Structure of a partially disrupted IgE high affinity receptor complex bound to an omalizumab variant

2024-10-23 REL RCSB RCSB RCSB 2021-10-11 2021-12-15 2021-12-15 2024-10-23 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI115469 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 5F30AI120510-03 United States Structure of a partially disrupted IgE high affinity receptor complex bound to an omalizumab variant Pennington LF Jardetzky TS IgE, allergy, Xolair, Omalizumab, IMMUNE SYSTEM Pennington LF Gasser P Kleinboelting S Zhang C Skiniotis G Eggel A Jardetzky TS Directed evolution of and structural insights into antibody-mediated disruption of a stable receptor-ligand complex. Nat Commun UK 12 7069 7069 2021 34862384 doi:10.1038/s41467-021-27397-z 2041-1723 7sht FULLOVERLAP Locked complex of IgE-Fc (G335C) and alpha chain of the high affinity IgE receptor (W156C) bound to clone_7 scFV Locked complex of IgE-Fc (G335C) and alpha chain of the high affinity IgE receptor (W156C) bound to clone_7 scFV 0 1 2 3 4 Homo sapiens High affinity immunoglobulin epsilon receptor subunit alpha Homo sapiens 0.022541798999999998 1 Homo sapiens LEVO APMAEGGGQNHHHHHHHHGGENLYFQGGSPKVSLNPPWNRIFKGENVTLTCNGNNFFEVSSTKWFHNGSLSEETNSSLNI VNAKFEDSGEYKCQHQQVNESEPVYLEVFSDWLLLQASAEVVMEGQPLFLRCHGWRNWDVYKVIYYKDGEALKYWYENHN ISITNATVEDSGTYYCTGKVCQLDYESEPLNITVIKA P12319 Immunoglobulin heavy constant epsilon Homo sapiens 0.035773160000000005 2 Homo sapiens LEVO ASFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTINITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWL SDRTYTCQVTYQGHTFEDSTKKCADSNPRCVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHS TRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACL IQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP GK P01854 clone_7 Variable fragment heavy chain Homo sapiens 0.013451814 2 Homo sapiens LEVO ASEVQLVESGGGLVQPDGSLRLSCAVSGYNITSGYSWNWIRQTPGKGLEWVASVTYDGSTNYNPSVKGRITISRDGSKNT FYLQMNSLRAEDTAVYYCAKGNNYFGHWHFAVWGQGTLVTVSS clone_7 Variable fragment light chain Homo sapiens 0.014641862999999998 2 Homo sapiens LEVO GSDIQLTQSPSSLSASVGDRVTITCRASKSVDSDGDSYMNWYQQKPGRAPKLLIYAASYLESGVPSRFSGSGSGTHFTLT ISSLQPEDFATYYCQQSHEDPYTFGQGTKVEIKGGSENLYFQGGSGHHHHHHHH 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 3 NAG singleParticle particle 4.5 7.5 Quantifoil R1.2/1.3 GOLD 200 CARBON HOLEY GLOW DISCHARGE ETHANE TFS KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K3 (6k x 4k) 1 523 2.0 44.0 1

Ab initio from preliminary relion models used at template for final refinements in cryoSPARC

7.29 FSC 0.143 CUT-OFF cryoSPARC 24396 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_25136.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 218.1376 218.1376 218.1376 90.0 90.0 90.0 X Y Z -0.467892 1.032226 0.0063388236 0.060340285 0.8521 0.8521 0.8521 0.3 AUTHOR ::::EMDATABANK.org::::EMD-25136:::: 1F6A A 1-329 PDB experimental model 1F6A B 335-544 PDB experimental model 4J4P B 1-329 PDB experimental model FLEXIBLE FIT

Initial local fitting done in Chimera, followed by auto dock, and a single round of real space refinement. Carbohydrates were automatically built in phenix when possible, and a handful of flagged outliers in geometry were fixed manually in Phenix.