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- EMDB-20557: Atomic structure of the Human Herpesvirus 6B Capsid and Capsid-As... -

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Entry
Database: EMDB / ID: EMD-20557
TitleAtomic structure of the Human Herpesvirus 6B Capsid and Capsid-Associated Tegument Complexes
Map dataHHV-6B capsid associated with pU11 tegument proteins
Sample
  • Virus: Human herpesvirus 6 strain Z29
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Large structural phosphoprotein
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Triplex capsid protein 2
Keywordsbeta-herpesvirus / HHV-6B / murine cytomegalovirus / human cytomegalovirus / pp150 / pU11 / pUL32 / pM32 / pU14 / VIRUS
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Herpesvirus UL11/UL32 / Small capsid protein, Herpesviridae / Herpesvirus large structural phosphoprotein UL32 / Small capsid protein of Herpesviridae / Herpesvirus capsid protein 2 / Herpesvirus capsid shell protein 1 / Herpesvirus VP23 like capsid protein / Herpesvirus capsid shell protein VP19C / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
Large structural phosphoprotein / Major capsid protein / Triplex capsid protein 2 / Small capsomere-interacting protein / Triplex capsid protein 1
Similarity search - Component
Biological speciesHuman herpesvirus 6B (strain Z29) / Human herpesvirus 6 strain Z29
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsZhang YB / Liu W
Funding support United States, 4 items
OrganizationGrant numberCountry
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
CitationJournal: Nat Commun / Year: 2019
Title: Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes.
Authors: Yibo Zhang / Wei Liu / Zihang Li / Vinay Kumar / Ana L Alvarez-Cabrera / Emily C Leibovitch / Yanxiang Cui / Ye Mei / Guo-Qiang Bi / Steve Jacobson / Z Hong Zhou /
Abstract: Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B ...Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B capsid and capsid-associated tegument complex (CATC) obtained by cryoEM and sub-particle reconstruction. Compared to other β-herpesviruses, HHV-6B exhibits high similarity in capsid structure but organizational differences in its CATC (pU11 tetramer). 180 "VΛ"-shaped CATCs are observed in HHV-6B, distinguishing from the 255 "Λ"-shaped dimeric CATCs observed in murine cytomegalovirus and the 310 "Δ"-shaped CATCs in human cytomegalovirus. This trend in CATC quantity correlates with the increasing genomes sizes of these β-herpesviruses. Incompatible distances revealed by the atomic structures rationalize the lack of CATC's binding to triplexes Ta, Tc, and Tf in HHV-6B. Our results offer insights into HHV-6B capsid assembly and the roles of its tegument proteins, including not only the β-herpesvirus-specific pU11 and pU14, but also those conserved across all subfamilies of Herpesviridae.
History
DepositionAug 3, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseDec 11, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6q1f
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6q1f
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20557.png

Downloads & links

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Map

FileDownload / File: emd_20557.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHHV-6B capsid associated with pU11 tegument proteins
Voxel sizeX=Y=Z: 2.17 Å
Density
Contour LevelBy AUTHOR: 0.036 / Movie #1: 0.036
Minimum - Maximum-0.07712099 - 0.12517424
Average (Standard dev.)0.0005919783 (±0.012241783)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-319-319-319
Dimensions640640640
Spacing640640640
CellA=B=C: 1388.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.172.172.17
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z1388.8001388.8001388.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS-319-319-319
NC/NR/NS640640640
D min/max/mean-0.0770.1250.001

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Supplemental data

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Sample components

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Entire : Human herpesvirus 6 strain Z29

EntireName: Human herpesvirus 6 strain Z29
Components
  • Virus: Human herpesvirus 6 strain Z29
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Large structural phosphoprotein
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Triplex capsid protein 2

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Supramolecule #1: Human herpesvirus 6 strain Z29

