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- EMDB-38192: Penton capsomer of the VZV B-Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-38192
TitlePenton 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: Tri2A
    • Protein or peptide: Tri2B
    • Protein or peptide: Tri1
KeywordsVZV / capsid structures / VIRUS
Function / homologyT=16 icosahedral viral capsid / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / host cell nucleus / structural molecule activity / Major capsid protein
Function and homology information
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38192.png

Downloads & links

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Map

FileDownload / File: emd_38192.map.gz / Format: CCP4 / Size: 113.6 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 310 pix.
= 418.5 Å		1.35 Å/pix.
x 310 pix.
= 418.5 Å		1.35 Å/pix.
x 310 pix.
= 418.5 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-0.029236393 - 0.057222866
Average (Standard dev.)0.00046959287 (±0.00423845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions310310310
Spacing310310310
CellA=B=C: 418.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38192_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_38192_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: 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: 5 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 152.365312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IPAGIIPTGN VLSTIEVCIF FCIFDFFKQI RSDDNSLYSA QFDILLGTYC NTLNFVRFLE LGLSVACICT KFPELAYVRD GVIQFEVQQ PMIARDGPHP VDQPVHNYMV KRIHKRSLSA AFAIASEALS LLSNTYVAAT EIDSSLRIRA IQQMARNLRT V SDSFERGT ...String:
IPAGIIPTGN VLSTIEVCIF FCIFDFFKQI RSDDNSLYSA QFDILLGTYC NTLNFVRFLE LGLSVACICT KFPELAYVRD GVIQFEVQQ PMIARDGPHP VDQPVHNYMV KRIHKRSLSA AFAIASEALS LLSNTYVAAT EIDSSLRIRA IQQMARNLRT V SDSFERGT ADQLLGVLLE KAPPLSLLSP INKFQPEGHL NRVARAALLS DLKRRVCADM FFMTRHAREP RLISAYLSDM VS CTQPSVM VSRITHTNTR GRQVDGVLVT TATLKRQLLQ GILQIDDTAA DVPVTYGEMV LQGTNLVTAL VMGKAVRGMD DVA RHLLDI TDPNTLNIPS IPPQSNSDST TAGLPVNARV PADLVIVGDK LVFLEALERR VYQATRVAYP LIGNIDITFI MPMG VFQAN SMDRYTRHAG DFSTVSEQDP RQFPPQGIFF YNKDGILTQL TLRDAMGTIC HSSLLDVEAT LVALRQQHLD RQCYF GVYV AEGTEDTLDV QMGRFMETWA DMMPHHPHWV NEHLTILQFI APSNPRLRFE LNPAFDFFVA PGDVDLPGPQ RPPEAM PTV NATLRIINGN IPVPLCPISF RDCRGTQLGL GRHTMTPATI KAVKDTFEDR AYPTIFYMLE AVIHGNERNF CALLRLL TQ CIRGYWEQSH RVAFVNNFHM LMYITTYLGN GELPEVCINI YRDLLQHVRA LRQTITDFTI QGEGHNGETS EALNNILT D DTFIAPILWD CDALIYRDEA ARDRLPAIRV SGRNGYQALH FVDMAGHNFQ RRDNVLIHGR PVRGDTGQAI PITPHHDRE WGILSKIYYY IVIPAFSRGS CCTMGVRYDR LYPALQAVIV PEIPADEEAP TTPEDPRHPL HAHQLVPNSL NVYFHNAHLT VDGDALLTL QELMGDMAER TTAILVSSAP DAGAATATTR NMRIYDGALY HGLIMMAYQA YDETIATGTF FYPVPVNPLF A CPEHLASL RGMTNARRVL AKMVPPIPPF LGANHHATIR QPVAYHVTHS KSDFNTLTYS LLGGYFKFTP ISLTHQLRTG FH PGIAFTV VRQDRFATEQ LLYAERASES YFVGQIQVHH HDAIGGVNFT LTQPRAHVDL GVGYTAVCAT AALRCPLTDM GNT AQNLFF SRGGVPMLHD NVTESLRRIT ASGGRLNPTE PLPIFGGLRP ATSAGIARGQ ASVCEFVAMP VSTDLQYFRT ACNP RGRAS GMLYMGDRDA DIEAIMFDHT QSDVAYTDRA TLNPWASQKH SYGDRLYNGT YNLTGASPIY SPCFKFFTPA EVNTN CNTL DRLLMEAKAV ASQSSTDTEY QFKRPPGSTE MTQDPCGLFQ EAYPPLCSSD AAMLRTAHAG ETGADEVHLA QYLIRD ASP LRGCLPL

UniProtKB: Major capsid protein

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Macromolecule #2: Tri2A

MacromoleculeName: Tri2A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 #3: Tri2B

MacromoleculeName: Tri2B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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 #4: Tri1

MacromoleculeName: Tri1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 32.26891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FKSTTQLIQQ VSLTDFFRPD IEHAGSTVLI LRHPTDLPAL ARHRAPPGRQ TERLAEAWGQ LLEASRAYVT SLSFIAACRA EEYTDKQAA EANRTAIVSA YGCSRMGARL IRFSECLRAM VQCHVFPHRF ISFFGSLLEY TIQDNLCNIT AVAKGPQEAA R TDKTSTRR ...String:
FKSTTQLIQQ VSLTDFFRPD IEHAGSTVLI LRHPTDLPAL ARHRAPPGRQ TERLAEAWGQ LLEASRAYVT SLSFIAACRA EEYTDKQAA EANRTAIVSA YGCSRMGARL IRFSECLRAM VQCHVFPHRF ISFFGSLLEY TIQDNLCNIT AVAKGPQEAA R TDKTSTRR VTANIPACVF WDVDKDLHLS ADGLKHVFLV FVYTQRRQRE GVRLHLALSQ LNEQCFGRGI GFLLGARICM YA AYTLIGT 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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 267174
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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