CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and neutralizing fabs 8I21 and 13H11

2024-10-30 REL RCSB RCSB RCSB 2021-12-10 2022-03-23 2022-03-23 2024-10-30 Not funded CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and neutralizing fabs 8I21 and 13H11 Kschonsak M Johnson MC glycoprotein complex, antibody complex, Neuropilin 2, VIRAL PROTEIN, VIRAL PROTEIN-Immune System complex Kschonsak M Johnson MC Schelling R Green EM Rouge L Ho H Patel N Kilic C Kraft E Arthur CP Rohou AL Comps-Agrar L Martinez-Martin N Perez L Payandeh J Ciferri C Structural basis for HCMV Pentamer receptor recognition and antibody neutralization. Sci Adv US 8 eabm2536 eabm2536 2022 35275719 doi:10.1126/sciadv.abm2536 2375-2548 7t4s FULLOVERLAP Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to Neuropilin 2 and fabs of human neutralizing antibodies 8I21 and 13H11 Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to Neuropilin 2 and fabs of human neutralizing antibodies 8I21 and 13H11 0 1 2 3 4 5 6 7 8 9 10 0.36 Envelope glycoprotein H Human betaherpesvirus 5 0.087311273 1 Homo sapiens LEVO MRPGLPSYLIILAVCLFSHLLSSRYGAEAVSEPLDKAFHLLLNTYGRPIRFLRENTTQCTYNSSLRNSTVVRENAISFNF FQSYNQYYVFHMPRCLFAGPLAEQFLNQVDLTETLERYQQRLNTYALVSKDLASYRSFSQQLKAQDSLGEQPTTVPPPID LSIPHVWMPPQTTPHGWTESHTTSGLHRPHFNQTCILFDGHDLLFSTVTPCLHQGFYLIDELRYVKITLTEDFFVVTVSI DDDTPMLLIFGHLPRVLFKAPYQRDNFILRQTEKHELLVLVKKDQLNRHSYLKDPDFLDAALDFNYLDLSALLRNSFHRY AVDVLKSGRCQMLDRRTVEMAFAYALALFAAARQEEAGAQVSVPRALDRQAALLQIQEFMITCLSQTPPRTTLLLYPTAV DLAKRALWTPNQITDITSLVRLVYILSKQNQQHLIPQWALRQIADFALKLHKTHLASFLSAFARQELYLMGSLVHSMLVH TTERREIFIVETGLCSLAELSHFTQLLAHPHHEYLSDLYTPCSSSGRRDHSLERLTRLFPDATVPATVPAALSILSTMQP STLETFPDLFCLPLGESFSALTVSEHVSYIVTNQYLIKGISYPVSTTVVGQSLIITQTDSQTKCELTRNMHTTHSITVAL NISLENCAFCQSALLEYDDTQGVINIMYMHDSDDVLFALDPYNEVVVSSPRTHYLMLLKNGTVLEVTDVVVDATDGTKLG PEQKLISEEDLNSAVDGSGLNDIFEAQKIEWHENLYFQGHHHHHHHH F5H9T3 Envelope glycoprotein L Human betaherpesvirus 5 0.030846491999999996 1 Homo sapiens LEVO MCRRPDCGFSFSPGPVILLWCCLLLPIVSSAAVSVAPTAAEKVPAECPELTRRCLLGEVFEGDKYESWLRPLVNVTGRDG PLSQLIRYRPVTPEAANSVLLDEAFLDTLALLYNNPDQLRALLTLLSSDTAPRWMTVMRGYSECGDGSPAVYTCVDDLCR GYDLTRLSYGRSIFTEHVLGFELVPPSLFNVVVAIRNEATRTNRAVRLPVSTAAAPEGITLFYGLYNAVKEFCLRHQLDP PLLRHLDKYYAGLPPELKQTRVNLPAHSRYGPQAVDAR Q71DN9 Envelope protein UL128 Human betaherpesvirus 5 0.019746023 1 Homo sapiens LEVO MSPKNLTPFLTALWLLLGHSRVPRVRAEECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTM THSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLD VCRAKMGYMLQ Q38LY2 Envelope glycoprotein UL130 Human betaherpesvirus 5 0.028866811 1 Homo sapiens LEVO MLRLLLRHHFHCLLLCAVWATPCLASPWFTLTANQNPSPPWSKLTYPKPHDAATFYCPFLYPSPPRSPSQFSGFQRVSTG PECRNETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQTILQRMPRTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLR