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- EMDB-38193: C-hexon capsomer of the VZV B-Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-38193
TitleC-hexon capsomer of the VZV B-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: 3.7 Å
AuthorsWang N / Cao L / Wang X
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_38193.png

Downloads & links

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Map

FileDownload / File: emd_38193.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: 0.02
Minimum - Maximum-0.20132303 - 0.2670297
Average (Standard dev.)0.00057829806 (±0.015338207)
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: #2

Fileemd_38193_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38193_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: 153.585562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TESDRIAGIF NIPAGIIPTG NVLSTIEVCA HRCIFDFFKQ IRSDDNSLYS AQFDILLGTY CNTLNFVRFL ELGLSVACIC TKFPELAYV RDGVIQFEVQ QPMIARDGPH PVDQPVHNYM VKRIHKRSLS AAFAIASEAL SLLSNTYVDG TEIDSSLRIR A IQQMARNL ...String:
TESDRIAGIF NIPAGIIPTG NVLSTIEVCA HRCIFDFFKQ IRSDDNSLYS AQFDILLGTY CNTLNFVRFL ELGLSVACIC TKFPELAYV RDGVIQFEVQ QPMIARDGPH PVDQPVHNYM VKRIHKRSLS AAFAIASEAL SLLSNTYVDG TEIDSSLRIR A IQQMARNL RTVLDSFERG TADQLLGVLL EKAPPLSLLS PINKFQPEGH LNRVARAALL SDLKRRVCAD MFFMTRHARE PR LISAYLS DMVSCTQPSV MVSRITHTNT RGRQVDGVLV TTATLKRQLL QGILQIDDTA ADVPVTYGEM VLQGTNLVTA LVM GKAVRG MDDVARHLLD ITDPNTLNIP SIPPQSNSDS TTAGLPVNAR VPADLVIVGD KLVFLEALER RVYQATRVAY PLIG NIDIT FIMPMGVFQA NSMDRYTRHA GDFSTVSEQD PRQFPPQGIF FYNKDGILTQ LTLRDAMGTI CHSSLLDVEA TLVAL RQQH LDRQCYFGVY VAEGTEDTLD VQMGRFMETW ADMMPHHPHW VNEHLTILQF IAPSNPRLRF ELNPAFDFFV APGDVD LPG PQRPPEAMPT VNATLRIING NIPVPLCPIS FRDCRGTQLG LGRHTMTPAT IKAVKDTFED RAYPTIFYML EAVIHGN ER NFCALLRLLT QCIRGYWEQS HRVAFVNNFH MLMYITTYLG NGELPEVCIN IYRDLLQHVR ALRQTITDFT IQGEGHNG E TSEALNNILT DDTFIAPILW DCDALIYRDE AARDRLPAIR VSGRNGYQAL HFVDMAGHNF QRRDNVLIHG RPVRGDTGQ AIPITPHHDR EWGILSKIYY YIVIPAFSRG SCCTMGVRYD RLYPALQAVI VPEIPADEEA PTTPEDPRHP LHAHQLVPNS LNVYFHNAH LTVDGDALLT LQELMGDMAE RTTAILVSSA PDAGAATATT RNMRIYDGAL YHGLIMMAYQ AYDETIATGT F FYPVPVNP LFACPEHLAS LRGMTNARRV LAKMVPPIPP FLGANHHATI RQPVAYHVTH SKSDFNTLTY SLLGGYFKFT PI SLTHQLR TGFHPGIAFT VVRQDRFATE QLLYAERASE SYFVGQIQVH HHDAIGGVNF TLTQPRAHVD LGVGYTAVCA TAA LRCPLT DMGNTAQNLF FSRGGVPMLH DNVTESLRRI TASGGRLNPT EPLPIFGGLR PATSAGIARG QASVCEFVAM PVST DLQYF RTACNPRGRA SGMLYMGDRD ADIEAIMFDH TQSDVAYTDR ATLNPWASQK HSYGDRLYNG TYNLTGASPI YSPCF KFFT PAEVNTNCNT LDRLLMEAKA VASQSSTDTE YQFKRPPGST EMTQDPCGLF QEAYPPLCSS DAAMLRTAHA GETGAD EVH LAQYLIRDAS PLRGCLPL

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: 42.776746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SIQVTPRSIV INRMNNIQIN PTSIGNPNNG LHMTYNNAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAS IQVTPRSIVI NRMNNIQIN PTSIGNPQVT IRLPLNNFKS TTQLIQQVSL TDFFRPDIEH AGSTVLILRH PTDLPALARH RAPPGRQTER L AEAWGQLL ...String:
SIQVTPRSIV INRMNNIQIN PTSIGNPNNG LHMTYNNAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAS IQVTPRSIVI NRMNNIQIN PTSIGNPQVT IRLPLNNFKS TTQLIQQVSL TDFFRPDIEH AGSTVLILRH PTDLPALARH RAPPGRQTER L AEAWGQLL EASRAYVTSL SFIAACRAEE YTDKQAAEAN RTAIVSAYGC SRMGARLIRF SECLRAMVQC HVFPHRFISF FG SLLEYTI QDNLCNITAV AKGPQEAART DKTSTRRVTA NIPACVFWDV DKDLHLSADG LKHVFLVFVY TQRRQREGVR LHL ALSQLN EQCFGRGIGF LLGARICMYA AYTLIGTIPS ESVRYTRRME RFGGYNVPTI WLEGVVWGGT NTWNEC

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
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: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1442742
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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