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- EMDB-38186: portal vertex capsomer of the VZV C-Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-38186
Titleportal vertex 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: coiled-coil domain of portal
    • Protein or peptide: Tri2A
    • Protein or peptide: Tri2B
    • Protein or peptide: Tri1
    • Protein or peptide: CVC1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Large tegument protein deneddylase
KeywordsVZV / capsid structure / VIRAL PROTEIN
Function / homology
Function and homology information


nuclear capsid assembly / deNEDDylase activity / viral genome packaging / T=16 icosahedral viral capsid / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / viral penetration into host nucleus / viral capsid ...nuclear capsid assembly / deNEDDylase activity / viral genome packaging / T=16 icosahedral viral capsid / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / viral penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus UL25 / Herpesvirus UL25 family / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily ...Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus UL25 / Herpesvirus UL25 family / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Major capsid protein / Capsid vertex component 2 / Large tegument protein deneddylase
Similarity search - Component
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsNan W / Lei C / Jiangxi 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_38186.png

Downloads & links

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Map

FileDownload / File: emd_38186.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 345.6 Å		1.35 Å/pix.
x 256 pix.
= 345.6 Å		1.35 Å/pix.
x 256 pix.
= 345.6 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: 0.006
Minimum - Maximum-0.016273504 - 0.030610416
Average (Standard dev.)0.0008944923 (±0.003113286)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38186_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_38186_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: coiled-coil domain of portal
    • Protein or peptide: Tri2A
    • Protein or peptide: Tri2B
    • Protein or peptide: Tri1
    • Protein or peptide: CVC1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Large tegument protein deneddylase

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 153.965938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AAAAAATESD RIAGIFNIPA GIIPTGNVLS TIEVCAHRCI FDFFKQIRSD DNSLYSAQFD ILLGTYCNTL NFVRFLELGL SVACICTKF PELAYVRDGV IQFEVQQPMI ARDGPHPVDQ PVHNYMVKRI HKRSLSAAFA IASEALSLLS NTYVDGTEID S SLRIRAIQ ...String:
AAAAAATESD RIAGIFNIPA GIIPTGNVLS TIEVCAHRCI FDFFKQIRSD DNSLYSAQFD ILLGTYCNTL NFVRFLELGL SVACICTKF PELAYVRDGV IQFEVQQPMI ARDGPHPVDQ PVHNYMVKRI HKRSLSAAFA IASEALSLLS NTYVDGTEID S SLRIRAIQ QMARNLRTVL DSFERGTADQ LLGVLLEKAP PLSLLSPINK FQPEGHLNRV ARAALLSDLK RRVCADMFFM TR HAREPRL ISAYLSDMVS CTQPSVMVSR ITHTNTRGRQ VDGVLVTTAT LKRQLLQGIL QIDDTAADVP VTYGEMVLNG ANL VTALVM GKAVRSLDDV GRHLLDITDP NTLNIPSIPP QSNSDSTTAG LPVNARVPAD LVIVGDKLVF LEALERRVYQ ATRV AYPLI GNIDITFIMP MGVFQANSMD RYTRHAGDFS TVSEQDPRQF PPQGIFFYNK DGILTQLTLR DAMGTICHSS LLDVE ATLV ALRQQHLDRQ CYFGVYVAEG TEDTLDVQMG RFMETWADMM PHHPHWVNEH LTILQFIAPS NPRLRFELNP AFDFFV APG DVDLPGPQRP PEAMPTVNAT LRIINGNIPV PLCPISFRDC RGTQLGLGRH TMTPATIKAV KDTFEDRAYP TIFYMLE AV IHGNERNFCA LLRLLTQCIR GYWEQSHRVA FVNNFHMLMY ITTYLGNGEL PEVCINIYRD LLQHVRALRQ TITDFTIQ G EGHNGETSEA LNNILTDDTF IAPILWDCDA LIYRDEAARD RLPAIRVSGR NGYQALHFVD MAGHNFQRRD NVLIHGRPV RGDTGQAIPI TPHHDREWGI LSKIYYYIVI PAFSRGSCCT MGVRYDRLYP ALQAVIVPEI PADEEAPTTP EDPRHPLHAH QLVPNSLNV YFHNAHLTVD GDALLTLQEL MGDMAERTTA ILVSSAPDAG AATATTRNMR IYDGALYHGL IMMAYQAYDE T IATGTFFY PVPVNPLFAC PEHLASLRGM TNARRVLAKM VPPIPPFLGA NHHATIRQPV AYHVTHSKSD FNTLTYSLLG GY FKFTPIS LTHQLRTGFH PGIAFTVVRQ DRFATEQLLY AERASESYFV GQIQVHHHDA IGGVNFTLTQ PRAHVDLGVG YTA VCATAA LRCPLTDMGN TAQNLFFSRG GVPMLHDNVT ESLRRITASG GRLNPTEPLP IFGGLRPATS AGIARGQASV CEFV AMPVS TDLQYFRTAC NPRGRASGML YMGDRDADIE AIMFDHTQSD VAYTDRATLN PWASQKHSYG DRLYNGTYNL TGASP IYSP CFKFFTPAEV NTNCNTLDRL LMEAKAVASQ SSTDTEYQFK RPPGSTEMTQ DPCGLFQEAY PPLCSSDAAM LRTAHA GET GADEVHLAQY LIRDASPLRG CLPL