FVVNDGTRYQMCVMKLESWAHVFRDYSVSFQVRLTFTEANNQTYTFCTHPNLIVGSENLYFQGSAWSHPQFEKGGGSGGG SGGGSAWSHPQFEK Q38M07 Envelope protein UL131A Human betaherpesvirus 5 0.015011042999999998 1 Homo sapiens LEVO MRLCRVWLSVCLCAVVLGQCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLTLNYHYDASHGLDNFDVLKRI NVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSLEFSVRLFAN Q8AZ45 Neuropilin-2 Homo sapiens 0.098923211 1 Homo sapiens LEVO MDMFPLTWVFLALYFSRHQVRGQPDPPCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNFNPHFEIEK HDCKYDFIEIRDGDSESADLLGKHCGNIAPPTIISSGSMLYIKFTSDYARQGAGFSLRYEIFKTGSEDCSKNFTSPNGTI ESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDLEHDPLQVGEGDCKYDWLDIWDGIPHVGPLIGKYCGTKTPSELRS STGILSLTFHTDMAVAKDGFSARYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTP NLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHA PLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQ AQPGEEWLQVDLGTPKTVKGVIIQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDI RRFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWTDSKPTVETLGPTVKSEETTTPYPTEEEATECGENCSFEDDKDLQL PSGFNCNFDFLEEPCGWMYDHAKWLRTTWASSSSPNDRTFPDDRNFLRLQSDSQREGQYARLISPPVHLPRSPVCMEFQY QATGGRGVALQVVREASQESKLLWVIREDQGGEWKHGRIILPSYDMEYQIVFEGVIGKGRSGEIAIDDIRISTDVPLENC MEPISAFAGENFKVDIPEIHEREGYEDEIDDEYEVDWSNSSSATSGSGAPSTDKEKSWLYTLDPGNSDYKDDDDK O60462 Fab 8I21 heavy chain Homo sapiens 0.026816311 1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYALVELVESGGGVVQPGRSLRLSCAASGFTFSSDGMHWVRQSPGRGLEWVAFISSDGST PYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAMYFCAKDWALFRWLRTFDHWGQGTLVTVSSASTKGPSVFPLAPSS KSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVD KKVEPKSCD Fab 13H11 heavy chain Homo sapiens 0.026600086 1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYAQVQLVQSGAEVKKPGASVKVSCKASGYTFTNYYIHWVRQAPGQGLEWMGIIHPSSGG TSYAQKFQGRVTMTRDTSTSTVSMDLSSLRSEDTAVYYCGRAFRILGLSDVFVNDWGQGTVVTVSSASTKGPSVFPLAPS SKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV DKKVEPKSCD Fab 13H11 light chain Homo sapiens 0.02578002 1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYADIQMTQSPSSLSASVGDRVTITCRASQGINNYLAWYQQKPGKVPKLLIYAASTLQSG VPSRFSGSGSGTAFTLTILSLQPEDVATYYCQKYNSAPFTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLN NFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC Fab 8I21 light chain Homo sapiens 0.02599508 1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYAETVMTQSPATLSVSPGGRATLSCRASQSVGINLAWYQQKPGQAPRLLIYGASTRASG FPARFSGSGSGTEFTLTITSLQSEDFAVYYCQQYNDWPPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLL NNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 9 NAG CALCIUM ION 4.0078e-05 1 CA singleParticle particle 1 7.5 300.0 NaCl sodium chloride 25.0 HEPES HEPES UltrAuFoil R0.6/1 GOLD 300 PLASMA CLEANING 20 ETHANE 100 277.15 LEICA EM GP

