Structure of the HIV-Nef tetherin cargo bound AP-1:Arf1 stable closed trimer

2025-05-14 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name AUTHOR_SUPPORTING_EVIDENCE pdbx_audit_support _pdbx_audit_support.funding_organization DERIVED_CALCULATIONS chem_comp_atom chem_comp_bond database_2 struct_conn _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_label_asym_id STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name RCSB RCSB 2018-03-18 2018-04-11 2018-08-01 2025-05-14 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01 AI 120691 United States Structure of the HIV-Nef tetherin cargo bound AP-1:Arf1 stable closed trimer Morris KL Buffalo CZ Hurley JH AP, HIV, Nef, trafficking, VIRAL PROTEIN, PROTEIN TRANSPORT Morris KL Buffalo CZ Sturzel CM Heusinger E Kirchhoff F Ren X Hurley JH HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation. Cell 174 659 671.e14 2018 30053425 doi:10.1016/j.cell.2018.07.004 1097-4172 EMD-7458 other EM volume EMD-7457 other EM volume EMD-7456 other EM volume EMD-7455 other EM volume 6cri FULLOVERLAP Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer 0 1 2 3 4 5 6 Homo sapiens 0.70 Bone marrow stromal antigen 2, Protein Nef chimera Human immunodeficiency virus 1 0.029964326 6 Escherichia coli LEVO MSYYHHHHHHDYDIPTTENLYFQGAMGSASTSYDYCRVPMEDGDKRCKGSDEASEGSGMGGKWSKSSVIGWPAVRERMRR AEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIH SQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVLE WRFDSRLAFHHVARELHPEYFKNC Q10589 Q90VU7 AP-1 complex subunit beta-1 Homo sapiens 0.064458656 3 Escherichia coli LEVO EIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVK DCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSN PMVVANAVAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQSICERVTPRLSHANS AVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPELQYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIY VKLEKLDIMIRLASQANIAQVLAELREYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVV IKDIFRKYPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKSTQVQLQLLTAIVKLFL KKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAKEVVLAEKPLISEETDLIEPTLLDELICYIGTLASV YHKPPSAFVE Q10567 ADP-ribosylation factor 1 Homo sapiens 0.018936599999999998 6 Escherichia coli LEVO EMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSND RERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQ LRNQK P84077 AP-1 complex subunit gamma-1 Mus musculus 0.06640105499999999 3 Escherichia coli LEVO PIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLGYPAHFGQLECLKLIASQKFTDKR IGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQGLALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVH VIRKVPELMEMFLPATKNLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGISDP FLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIKSESGLRVLAINILGRFLLNNDKN IRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVSIKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASG IFLAAEKYAPSKRWHIDTIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCIGEY GDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCTVNRIKKVVSIYGSSIDVELQQRA VEYNALFKKYDHMRSALLERMPVME P22892 AP-1 complex subunit mu-1 Mus musculus 0.048475535 3 Escherichia coli LEVO SASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWIKHNNLYLVATSKKNACVSLVF SFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDFGYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRS EGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQC VRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQFKRRSTANNVEIHIPVPNDAD SPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKS GYQALPWVRYITQNGDYQLRTQ P35585 AP-1 complex subunit sigma-3 Homo sapiens 0.01699885 3 Escherichia coli LEVO MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYKRYASLYFCCAIENQDNELLT LEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIGGEIQETSKKIAVKAIEDSDMLQ Q96PC3 GUANOSINE-5'-TRIPHOSPHATE 0.0005231799999999999 6 GTP MAGNESIUM ION 2.4305e-05 6 MG singleParticle particle 0.07 8.0

20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP

PLASMA CLEANING

unspecified

ETHANE 100 296 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 62.4 1 PHASE FLIPPING AND AMPLITUDE CORRECTION

CRYOSPARC

C1 6.8 FSC 0.143 CUT-OFF RELION 11108 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD RELION emd_7563.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 409.72803 409.72803 409.72803 90.0 90.0 90.0 X Y Z -0.017942984 0.058546383 0.0003145799 0.002489533 1.067 1.067 1.067 0.0149 AUTHOR ::::EMDATABANK.org::::EMD-7563:::: HIV-Nef tetherin cargo bound AP-1:Arf1 stable closed trimer FLEXIBLE FIT Correlation coefficient REAL 425.0