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- EMDB-0880: The atomic structure of varicella-zoster virus A-capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-0880
TitleThe atomic structure of varicella-zoster virus A-capsid
Map dataCryo-EM structure of varicella-zoster virus A-capsid
Sample
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Triplex capsid protein 2
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral capsid assembly / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Herpesvirus UL35 / Herpesvirus UL35 family / 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
Triplex capsid protein 2 / Major capsid protein / Small capsomere-interacting protein / Triplex capsid protein 1
Similarity search - Component
Biological speciesHHV-3,Human alphaherpesvirus 3 / Human alphaherpesvirus 3 (Varicella-zoster virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsZheng Q / Li S
CitationJournal: Nat Microbiol / Year: 2020
Title: Near-atomic cryo-electron microscopy structures of varicella-zoster virus capsids.
Authors: Wei Wang / Qingbing Zheng / Dequan Pan / Hai Yu / Wenkun Fu / Jian Liu / Maozhou He / Rui Zhu / Yuze Cai / Yang Huang / Zhenghui Zha / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Yuqiong Que ...Authors: Wei Wang / Qingbing Zheng / Dequan Pan / Hai Yu / Wenkun Fu / Jian Liu / Maozhou He / Rui Zhu / Yuze Cai / Yang Huang / Zhenghui Zha / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Yuqiong Que / Ting Wu / Jun Zhang / Shaowei Li / Hua Zhu / Z Hong Zhou / Tong Cheng / Ningshao Xia /
Abstract: Varicella-zoster virus (VZV) is a medically important human herpesvirus that causes chickenpox and shingles, but its cell-associated nature has hindered structure studies. Here we report the cryo- ...Varicella-zoster virus (VZV) is a medically important human herpesvirus that causes chickenpox and shingles, but its cell-associated nature has hindered structure studies. Here we report the cryo-electron microscopy structures of purified VZV A-capsid and C-capsid, as well as of the DNA-containing capsid inside the virion. Atomic models derived from these structures show that, despite enclosing a genome that is substantially smaller than those of other human herpesviruses, VZV has a similarly sized capsid, consisting of 955 major capsid protein (MCP), 900 small capsid protein (SCP), 640 triplex dimer (Tri2) and 320 triplex monomer (Tri1) subunits. The VZV capsid has high thermal stability, although with relatively fewer intra- and inter-capsid protein interactions and less stably associated tegument proteins compared with other human herpesviruses. Analysis with antibodies targeting the N and C termini of the VZV SCP indicates that the hexon-capping SCP-the largest among human herpesviruses-uses its N-terminal half to bridge hexon MCP subunits and possesses a C-terminal flexible half emanating from the inner rim of the upper hexon channel into the tegument layer. Correlation of these structural features and functional observations provide insights into VZV assembly and pathogenesis and should help efforts to engineer gene delivery and anticancer vectors based on the currently available VZV vaccine.
History
DepositionDec 5, 2019-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateAug 11, 2021-
Current statusAug 11, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lgl
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6lgl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0880.map.gz / Format: CCP4 / Size: 7.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of varicella-zoster virus A-capsid
Voxel sizeX=Y=Z: 1.307 Å
Density
Contour LevelBy AUTHOR: 3.0 / Movie #1: 5
Minimum - Maximum-13.588155 - 22.143972
Average (Standard dev.)-0.009036039 (±1.9782684)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128012801280
Spacing128012801280
CellA=B=C: 1672.9601 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3071.3071.307
M x/y/z128012801280
origin x/y/z0.0000.0000.000
length x/y/z1672.9601672.9601672.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128012801280
D min/max/mean-13.58822.144-0.009

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Supplemental data

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Sample components

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Entire : Human alphaherpesvirus 3

EntireName: Human alphaherpesvirus 3 (Varicella-zoster virus)
Components
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
    • Protein or peptide: Major capsid protein
    • 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 alphaherpesvirus 3