UniProtKB: Major capsid protein

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Macromolecule #2: coiled-coil domain of portal

MacromoleculeName: coiled-coil domain of portal / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 7.42214 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #3: Tri2A

MacromoleculeName: Tri2A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 32.225578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AMPFEIEVLL PGELSPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVFG SADSIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVEDL N PDPDLNVL ...String:
AMPFEIEVLL PGELSPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVFG SADSIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVEDL N PDPDLNVL YYNGARLSLV ADVQQLASDA AIRTLVLNLM FSINEGCLLI LALIPRLLAL GYVNALLQMQ SVTREAAQLI HP EAPMLMR RLPIYETISS WISTSSRLGD TLGTRAILRV CVFDGPSTVH PGDRTAVIQV

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Macromolecule #4: Tri2B

MacromoleculeName: Tri2B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 33.420516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AMPFEIEVLL PGEISPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVFG SADEIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVERT A AGRTPGEL ...String:
AMPFEIEVLL PGEISPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVFG SADEIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVERT A AGRTPGEL PGADVICYNG RRYELETNLQ HRDGSDAAIR TLVLNLMFSI NEGTTLILTL ITRLLVQGAH DGYVNLLIQT AN CVRETGQ PMPRIQDGHR RFPIYEAISS WISTSSRLGD TLGTRAILRV CVFDGPSTVH PGDRTAVIQV

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Macromolecule #5: Tri1

MacromoleculeName: Tri1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 32.583186 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TTQLIQQVSL TDFFRPDIEH AGSTVLILRH PTDLPHLARH RAPPGRQTER LAEAWGQLLE ASESGCARAY VTSLSFIAAC RAEEYTDKQ AAEANRTAIV SAYGCSRMGA RLIRFSECLR AMVQCHVFPH RFISFFGSLL EYTIQDNLCN ITAVAKGPQE A ARTDKTST ...String:
TTQLIQQVSL TDFFRPDIEH AGSTVLILRH PTDLPHLARH RAPPGRQTER LAEAWGQLLE ASESGCARAY VTSLSFIAAC RAEEYTDKQ AAEANRTAIV SAYGCSRMGA RLIRFSECLR AMVQCHVFPH RFISFFGSLL EYTIQDNLCN ITAVAKGPQE A ARTDKTST RRVTANIPAC VFWDVDKDLH LSADGLKHVF LVFVYTQRRQ REGVRLHLAL SQLNEQCFGR GIGFLLGARI CM YAAYTLI GTIPSESVRY TRRMERFGGY NVPTIWLEGV VWGGTNTWNE CY

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Macromolecule #6: CVC1

MacromoleculeName: CVC1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 59.751445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNAHLANEVQ YDLGHPSSLV HVIISSECLA AAGIPLAALM RANFQVEIQT RAHATGDCTP WCTAFAAYVP ADAVGELLAP VVPAHPGLL PRASSAGGLF VSLPVVCDAQ GVYDPYAVAA LRLAWGSGAS CARVILFSYD ELVPPNTRYA ADSTRIMRVC R HLCRYVAL ...String:
MNAHLANEVQ YDLGHPSSLV HVIISSECLA AAGIPLAALM RANFQVEIQT RAHATGDCTP WCTAFAAYVP ADAVGELLAP VVPAHPGLL PRASSAGGLF VSLPVVCDAQ GVYDPYAVAA LRLAWGSGAS CARVILFSYD ELVPPNTRYA ADSTRIMRVC R HLCRYVAL LGAAAPPAAK EAAAHLSMGL PPISPEEQLT APGGDTTAAQ DVSIAQENEE ILALVQRRSL VEWLDRGWEA LA GGDRPDW LWSRRSISVV LRHHYGTKQR FVVVSYENSV AWGGRRARPP LLSSALATAL TEACAAERVV RPHQLSPAGQ AEL LLRFPA LEVPLRHPRP VLPPFDIAAE VAFTARIHLA CLRALGQAIR AALQGGPRIS QRLRYDFGPD QRAWLGEVTR RFPI LLENL MRAVEGTAPD AFFHTAYALA VLAHLGGRVV PLGDDLPARF ADSDGHYVFD YYSTSGDTLR LNNRPIAVAM DEQSK CRFM EAPRRVCEQY LPGESYAYLC LGFNRRLCGI VVFPGGFAFT INIAAYLSLS DPVARAAVLR FCRKVS

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Macromolecule #7: Capsid vertex component 2

MacromoleculeName: Capsid vertex component 2 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 10.890343 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDPYCPFDAL DVWEHRRFIV ADSRNFITPE FPRDFWMSPV FNLPRETAAE QVVVLQAQRT AAAAALENAA MQAAELPVDI ERRLRPIER NVHEI

UniProtKB: Capsid vertex component 2

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Macromolecule #8: Large tegument protein deneddylase

MacromoleculeName: Large tegument protein deneddylase / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 5.50051 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QRTGRSALAV LIRACYRLQQ QLQRTRRALL HHSDAVLTSL HHVRMLL

UniProtKB: Large tegument protein deneddylase

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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 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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28556
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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