Atomic structure of the Human Herpesvirus 6B Capsid and Capsid-Associated Tegument Complexes

2024-03-20 REL RCSB RCSB RCSB 2019-08-03 2019-11-13 2019-12-11 2024-03-20 National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR) DE028583, DE025567 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI094386 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1S10RR23057, 1S10OD018111, and 1U24GM116792 United States National Science Foundation (NSF, United States) DBI-1338135 and DMR-1548924 United States Atomic structure of the Human Herpesvirus 6B Capsid and Capsid-Associated Tegument Complexes Zhang YB Liu W beta-herpesvirus, HHV-6B, murine cytomegalovirus, human cytomegalovirus, pp150, pU11, pUL32, pM32, pU14, VIRUS Zhang Y Liu W Li Z Kumar V Alvarez-Cabrera AL Leibovitch EC Cui Y Mei Y Bi GQ Jacobson S Zhou ZH Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes. Nat Commun UK 10 5346 5346 2019 31767868 doi:10.1038/s41467-019-13064-x 2041-1723 EMD-20558 other EM volume EMD-20559 other EM volume EMD-20560 other EM volume 6q1f FULLOVERLAP Human herpesvirus 6 strain Z29 Human herpesvirus 6 strain Z29 0 1 2 3 4 5 Human herpesvirus 6 strain Z29 Z29 VIRION STRAIN true false Major capsid protein Human herpesvirus 6B (strain Z29) Z29 0.15226004699999998 16 LEVO MENWQATEILPKIEAPLNIFNDIKTYTAEQLFDNLRIYFGDDPSRYNISFEALLGIYCNKIEWINFFTTPIAVAANVIRF NDVSRMTLGKVLFFIQLPRVATGNDVTAPKETTIMVAKHSEKHPINISFDLSAACLEHLENTFKNTVIDQILNINALHTV LRSLKNSADSLERGLIHAFMQTLLRKSPPQFIVLTMNENKVHNKQALSRVQRSNMFQSLKNRLLTSLFFLNRNNNSSYIY RILNDMMESVTESILNDTNNYTSKENIPLDGVLLGPIGSIQKLTNILSQYISTQVVSAPISYGHFIMGKENAVTAIAYRA IMADFTQFTVNAGTEQQDTNNKSEIFDKSRAYADLKLNTLKLGDKLVAFDHLHKVYKNTDVNDPLEQSLQLTFFFPLGIY IPTETGFSTMETRVKLNDTMENNLPTSVFFHNKDQVVQRIDFADILPSVCHPIVHDSTIVERLMKNEPLPTGHRFSQLCQ LKITRENPTRILQTLYNLYESRQEVPKNTNVLKNELNVEDFYKPDNPTLPTERHPFFDLTYIQKNRATEVLCTPRIMIGN MPLPLAPISFHEARTNQMLEHAKTNSHNYDFTLKIVTESLTSGSYPELAYVIEILVHGNKHAFMILKQVISQCISYWFNM KHILLFCNSFEMIMLISNHMGDELIPGAAFAHYRNLVSLIRLVKRTISISNINEQLCGEPLVNFANALFDGRLFCPFVHT MPRNDTNAKITADDTPLTQNTVRVRNYEISDVQRMNLIDSSVVFTDNDRPSNENTILSKIFYFCVLPALSNNKACGAGVN VKELVLDLFYTEPFICPDDCFQENPISSDVLMSLIREAMGPGYTVANTSSIAKQLFKSLIYINENTKILEVEVSLDPAQR HGNSVHFQSLQHILYNGLCLISPITTLRRYYQPIPFHRFFSDPGICGTMNADIQVFLNTFPHYQRNDGGFPLPPPLALEF YNWQRTPFSVYSAFCPNSLLSIMTLAAMHSKLSPVAIAIQSKSKIHPGFAATLVRTDNFDVECLLYSSRAATSIILDDPT VTAEAKDIVTTYNFTQHLSFVDMGLGFSSTTATANLKRIKSDMGSKIQNLFSAFPIHAFTNTDINTWIRHHVGIEKPNPS EGEALNIITFGGINKNPPSILLHGQQAICEVILTPVTTNINFFKLPHNPRGRESCMMGTDPHNEEAARKALYDHTQTDSD TFAATTNPWASLPGSLGDILYNTAHREQLCYNPKTYSPNAQFFTESDILKTNKMMYKVINEYCMKSNSCLNSDSEIQYSC SEGTDSFVSRPCQFLQNALPLHCSSNQALLESRSKTGNTQISETHYCNYAIGETIPLQLIIESSI Q9QJ26 Large structural