SupramoleculeName: Human alphaherpesvirus 3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10335 / Sci species name: Human alphaherpesvirus 3 / 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: HHV-3,Human alphaherpesvirus 3
Molecular weightTheoretical: 155.145359 KDa
SequenceString: MTTVSCPANV ITTTESDRIA GLFNIPAGII PTGNVLSTIE VCAHRCIFDF FKQIRSDDNS LYSAQFDILL GTYCNTLNFV RFLELGLSV ACICTKFPEL AYVRDGVIQF EVQQPMIARD GPHPVDQPVH NYMVKRIHKR SLSAAFAIAS EALSLLSNTY V DGTEIDSS ...String:
MTTVSCPANV ITTTESDRIA GLFNIPAGII PTGNVLSTIE VCAHRCIFDF FKQIRSDDNS LYSAQFDILL GTYCNTLNFV RFLELGLSV ACICTKFPEL AYVRDGVIQF EVQQPMIARD GPHPVDQPVH NYMVKRIHKR SLSAAFAIAS EALSLLSNTY V DGTEIDSS LRIRAIQQMA RNLRTVLDSF ERGTADQLLG VLLEKAPPLS LLSPINKFQP EGHLNRVARA ALLSDLKRRV CA DMFFMTR HAREPRLISA YLSDMVSCTQ PSVMVSRITH TNTRGRQVDG VLVTTATLKR QLLQGILQID DTAADVPVTY GEM VLQGTN LVTALVMGKA VRGMDDVARH LLDITDPNTL NIPSIPPQSN SDSTTAGLPV NARVPADLVI VGDKLVFLEA LERR VYQAT RVAYPLIGNI DITFIMPMGV FQANSMDRYT RHAGDFSTVS EQDPRQFPPQ GIFFYNKDGI LTQLTLRDAM GTICH SSLL DVEATLVALR QQHLDRQCYF GVYVAEGTED TLDVQMGRFM ETWADMMPHH PHWVNEHLTI LQFIAPSNPR LRFELN PAF DFFVAPGDVD LPGPQRPPEA MPTVNATLRI INGNIPVPLC PISFRDCRGT QLGLGRHTMT PATIKAVKDT FEDRAYP TI FYMLEAVIHG NERNFCALLR LLTQCIRGYW EQSHRVAFVN NFHMLMYITT YLGNGELPEV CINIYRDLLQ HVRALRQT I TDFTIQGEGH NGETSEALNN ILTDDTFIAP ILWDCDALIY RDEAARDRLP AIRVSGRNGY QALHFVDMAG HNFQRRDNV LIHGRPVRGD TGQGIPITPH HDREWGILSK IYYYIVIPAF SRGSCCTMGV RYDRLYPALQ AVIVPEIPAD EEAPTTPEDP RHPLHAHQL VPNSLNVYFH NAHLTVDGDA LLTLQELMGD MAERTTAILV SSAPDAGAAT ATTRNMRIYD GALYHGLIMM A YQAYDETI ATGTFFYPVP VNPLFACPEH LASLRGMTNA RRVLAKMVPP IPPFLGANHH ATIRQPVAYH VTHSKSDFNT LT YSLLGGY FKFTPISLTH QLRTGFHPGI AFTVVRQDRF ATEQLLYAER ASESYFVGQI QVHHHDAIGG VNFTLTQPRA HVD LGVGYT AVCATAALRC PLTDMGNTAQ NLFFSRGGVP MLHDNVTESL RRITASGGRL NPTEPLPIFG GLRPATSAGI ARGQ ASVCE FVAMPVSTDL QYFRTACNPR GRASGMLYMG DRDADIEAIM FDHTQSDVAY TDRATLNPWA SQKHSYGDRL YNGTY NLTG ASPIYSPCFK FFTPAEVNTN CNTLDRLLME AKAVASQSST DTEYQFKRPP GSTEMTQDPC GLFQEAYPPL CSSDAA MLR TAHAGETGAD EVHLAQYLIR DASPLRGCLP LPR

