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- EMDB-38187: C-hexon capsomer of the VZV C-Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-38187
TitleC-hexon capsomer of the VZV C-Capsid
Map data
Sample
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Tri2A
    • Protein or peptide: Tri2B
    • Protein or peptide: Tri1
KeywordsVZV / capsid structure / VIRUS
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral process / viral capsid / host cell nucleus / structural molecule activity
Similarity search - Function
Herpesvirus UL35 / Herpesvirus UL35 family / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
Major capsid protein / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNan W / Lei C / Xiangxi W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Hlife / Year: 2024
Title: Insights into varicella-zoster virus assembly from the B- and C-capsid at near-atomic resolution structures
Authors: Cao L / Wang N / Lv Z / Chen W / Chen Z / Song L / Sha X / Wang G / Hu Y / Lian X / Cui G / Fan J / Quan Y / Liu H / Hou H / Wang X
History
DepositionDec 1, 2023-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38187.png

Downloads & links

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Map

FileDownload / File: emd_38187.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 240 pix.
= 324. Å		1.35 Å/pix.
x 240 pix.
= 324. Å		1.35 Å/pix.
x 240 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.06980323 - 0.1228242
Average (Standard dev.)0.000569557 (±0.008490582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38187_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38187_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: Tri2A
    • Protein or peptide: Tri2B
    • Protein or peptide: Tri1

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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: OTHER / 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: 6 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 152.267125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PAGIIPTGNV LSTIEVCAHR CIFDFFKQIR SDDNSLYSAQ FDILLGTYCN TLNFVRFLEL GLSVACICTK FPELAYVRDG VIQFEVQQP MIARDGPHPV DQPVHNYMVK RIHKRSLSAA FAIASEALSL LSNTYVDGTE IDSSLRIRAI QQMARNLRTV L DSFERGTA ...String:
PAGIIPTGNV LSTIEVCAHR CIFDFFKQIR SDDNSLYSAQ FDILLGTYCN TLNFVRFLEL GLSVACICTK FPELAYVRDG VIQFEVQQP MIARDGPHPV DQPVHNYMVK RIHKRSLSAA FAIASEALSL LSNTYVDGTE IDSSLRIRAI QQMARNLRTV L DSFERGTA DQLLGVLLEK APPLSLLSPI NKFQPEGHLN RVARAALLSD LKRRVCADMF FMTRHAREPR LISAYLSDMV SC TQPSVMV SRITHTNTRG RQVDGVLVTT ATLKRQLLQG ILQIDDTAAD VPVTYGEMVL QGTNLVTALV MGKAVRGMDD VAR HLLDIT DPNTLNIPSI PPQSNSDSTT AGLPVNARVP ADLVIVGDKL VFLEALERRV YQATRVAYPL IGNIDITFIM PMGV FQANS MDRYTRHAGD FSTVSEQDPR QFPPQGIFFY NKDGILTQLT LRDAMGTICH SSLLDVEATL VALRQQHLDR QCYFG VYVA EGTEDTLDVQ MGRFMETWAD MMPHHPHWVN EHLTILQFIA PSNPRLRFEL NPAFDFFVAP GDVDLPGPQR PPEAMP TVN ATLRIINGNI PVPLCPISFR DCRGTQLGLG RHTMTPATIK AVKDTFEDRA YPTIFYMLEA VIHGNERNFC ALLRLLT QC IRGYWEQSHR VAFVNNFHML MYITTYLGNG ELPEVCINIY RDLLQHVRAL RQTITDFTIQ GEGHNGETSE ALNNILTD D TFIAPILWDC DALIYRDEAA RDRLPAIRVS GRNGYQALHF VDMAGHNFQR RDNVLIHGRP VRGDTGQAIP ITPHHDREW GILSKIYYYI VIPAFSRGSC CTMGVRYDRL YPALQAVIVP EIPADEEAPT TPEDPRHPLH AHQLVPNSLN VYFHNAHLTV DGDALLTLQ ELMGDMAERT TAILVSSAPD AGAATATTRN MRIYDGALYH GLIMMAYQAY DETIATGTFF YPVPVNPLFA C PEHLASLR GMTNARRVLA KMVPPIPPFL GANHHATIRQ PVAYHVTHSK SDFNTLTYSL LGGYFKFTPI SLTHQLRTGF HP GIAFTVV RQDRFATEQL LYAERASESY FVGQIQVHHH DAIGGVNFTL TQPRAHVDLG VGYTAVCATA ALRCPLTDMG NTA QNLFFS RGGVPMLHDN VTESLRRITA SGGRLNPTEP LPIFGGLRPA TSAGIARGQA SVCEFVAMPV STDLQYFRTA CNPR GRASG MLYMGDRDAD IEAIMFDHTQ SDVAYTDRAT LNPWASQKHS YGDRLYNGTY NLTGASPIYS PCFKFFTPAE VNTNC NTLD RLLMEAKAVA SQSSTDTEYQ FKRPPGSTEM TQDPCGLFQE AYPPLCSSDA AMLRTAHAGE TGADEVHLAQ YLIRDA SPL RGCLPL