phosphoprotein Human herpesvirus 6B (strain Z29) Z29 0.095738125 12 LEVO MDLKAQSIPFAWLDRDKVQRLTNFLSNLENLENVDLREHPYVTNSCVVREGEDVDELKTLYNTFILWLMYHYVLSKRKPD YNAIWQDITKLQNVVNEYLKSKGLNKGNFENMFTNKEKFESQFSDIHRALLRLGNSIRWGSNVPIDTPYVNLTAEDSSEI ENNLQDAEKNMLWYTVYNINDPWDENGYLVTSINKLVYLGKLFVTLNQSWSKLEKVAMSQIVTTQNHLSGHLRKNENFNA VYSQRVLQTPLTGQRVESFLKIITSDYEIIKSSLESYSASKAFSVPENGPHSLMDFASLDGRMPSDLSLPSISIDTKRPS ADLARLKISQPKSLDAPLKTQRRHKFPESDSVDNAGGKILIKKETLGGRDVRATTPVSSVSLMSGVEPLSSLTSTNLDLR DKSHGNYRIGPSGILDFGVKLPAEAQSNTGDVDLLQDKTSIRSPSSGITDVVNGLANLNLRQNKSDVSRPWSKNTAANAD VFDPVHRLVSEQTGTPFVLNNSDVAGSEAKLTTHSTETGVSPHNVSLIKDLRDKDGFRKQKKLDLLGSWTKEKNDKAIVH SREVTGDSGDATETVTARDSPVLRKTKHANDIFAGLNKKYARDVSRGGKGNSRDLYSGGNAEKKETSGKFNVDKEMTQNE QEPLPNLMEAARNAGEEQYVQAGLGQRVNKILAEFTNLISLGEKGIQDILHNQSGTELKLPTENKLGRESEEANVERILE VSDPQNLFKNFKLQNDLDSVQSPFRLPNADLSRDLDSVSFKDALDVKLPGNGEREIDLALQKVKAGERETSDFKVGQDET LIPTQLMKVETPEEKDDVIEKMVLRIRQDGETDEETVPGPGVAESLGIAAKDKSVIAS Q69535 Small capsomere-interacting protein Human herpesvirus 6B (strain Z29) Z29 0.009827329 16 LEVO MTTIRGDDLSNQITQISGSSSKKEEEKKKQQMLTGVLGLQPTMANHPVLGVFLPKYAKQNGGNVDKTAFRLDLIRMLALH RLNTKTGSD Q9WT32 Triplex capsid protein 1 Human herpesvirus 6B (strain Z29) Z29 0.034162508 5 LEVO MNSKSSARAAIVDTVEAVKKRKYISIEAGTLNNVVEKERKFLKQFLSGRENLRIAARVFTPCELLAPELENLGMLMYRFE TDVDNPKILFVGLFFLCSNAFNVSACVRTALTTMYTNSMVDNVLSMINTCKYLEDKVSLFGVTSLVSCGSSCLLSCVMQG NVYDANKENIHGLTVLKEIFLEPDWEPRQHSTQYVYVVHVYKEVLSKLQYGIYVVLTSFQNEDLVVDILRQYFEKERFLF LNYLINSNTTLSYFGSVQRIGRCATEDIKSGFLQYRGITLPVIKLENIFVDLSEKKVFV Q9WT35 Triplex capsid protein 2 Human herpesvirus 6B (strain Z29) Z29 0.033514332 10 LEVO METVYCTFDHKLSLSDISTLCKLMNIVIPIPAHHHLIGSGNLGLYPIVSSNKDYVHIRNVLRTMVVTILQKVEGNQLVLR KPMTGQQYAIKNTGPFPWEKGDTLTLIPPLSTHSEEKLLKLGDWELTVPLVVPTAIAAEINIRLLCIGLIAVHREYNEMQ TIIDELCSIQYRDVLIKLPDIVNDKQSMYSMKTACISLSMITAMAPDIVRTYIDRLTLEDHSMLLIKCQELLSKRTTLST QRCGQLHATDIKDELKKIKSVLTMIDQINSLTNEKTYFVVCDVSADNRMATCIYKN Q9QJ27 singleParticle particle 7.4

PBS buffer, pH 7.4

COPPER 200 CARBON HOLEY GLOW DISCHARGE 30 AIR 101.325 ETHANE HOMEMADE PLUNGER

The grids were manually plunged into the ethane..

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 2.2 2.2 3.2 3.2 64000.0 64000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) 4828 23.0 1 7430

a sphere density map

I 9.0 FSC 0.143 CUT-OFF

bin4 reconstrction

6443 PROJECTION MATCHING PROJECTION MATCHING emd_20557.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 -319 -319 -319 640 640 640 1388.8 1388.8 1388.8 90.0 90.0 90.0 X Y Z -0.07712099 0.12517424 0.0005919783 0.012241783 2.17 2.17 2.17 0.036 AUTHOR ::::EMDATABANK.org::::EMD-20557:::: HHV-6B capsid associated with pU11 tegument proteins OTHER