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Macromolecule #2: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: HHV-3,Human alphaherpesvirus 3
Molecular weightTheoretical: 24.440119 KDa
SequenceString: MTQPASSRVV FDPSNPTTFS VEAIAAYTPV ALIRLLNASG PLQPGHRVDI ADARSIYTVG AAASAARARA NHNANTIRRT AMFAETDPM TWLRPTVGLK RTFNPRIIRP QPPNPSMSLG ISGPTILPQK TQSADQSALQ QPAALAFSGS SPQHPPPQTT S ASVGQQQH ...String:
MTQPASSRVV FDPSNPTTFS VEAIAAYTPV ALIRLLNASG PLQPGHRVDI ADARSIYTVG AAASAARARA NHNANTIRRT AMFAETDPM TWLRPTVGLK RTFNPRIIRP QPPNPSMSLG ISGPTILPQK TQSADQSALQ QPAALAFSGS SPQHPPPQTT S ASVGQQQH VVSGSSGQQP QQGAQSSTVQ PTTGSPPAAQ GVPQSTPPPT QNTPQGGKGQ TLSHTGQSGN ASRSRRV

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Macromolecule #3: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: HHV-3,Human alphaherpesvirus 3
Molecular weightTheoretical: 54.02818 KDa
SequenceString: MGSQPTNSHF TLNEQTLCGT NISLLGNNRF IQIGNGLHMT YAPGFFGNWS RDLTIGPRFG GLNKQPIHVP PKRTETASIQ VTPRSIVIN RMNNIQINPT SIGNPQVTIR LPLNNFKSTT QLIQQVSLTD FFRPDIEHAG SIVLILRHPS DMIGEANTLT Q AGRDPDVL ...String:
MGSQPTNSHF TLNEQTLCGT NISLLGNNRF IQIGNGLHMT YAPGFFGNWS RDLTIGPRFG GLNKQPIHVP PKRTETASIQ VTPRSIVIN RMNNIQINPT SIGNPQVTIR LPLNNFKSTT QLIQQVSLTD FFRPDIEHAG SIVLILRHPS DMIGEANTLT Q AGRDPDVL LEGLRNLFNA CTAPWTVGEG GGLRAYVTSL SFIAACRAEE YTDKQAADAN RTAIVSAYGC SRMETRLIRF SE CLRAMVQ CHVFPHRFIS FFGSLLEYTI QDNLCNITAV AKGPQEAART DKTSTRRVTA NIPACVFWDV DKDLHLSADG LKH VFLVFV YTQRRQREGV RLHLALSQLN EQCFGRGIGF LLGRIRAENA AWGTEGVANT HQPYNTRALP LVQLSNDPTS PRCS IGEIT GVNWNLARQR LYQWTGDFRG LPTQLSCMYA AYTLIGTIPS ESVRYTRRME RFGGYNVPTI WLEGVVWGGT NTWNE CYY

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Macromolecule #4: Triplex capsid protein 2

MacromoleculeName: Triplex capsid protein 2 / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: HHV-3,Human alphaherpesvirus 3
Molecular weightTheoretical: 34.421914 KDa
SequenceString: MAMPFEIEVL LPGELSPAET SALQKCEGKI ITFSTLRHRA SLVDIALSSY YINGAPPDTL SLLEAYRMRF AAVITRVIPG KLLAHAIGV GTPTPGLFIQ NTSPVDLCNG DYICLLPPVF GSADSIRLDS VGLEIVFPLT IPQTLMREII AKVVARAVER T AAGAQILP ...String:
MAMPFEIEVL LPGELSPAET SALQKCEGKI ITFSTLRHRA SLVDIALSSY YINGAPPDTL SLLEAYRMRF AAVITRVIPG KLLAHAIGV GTPTPGLFIQ NTSPVDLCNG DYICLLPPVF GSADSIRLDS VGLEIVFPLT IPQTLMREII AKVVARAVER T AAGAQILP HEVLRGADVI CYNGRRYELE TNLQHRDGSD AAIRTLVLNL MFSINEGCLL LLALIPTLLV QGAHDGYVNL LI QTANCVR ETGQLINIPP MPRIQDGHRR FPIYETISSW ISTSSRLGDT LGTRAILRVC VFDGPSTVHP GDRTAVIQV

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 56.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22983

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Target criteria: REAL
Output model

PDB-6lgl:
The atomic structure of varicella-zoster virus A-capsid

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