SupramoleculeName: Human herpesvirus 6 strain Z29 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 36351 / Sci species name: Human herpesvirus 6 strain Z29 / Sci species strain: Z29 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 6B (strain Z29) / Strain: Z29
Molecular weightTheoretical: 152.260047 KDa
SequenceString: MENWQATEIL PKIEAPLNIF NDIKTYTAEQ LFDNLRIYFG DDPSRYNISF EALLGIYCNK IEWINFFTTP IAVAANVIRF NDVSRMTLG KVLFFIQLPR VATGNDVTAP KETTIMVAKH SEKHPINISF DLSAACLEHL ENTFKNTVID QILNINALHT V LRSLKNSA ...String:
MENWQATEIL PKIEAPLNIF NDIKTYTAEQ LFDNLRIYFG DDPSRYNISF EALLGIYCNK IEWINFFTTP IAVAANVIRF NDVSRMTLG KVLFFIQLPR VATGNDVTAP KETTIMVAKH SEKHPINISF DLSAACLEHL ENTFKNTVID QILNINALHT V LRSLKNSA DSLERGLIHA FMQTLLRKSP PQFIVLTMNE NKVHNKQALS RVQRSNMFQS LKNRLLTSLF FLNRNNNSSY IY RILNDMM ESVTESILND TNNYTSKENI PLDGVLLGPI GSIQKLTNIL SQYISTQVVS APISYGHFIM GKENAVTAIA YRA IMADFT QFTVNAGTEQ QDTNNKSEIF DKSRAYADLK LNTLKLGDKL VAFDHLHKVY KNTDVNDPLE QSLQLTFFFP LGIY IPTET GFSTMETRVK LNDTMENNLP TSVFFHNKDQ VVQRIDFADI LPSVCHPIVH DSTIVERLMK NEPLPTGHRF SQLCQ LKIT RENPTRILQT LYNLYESRQE VPKNTNVLKN ELNVEDFYKP DNPTLPTERH PFFDLTYIQK NRATEVLCTP RIMIGN MPL PLAPISFHEA RTNQMLEHAK TNSHNYDFTL KIVTESLTSG SYPELAYVIE ILVHGNKHAF MILKQVISQC ISYWFNM KH ILLFCNSFEM IMLISNHMGD ELIPGAAFAH YRNLVSLIRL VKRTISISNI NEQLCGEPLV NFANALFDGR LFCPFVHT M PRNDTNAKIT ADDTPLTQNT VRVRNYEISD VQRMNLIDSS VVFTDNDRPS NENTILSKIF YFCVLPALSN NKACGAGVN VKELVLDLFY TEPFICPDDC FQENPISSDV LMSLIREAMG PGYTVANTSS IAKQLFKSLI YINENTKILE VEVSLDPAQR HGNSVHFQS LQHILYNGLC LISPITTLRR YYQPIPFHRF FSDPGICGTM NADIQVFLNT FPHYQRNDGG FPLPPPLALE F YNWQRTPF SVYSAFCPNS LLSIMTLAAM HSKLSPVAIA IQSKSKIHPG FAATLVRTDN FDVECLLYSS RAATSIILDD PT VTAEAKD IVTTYNFTQH LSFVDMGLGF SSTTATANLK RIKSDMGSKI QNLFSAFPIH AFTNTDINTW IRHHVGIEKP NPS EGEALN IITFGGINKN PPSILLHGQQ AICEVILTPV TTNINFFKLP HNPRGRESCM MGTDPHNEEA ARKALYDHTQ TDSD TFAAT TNPWASLPGS LGDILYNTAH REQLCYNPKT YSPNAQFFTE SDILKTNKMM YKVINEYCMK SNSCLNSDSE IQYSC SEGT DSFVSRPCQF LQNALPLHCS SNQALLESRS KTGNTQISET HYCNYAIGET IPLQLIIESS I

UniProtKB: Major capsid protein

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Macromolecule #2: Large structural phosphoprotein

MacromoleculeName: Large structural phosphoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 6B (strain Z29) / Strain: Z29
Molecular weightTheoretical: 95.738125 KDa
SequenceString: MDLKAQSIPF AWLDRDKVQR LTNFLSNLEN LENVDLREHP YVTNSCVVRE GEDVDELKTL YNTFILWLMY HYVLSKRKPD YNAIWQDIT KLQNVVNEYL KSKGLNKGNF ENMFTNKEKF ESQFSDIHRA LLRLGNSIRW GSNVPIDTPY VNLTAEDSSE I ENNLQDAE ...String:
MDLKAQSIPF AWLDRDKVQR LTNFLSNLEN LENVDLREHP YVTNSCVVRE GEDVDELKTL YNTFILWLMY HYVLSKRKPD YNAIWQDIT KLQNVVNEYL KSKGLNKGNF ENMFTNKEKF ESQFSDIHRA LLRLGNSIRW GSNVPIDTPY VNLTAEDSSE I ENNLQDAE KNMLWYTVYN INDPWDENGY LVTSINKLVY LGKLFVTLNQ SWSKLEKVAM SQIVTTQNHL SGHLRKNENF NA VYSQRVL QTPLTGQRVE SFLKIITSDY EIIKSSLESY SASKAFSVPE NGPHSLMDFA SLDGRMPSDL SLPSISIDTK RPS ADLARL KISQPKSLDA PLKTQRRHKF PESDSVDNAG GKILIKKETL GGRDVRATTP VSSVSLMSGV EPLSSLTSTN LDLR DKSHG NYRIGPSGIL DFGVKLPAEA QSNTGDVDLL QDKTSIRSPS SGITDVVNGL ANLNLRQNKS DVSRPWSKNT AANAD VFDP VHRLVSEQTG TPFVLNNSDV AGSEAKLTTH STETGVSPHN VSLIKDLRDK DGFRKQKKLD LLGSWTKEKN DKAIVH SRE VTGDSGDATE TVTARDSPVL RKTKHANDIF AGLNKKYARD VSRGGKGNSR DLYSGGNAEK KETSGKFNVD KEMTQNE QE PLPNLMEAAR NAGEEQYVQA GLGQRVNKIL AEFTNLISLG EKGIQDILHN QSGTELKLPT ENKLGRESEE ANVERILE V SDPQNLFKNF KLQNDLDSVQ SPFRLPNADL SRDLDSVSFK DALDVKLPGN GEREIDLALQ KVKAGERETS DFKVGQDET LIPTQLMKVE TPEEKDDVIE KMVLRIRQDG ETDEETVPGP GVAESLGIAA KDKSVIAS