UniProtKB: Major capsid protein

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Macromolecule #2: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 10.185611 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SNPTTFSVEA IAAYTPVALI RLLNASGPLQ PGHRVDIADA RSIYTVGAAA SAARARANHN ANTIRRTAMF AETDPMTWLR PTVGLRRTF NPRII

UniProtKB: Small capsomere-interacting protein

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Macromolecule #3: Tri2A

MacromoleculeName: Tri2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 27.729641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AMPFEIEVLL PGELSPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVYG SADSIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVEDL N LMFSINEG ...String:
AMPFEIEVLL PGELSPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVYG SADSIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVEDL N LMFSINEG CLLILALIPR LLALLIPRLL ALVTREAAQL IHPEAPMLML PIYETISSWI STSSRLGDTL GTRAILRVCV FD GPSTVHP GDRTAVIQV

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Macromolecule #4: Tri2B

MacromoleculeName: Tri2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 28.721295 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AMPFEIEVLL PGEISPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVFG SADEIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVERT A ADVICYNG ...String:
AMPFEIEVLL PGEISPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVFG SADEIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVERT A ADVICYNG RRYELETNLQ HRDGSDAAIR TLVLNLMFSI NEGTTLILTL ITRLLRFPIY EAISSWISTS SRLGDTLGTR AI LRVCVFD GPSTVHPGDR TAVIQV

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Macromolecule #5: Tri1

MacromoleculeName: Tri1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 33.690453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AAAAAAAAAA AAAAAAAAAA FKSTTQLIQQ VSLTDFFRPD IEHAGSTVLI LRHPTDLPAL ARHRAPPGRQ TERLAEAWGQ LLEASRAYV TSLSFIAACR AEEYTDKQAA EANRTAIVSA YGCSRMGARL IRFSECLRAM VQCHVFPHRF ISFFGSLLEY T IQDNLCNI ...String:
AAAAAAAAAA AAAAAAAAAA FKSTTQLIQQ VSLTDFFRPD IEHAGSTVLI LRHPTDLPAL ARHRAPPGRQ TERLAEAWGQ LLEASRAYV TSLSFIAACR AEEYTDKQAA EANRTAIVSA YGCSRMGARL IRFSECLRAM VQCHVFPHRF ISFFGSLLEY T IQDNLCNI TAVAKGPQEA ARTDKTSTRR VTANIPACVF WDVDKDLHLS ADGLKHVFLV FVYTQRRQRE GVRLHLALSQ LN EQCFGRG IGFLLGARIC MYAAYTLIGT IPSESVRYTR RMERFGGYNV PTIWLEGVVW GGTNTWNEC

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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: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1755031
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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