blot for 3.5 seconds before plunging.

Sample was mildly crosslinked with 0.025% glutaraldehyde, incubated for 10 min at room temperature and quenched with 9 mM TRIS pH 7.5

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 1.5 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 4 21357 10.0 52.0

Images were collected in movie-mode at 4 frames/second.

Movie frames were corrected for motion and aligned. Images with a CTF fit resolution of 6.0 A or better were selected for particle picking.

2532206

template-matching particle picking

ab-initio 3D model generation from select particles within cisTEM

44 C1 3.1 FSC 0.143 CUT-OFF cisTEM 1.02

A composite map was generated from the three individual focused 3D maps.

2252924 OTHER cisTEM 1.02

Auto-refine in cisTEM

OTHER cisTEM 1.02

Manual refine in cisTEM. Map was divided in 3 sections to refine map with focused refinements.

100 RELION 3.1 emd_25687.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 284 284 284 0 0 0 284 284 284 383.7976 383.7976 383.7976 90.0 90.0 90.0 X Y Z 0.0 15.305042 0.011590637 0.18164654 1.3514 1.3514 1.3514 0.8 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Composite map of combined focused refinement maps. Used for model refinements. 2QQO PDB experimental model 5VOB PDB experimental model emd_25687_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 378.392 378.392 378.392 90.0 90.0 90.0 X Y Z -7.711302 21.565449000000001 -0.00996478 0.39309382 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Non-sharpened, full map of overall (non-focused)refinement emd_25687_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 378.392 378.392 378.392 90.0 90.0 90.0 X Y Z -10.270587000000001 25.800846 -0.013299483 0.32925087 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Non-sharpened, full map of focused refinement on NRP2-UL region emd_25687_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 378.392 378.392 378.392 90.0 90.0 90.0 X Y Z -9.671236 25.268902000000001 -0.039474353 0.495079 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Half map 1 of focused refinement on NRP2-UL region emd_25687_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 378.392 378.392 378.392 90.0 90.0 90.0 X Y Z -10.269913000000001 25.255790000000001 -0.03919688 0.49540535 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Half map 2 of focused refinement on NRP2-UL region emd_25687_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 378.392 378.392 378.392 90.0 90.0 90.0 X Y Z -9.185313000000001 25.477692000000001 -0.037474558 0.49824408 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Half map 2 of focused refinement on 8I21-UL128 region emd_25687_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 378.392 378.392 378.392 90.0 90.0 90.0 X Y Z -9.589352 23.313607999999999 -0.008639139 0.3969938 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Non-sharpened, full map of focused refinement on 13H11-gH region emd_25687_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 378.392 378.392 378.392 90.0 90.0 90.0 X Y Z -8.873863 23.212924999999998 -0.03275691 0.5255626 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Half map 1 of focused refinement on 13H11-gH region emd_25687_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 378.392 378.392 378.392 90.0 90.0 90.0 X Y Z -10.17572 22.771249999999998 -0.032426596 0.52593434 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Half map 2 of focused refinement on 13H11-gH region emd_25687_additional_9.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 85 75 96 113 87 58 96 75 85 129.7344 101.355 114.869 90.0 90.0 90.0 Z Y X -9.846678000000001 15.305338000000001 0.000000000024496 1.0 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Density modified map of focused refined 13H11-gH region. Map used for composite map generation. emd_25687_additional_10.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 378.392 378.392 378.392 90.0 90.0 90.0 X Y Z -9.634181999999999 24.952818000000001 -0.012554773 0.36907566 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Non-sharpened, full map of focused refinement on 8I21-UL128 region emd_25687_additional_11.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 378.392 378.392 378.392 90.0 90.0 90.0 X Y Z -10.417306999999999 23.393353000000001 -0.0375993 0.49823883 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Half map 1 of focused refinement on 8I21-UL128 region emd_25687_additional_12.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 64 73 73 90 112 114 73 73 64 98.6522 98.6522 86.4896 90.0 90.0 90.0 Z Y X -9.599861000000001 13.122127000000001 -0.000000000031918 1.0 1.3514 1.3514 1.3514 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Density modified map of focused refined 8I12-UL128 region. Map used for composite map generation. emd_25687_additional_13.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 59 64 61 114 133 154 61 64 59 82.4354 86.4896 79.7326 90.0 90.0 90.0 Z Y X -6.6689754 10.67742 -0.000000000017851 1.0 1.3514 1.3514 1.3513999 AUTHOR ::::EMDATABANK.org::::EMD-25687:::: Density modified map of focused refined NRP2-UL region. Map used for composite map generation.