UniProtKB: Large structural phosphoprotein

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Macromolecule #3: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 3 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 6B (strain Z29) / Strain: Z29
Molecular weightTheoretical: 9.827329 KDa
SequenceString:
MTTIRGDDLS NQITQISGSS SKKEEEKKKQ QMLTGVLGLQ PTMANHPVLG VFLPKYAKQN GGNVDKTAFR LDLIRMLALH RLNTKTGSD

UniProtKB: Small capsomere-interacting protein

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Macromolecule #4: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 6B (strain Z29) / Strain: Z29
Molecular weightTheoretical: 34.162508 KDa
SequenceString: MNSKSSARAA IVDTVEAVKK RKYISIEAGT LNNVVEKERK FLKQFLSGRE NLRIAARVFT PCELLAPELE NLGMLMYRFE TDVDNPKIL FVGLFFLCSN AFNVSACVRT ALTTMYTNSM VDNVLSMINT CKYLEDKVSL FGVTSLVSCG SSCLLSCVMQ G NVYDANKE ...String:
MNSKSSARAA IVDTVEAVKK RKYISIEAGT LNNVVEKERK FLKQFLSGRE NLRIAARVFT PCELLAPELE NLGMLMYRFE TDVDNPKIL FVGLFFLCSN AFNVSACVRT ALTTMYTNSM VDNVLSMINT CKYLEDKVSL FGVTSLVSCG SSCLLSCVMQ G NVYDANKE NIHGLTVLKE IFLEPDWEPR QHSTQYVYVV HVYKEVLSKL QYGIYVVLTS FQNEDLVVDI LRQYFEKERF LF LNYLINS NTTLSYFGSV QRIGRCATED IKSGFLQYRG ITLPVIKLEN IFVDLSEKKV FV

UniProtKB: Triplex capsid protein 1

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Macromolecule #5: Triplex capsid protein 2

MacromoleculeName: Triplex capsid protein 2 / type: protein_or_peptide / ID: 5 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 6B (strain Z29) / Strain: Z29
Molecular weightTheoretical: 33.514332 KDa
SequenceString: METVYCTFDH KLSLSDISTL CKLMNIVIPI PAHHHLIGSG NLGLYPIVSS NKDYVHIRNV LRTMVVTILQ KVEGNQLVLR KPMTGQQYA IKNTGPFPWE KGDTLTLIPP LSTHSEEKLL KLGDWELTVP LVVPTAIAAE INIRLLCIGL IAVHREYNEM Q TIIDELCS ...String:
METVYCTFDH KLSLSDISTL CKLMNIVIPI PAHHHLIGSG NLGLYPIVSS NKDYVHIRNV LRTMVVTILQ KVEGNQLVLR KPMTGQQYA IKNTGPFPWE KGDTLTLIPP LSTHSEEKLL KLGDWELTVP LVVPTAIAAE INIRLLCIGL IAVHREYNEM Q TIIDELCS IQYRDVLIKL PDIVNDKQSM YSMKTACISL SMITAMAPDI VRTYIDRLTL EDHSMLLIKC QELLSKRTTL ST QRCGQLH ATDIKDELKK IKSVLTMIDQ INSLTNEKTY FVVCDVSADN RMATCIYKN

UniProtKB: Triplex capsid protein 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: PBS buffer, pH 7.4
GridMaterial: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: The grids were manually plunged into the ethane..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.2 µm / Calibrated defocus min: 2.2 µm / Calibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 2.2 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 4828 / Average electron dose: 23.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7430
Startup modelType of model: OTHER / Details: a sphere density map
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Details: bin4 reconstrction / Number images used: 6443

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-6q1f:
Atomic structure of the Human Herpesvirus 6B Capsid and Capsid-Associated Tegument Complexes

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