVTQIDAQNKLEKSEAGLAGAPARAVSAVKNMNLPEIPRNINIGDISIKVPNLPSFK Q92572 ADP-ribosylation factor 1 Homo sapiens
Q71L mutation, myristoylated
LEVO GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQKSL P84077 LAMP1 Homo sapiens
synthetic peptide with oleic acid conjugation
LEVO GRKRSHAGYQTI P11279 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 cleaning. 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 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris 20 FEI FALCON IV (4k x 4k) 53.4
2 datasets collected, processed independently, and merged.
 1
Mixture of blob picker, template picker, crYOLO, and Topaz
 C2 4.2 FSC 0.143 CUT-OFF cryoSPARC 4.4.1
Non Uniform refinement in cryoSPARC
122155 MAXIMUM LIKELIHOOD cryoSPARC 4.4.1 OTHER cryoSPARC 4.4.1 cryoSPARC 4.4.1 emd_45210.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.19998 423.19998 423.19998 90.0 90.0 90.0 X Y Z -0.0017520386 2.1548645 0.0007638757 0.021565313 1.058 1.058 1.058 0.1 AUTHOR deepEMhancer sharpened map AlphaFold in silico model RIGID BODY FIT REAL emd_45210_msk_1.map emd_45210_msk_2.map emd_45210_msk_3.map emd_45210_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.19998 423.19998 423.19998 90.0 90.0 90.0 X Y Z -0.19537659 0.382507 0.00081596116 0.009991125 1.058 1.058 1.058 AUTHOR Full, unsharpened map emd_45210_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.19998 423.19998 423.19998 90.0 90.0 90.0 X Y Z -0.36469018 0.614422 0.00081596116 0.013559624 1.058 1.058 1.058 AUTHOR B factor sharpened map emd_45210_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.19998 423.19998 423.19998 90.0 90.0 90.0 X Y Z 0.0 13.813179 0.09383504 0.81131804 1.058 1.058 1.058 AUTHOR Locres file emd_45210_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.19998 423.19998 423.19998 90.0 90.0 90.0 X Y Z -0.3353175 0.48238084 0.0006462733 0.040724277 1.058 1.058 1.058 AUTHOR Half map 1 emd_45210_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.19998 423.19998 423.19998 90.0 90.0 90.0 X Y Z -0.31328097 0.4804073 0.00063308654 0.040816315 1.058 1.058 1.058 AUTHOR Half map 2