2025-06-11 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.title _citation.year _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _citation.page_last _em_admin.last_update RCSB RCSB 2025-01-17 2025-03-26 2025-03-26 2025-06-11 National Science Foundation (NSF, United States) DGE-1656518 United States Cryo-EM Structure of Human Enterovirus D68 USA/IL/14-18952 Xu L Pintilie G Varanese L Carette JE Chiu W Virus, Enterovirus Varanese L Xu L Peters CE Pintilie G Roberts DS Raj S Liu M Ooi YS Diep J Qiao W Richards CM Callaway J Bertozzi CR Jabs S de Vries E van Kuppeveld FJM Nagamine CM Chiu W Carette JE MFSD6 is an entry receptor for enterovirus D68. Nature UK 641 1268 1275 2025 40132641 doi:10.1038/s41586-025-08908-0 1476-4687 0006 NATUAS EMD-48713 other EM volume
Cryo-EM Structure of Human Enterovirus D68 USA/IL/14-18952 in Complex with MFSD6(L3)-Fc
 9mwz FULLOVERLAP enterovirus D68 enterovirus D68 0 1 2 3 4
Enterovirus D68 propagated and purified from infection of RD cells
enterovirus D68 14-18952 Homo sapiens VIRION STRAIN false false viral protein 1 enterovirus D68 USA/IL/14-18952 0.032854242 1 LEVO IESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHT SSAAQTDKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSSNNTYVGLPDLTLQAMFVPTGALTPEKQDS FHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKSGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVY MKPKHIKAWAPRPPRTLPYMSIANANYKGKGRAPNALNAIIGNRDSVKTMPHNIVTT A0A1I9KHM1 3.4.22.29 viral protein 2 enterovirus D68 USA/IL/14-18952 0.026527137
Residues 1-11 deleted
1 LEVO RVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEAGSTGWWWKLPDALNNIGM FGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTNTSPGFDDIMKGEEGGTFNHPYVLDDGTSLACAT IFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFNGLRHAITQ A0A1P7ZRE5 3.4.22.29 viral protein 3 enterovirus D68 USA/IL/14-18952 0.027156866999999998 1 LEVO GVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQL LFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHVVWDFGLQ SSVTLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQLDHLH AAEAAYQ A0A097BW17 3.4.22.29 viral protein 4 enterovirus D68 USA/IL/14-18952 0.003401665
Residues 1-27 and 58-68 deleted
1 LEVO QINFYKDSYAASASKQDFSQDPSKFTEPVV Q68T42 water 1.8015e-05 46 HOH singleParticle particle 0.089 8.0 20.0 Tris-HCl Tris-HCl, pH 8.0 120.0 NaCl sodium chloride 1.0 EDTA EDTA, pH 8.0
20 mM Tris-HCl (pH 8.0), 120 mM NaCl, and 1 mM EDTA (pH 8.0)
 Quantifoil COPPER 400 CARBON LACEY 3.0 GLOW DISCHARGE AIR ETHANE 100 277.15 FEI VITROBOT MARK IV
Freezing carried out with 4 s blot time, 1 s wait time..
TFS KRIOS FLOOD BEAM DARK FIELD FIELD EMISSION GUN 300 2.7 1.0 2.0 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 1 10400 3.28 50.0 1 23976 CTFFIND NONE AlphaFold3 model of VP1, VP2, VP3, and VP4 I FOURIER SPACE 2.0 FSC 0.143 CUT-OFF RELION cryoSPARC 12930 MAXIMUM LIKELIHOOD RELION cryoSPARC MAXIMUM LIKELIHOOD RELION cryoSPARC emd_48705.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 720 720 720 0 0 0 720 720 720 534.95996 534.95996 534.95996 90.0 90.0 90.0 Z Y X -4.3708944 16.894093000000002 -0.000000002932494 1.0 0.743 0.743 0.743 5.0 AUTHOR Enterovirus D68 USA/IL/14-18952 apo AlphaFold in silico model FLEXIBLE FIT
Initial rigid fitting was done using Chimera and then ISOLDE was used for flexible fitting.
 emd_48705_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 720 720 720 0 0 0 720 720 720 534.95996 534.95996 534.95996 90.0 90.0 90.0 X Y Z -0.529538 1.7680504 0.018074919 0.13007356 0.743 0.743 0.743 AUTHOR Enterovirus D68 USA/IL/14-18952 apo half map B emd_48705_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 720 720 720 0 0 0 720 720 720 534.95996 534.95996 534.95996 90.0 90.0 90.0 X Y Z -0.98821735 1.7082093 0.018087206 0.13002287 0.743 0.743 0.743 AUTHOR Enterovirus D68 USA/IL/14-18952 apo half map A