CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with neutralizing fabs 2C12, 7I13 and 13H11

2024-11-13 REL RCSB RCSB RCSB 2021-12-10 2022-03-23 2022-03-23 2024-11-13 Not funded CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with neutralizing fabs 2C12, 7I13 and 13H11 Kschonsak M Johnson MC Human Cytomegalovirus, glycoprotein complex, antibody complex, 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 7t4q FULLOVERLAP Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to fabs of human neutralizing antibodies 2C12, 7I13 and 13H11 Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to fabs of human neutralizing antibodies 2C12, 7I13 and 13H11 0 1 2 3 4 5 6 7 8 9 10 11 0.32 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 Fab 2C12 heavy chain Homo sapiens 0.027001769999999998 1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYAQITLRESGPTLVKPTQTLTLTCTFSGFSLNTNGVGVGWIRQPPGKALEWLALIYWNG NEGYSPSLKSRLTITKDTSKNQVVLTMTNMDPVDTATYYCVHWPQGLTTVTRLAFDIWGQGTMVTVSSASTKGPSVFPLA PSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNT KVDKKVEPKSCD Fab 2C12 light chain Homo sapiens 0.025594653999999998 1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYAQSALTQPRSVSGSPGQSVTISCTGTTSDVGRYNFVSWYQQHPGKAPKLLMYDVSQRP SGVPSRFSGSKSGNTASLTISGLQAEDEAVFYCCSYAGGNFFSYVFGTGTKVTVLGQPKAAPSVTLFPPSSEELQANKAT LVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC Fab 7I13 light chain Homo sapiens 0.0258449 1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYAEIVLTQSPGTLSLSPGERATLSCRASQSVSSDFLAWYQQKPGQAPRLLIYGASSRAT GIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYAASPPFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLN NFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC Fab 7I13 heavy chain Homo sapiens 0.027046506 1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYAQVQLVESGGGVVQPGRSLRLSCAASGFTFSNYGMHWVRQGPGKGLEWVAVISYDASS KYYTDSVQGRFTISRDNSKNTLFLQMNSLRGEDTAVYYCAKALRYLDWFLSDPFDYWGQGTLVTVSSASTKGPSVFPLAP SSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTK VDKKVEPKSCD 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 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 6 NAG singleParticle particle 1.77 7.5 300.0 NaCl sodium chloride 25.0 HEPES HEPES UltrAuFoil R0.6/1 GOLD 300

The grid was incubated with a thiol reactive self-assembling reaction mixture of 4mM monothiolalkane(C11)PEG6-OH (11-mercaptoundecyl) hexaethyleneglycol, (SPT-0011P6, SensoPath Technologies, Inc., Bozeman, MT)[23]. Grids were incubated with this self-assembled, monolayer (SAM) solution for 24 hours. Prior to grid freezing, grids were removed from the SAM solution and rinsed with EtOH.

ETHANE 100 277.15 LEICA EM GP

blot for 3.5s before plunging.

The sample was monodisperse.

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 1 18326 10.0 58.0

Images were collected in movie-mode at 5 frames/second.

Movie frames were corrected for motion and aligned. Images with a CTF fit resolution of 8.0 A or better were selected for particle picking.

5128264

template-matching particle picking

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

39 C1 2.9 FSC 0.143 CUT-OFF cisTEM 1.02

A composite map was generated from the three individual focused 3D maps using phenix combine_focused_maps

4792984 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_25685.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 Z Y X -15.368733000000001 30.294058 -0.025309997 0.59128356 1.1948 1.1948 1.1948 4.9 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Composite map generated by combining focused refined maps. Map used for model refinements 5VOB PDB experimental model emd_25685_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -10.643636000000001 23.505146 -0.048753247 0.47730136 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Half map 2 of focused refinement on 2C12, 7I13, UL region. emd_25685_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -26.043068000000002 44.754150000000003 -0.025508335 1.32211 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Sharpened map of focused refinement on gL region. Used for composite map generation. emd_25685_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -12.978583 27.671759999999999 -0.048126798 0.44256547 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Half map 2 of focused refinement on gL region. emd_25685_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -36.064810000000001 64.041579999999996 -0.026577035 2.202898 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Sharpened map of focused refinement on 2C12, 7I13, UL region. Used for composite map generation. emd_25685_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -11.847168999999999 27.217972 -0.017679224 0.30442172 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Non-sharpened map of focused refinement on gL region. emd_25685_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -6.402915 18.767880999999999 -0.018354349 0.35647687 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Non-sharpened map of overall (non-focused) refinement. emd_25685_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -11.107620000000001 27.387999000000001 -0.04841289 0.44299045 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Half map 1 of focused refinement on gL region. emd_25685_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -10.223356000000001 24.18798 -0.019026574 0.37088612 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Non-sharpened map of focused refinement on 2C12, 7I13, UL region. emd_25685_additional_9.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -10.865430999999999 25.370186 -0.049283057 0.477609 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Half map 1 of focused refinement on 2C12, 7I13, UL region. emd_25685_additional_10.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -31.220827 49.543895999999997 -0.02445136 1.615451 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Sharpened map of focused refinement on gH and 13H11 region. Used for composite map generation. emd_25685_additional_11.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -8.022531000000001 20.929594000000002 -0.017319284 0.31637934 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Non-sharpened map of focused refinement on gH and 13H11 region. emd_25685_additional_12.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -7.992114 21.090527000000002 -0.04701477 0.44484988 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Half map 2 of focused refinement on gH and 13H11 region. emd_25685_additional_13.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 382.336 382.336 382.336 90.0 90.0 90.0 X Y Z -7.6339617 20.349022000000001 -0.04806816 0.4450575 1.1948 1.1948 1.1948 AUTHOR ::::EMDATABANK.org::::EMD-25685:::: Half map 1 of focused refinement on gH and 13H11 region.