REL RCSB RCSB 2017-01-19 2017-02-15 2017-05-31 2017-06-21 CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 4 Liu Y Pan J Liu Y Pan J Jenni S Raymond DD Caradonna T Do KT Schmidt AG Harrison SC Grigorieff N CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen Interface. J. Mol. Biol. UK 429 1829 1839 2017 28506635 doi:10.1016/j.jmb.2017.05.011 1089-8638 0070 JMOBAK EMD-8561 other EM volume EMD-8562 other EM volume EMD-8563 other EM volume 5uk2 fullOverlap Influenza-virus hemagglutinin H1 complexed with K1915 single-chain variable-domain fragment 0 1 2 3
The complex consists of three hemagglutinin head domains bound to three single-chain variable-domain fragments.
Influenza A virus (A/Solomon Islands/3/2006(H1N1)) Trichoplusia ni Hi-5 0.32 Hemagglutinin HA1 0.036024344 Influenza A virus (A/Solomon Islands/3/2006(H1N1)) A/Solomon Islands/3/2006(H1N1) pFastBac levo EDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCLLKGIAPLQLGNCSVAGWILGNPECELLISRESWSYI VEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPN LSKSYANNKEKEVLVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDREGRINYYWTLLEPGDTI IFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAKLRMVTGLRN IPS Hemagglutinin HA2 0.019841041 Influenza A virus A/Solomon Islands/3/2006(H1N1) pFASTBAC levo GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMNTQFTAVGKEFNKLERRMENL NKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYP KYSEESKLNREKI scFv 0.027629385 Homo sapiens pVRC levo EIVLTQSPGTLSLSPGERATLSCRASQSISGYYLTWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLE PEDFAVYYCQQYGISPVITFGGGTNVEIKGGGGGSGGGGSGGGGSEVQLVESGGGLVQPGGSLRLSCAASGFTFNIYDMH WVRQAPGKGLEWVSGLTTGGDTSYSGSVRGRFSISRENAKNSLYLQMNNLRAGDTAAYFCVRGVREVGATGGDPFYYAMA VWGQGTTVTVSSASGSSGSGHHHHHH BETA-D-MANNOSE 0.000180156 3 BMA N-ACETYL-D-GLUCOSAMINE 0.000221208 30 NAG singleParticle particle 0.1 8.
Beta-octylglucoside was added to a final concentration of 0.07% w/v to induce more variable particle orientations.
 Quantifoil R 1.2/1.3 COPPER 200 CARBON HOLEY ARRAY Air ETHANE 90.0 298.0 FEI VITROBOT MARK I FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1000.0 9000.0 18000. 30444. FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 70.0 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 7676 7420 2.5 38 1 10281 13.0 40.0
The exposure rate was 8 electrons/physical pixel/second.
 1
The particle images were normalized to have constant variance and zero average. Movies were processed using Unblur.
252130 PHASE FLIPPING AND AMPLITUDE CORRECTION CTFFIND3 OTHER
A starting map was determined using rosettes formed from Ni-NTA nanogold and His-tagged particles.
 PROJECTION MATCHING 7.5 IMAGIC 142314 3 FOURIER SPACE 4.8 FSC 0.143 CUT-OFF Frealign 9.11
Refinement and classification were limited to 10 Angstrom resolution.
 PROJECTION MATCHING Frealign 9.11 emd_8564.map.gz 1 Image stored as floating point number (4 bytes) 120 120 120 -60 -60 -60 120 120 120 196.8 196.8 196.8 90.0 90.0 90.0 x y z -3.741372 8.258274999999999 0.071280874 0.45758796 1.64 1.64 1.64 2.52 emdb influenza virus receptor-binding site antibody-antigen interface - Class 4 OTHER
Domains were initially placed manually using Chimera. The HA trimer was from PDB ID 5UGY. Fab was initially obtained using MODELLER, with PDB ID 4K8R as template. The structure was refined using PHENIX.
Correlation coefficient REAL