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- EMDB-38191: Portal vertex capsomer of VZV B-capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-38191
TitlePortal vertex capsomer of VZV B-capsid
Map data
Sample
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: major capsid protein
    • Protein or peptide: Tri2A
    • Protein or peptide: Tri2B
    • Protein or peptide: Tri1
KeywordsVZV / capsid structure / VIRAL PROTEIN
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 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_38191.png

Downloads & links

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Map

FileDownload / File: emd_38191.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: 0.007
Minimum - Maximum-0.017551046 - 0.031555217
Average (Standard dev.)0.0010372361 (±0.003302288)
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: #2

Fileemd_38191_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_38191_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: 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: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 149.896484 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 VPVTVLNGAN LVTALVMGKA VRSLDDVGRH LLD MQEEQL ENARVPADLV IVGDKLVFLE ALERRVYQAT RVAYPLIGNI DITFIMPMGV FQANSMDRYT RHAGDFSTVS EQDP RQFPP QGIFFYNKDG ILTQLTLRDA MGTICHSSLL DVEATLVALR QQHLDRQCYF GVYVAEGTED TLDVQMGRFM ETWAD MMPH HPHWVNEHLT ILQFIAPSNP RLRFELNPAF DFFVAPGDVD LPGPQRPPEA MPTVNATLRI INGNIPVPLC PISFRD CRG TQLGLGRHTM TPATIKAVKD TFEDRAYPTI FYMLEAVIHG NERNFCALLR LLTQCIRGYW EQSHRVAFVN NFHMLMY IT TYLGNGELPE VCINIYRDLL QHVRALRQTI TDFTIQGEGH NGETSEALNN ILTDDTFIAP ILWDCDALIY RDEAARDR L PAIRVSGRNG YQALHFVDMA GHNFQRRDNV LIHGRPVRGD TGQAIPITPH HDREWGILSK IYYYIVIPAF SRGSCCTMG VRYDRLYPAL QAVIVPEIPA DEEAPTTPED PRHPLHAHQL VPNSLNVYFH NAHLTVDGDA LLTLQELMGD MAERTTAILV SSAPDAGAA TATTRNMRIY DGALYHGLIM MAYQAYDETI ATGTFFYPVP VNPLFACPEH LASLRGMTNA RRVLAKMVPP I PPFLGANH HATIRQPVAY HVTHSKSDFN TLTYSLLGGY FKFTPISLTH QLRTGFHPGI AFTVVRQDRF ATEQLLYAER AS ESYFVGQ IQVHHHDAIG GVNFTLTQPR AHVDLGVGYT AVCATAALRC PLTDMGNTAQ NLFFSRGGVP MLHDNVTESL RRI TASGGR LNPTEPLPIF GGLRPATSAG IARGQASVCE FVAMPVSTDL QYFRTACNPR GRASGMLYMG DRDADIEAIM FDHT QSDVA YTDRATLNPW ASQKHSYGDR LYNGTYNLTG ASPIYSPCFK FFTPAEVNTN CNTLDRLLME AKAVASQSST DTEYQ FKRP PGSTEMTQDP CGLFQEAYPP LCSSDAAMLR TAHAGETGAD EVHLAQYLIR DASPLRGCLP L

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Macromolecule #2: major capsid protein

MacromoleculeName: major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 144.341406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IPAGIIPTGN VLSTIEVCIF FRFLELGLSV ACICTKFPEL AYVRDGVIQF EVQQPMIARD GPHPVDQPVH NYMVKRIHKR SLSAAFAIA SEALSLLSNT YVDGTEIDSS LRIRAIQQMA RNLRTVSDSF ERGTADQLLG VLLEKAPPLS LLSPINKFQP E GHLNRVAR ...String:
IPAGIIPTGN VLSTIEVCIF FRFLELGLSV ACICTKFPEL AYVRDGVIQF EVQQPMIARD GPHPVDQPVH NYMVKRIHKR SLSAAFAIA SEALSLLSNT YVDGTEIDSS LRIRAIQQMA RNLRTVSDSF ERGTADQLLG VLLEKAPPLS LLSPINKFQP E GHLNRVAR AALLSDLKRR VCADMFFMTR HAREPRLISA YLSDMVSCTQ PSVMVSRITH TNTRGRQVDG VLVTTATLKR QL LQGILQI DDTAADVPVT YGEMVLQGTN LVTALVMGKA VRNARVPADL VIVGDKLVFL EALERRVYQA TRVAYPLIGN IDI TFIMPM GVFQANSMDR YTRHAGDFST VSEQDPRQFP PQGIFFYNKD GILTQLTLRD AMGTICHSSL LDVEATLVAL RQQH LDRQC YFGVYVAEGT EDTLDVQMGR FMETWADMMP HHPHWVNEHL TILQFIAPSN PRLRFELNPA FDFFVAPGDV DLPGP QRPP EAMPTVNATL RIINGNIPVP LCPISFRDCR GTQLGLGRHT MTPATIKAVK DTFEDRAYPT IFYMLEAVIH GNERNF CAL LRLLTQCIRG YWEQSHRVAF VNNFHMLMYI TTYLGNGELP EVCINIYRDL LQHVRALRQT ITDFTIQGEG HNGETSE AL NNILTDDTFI APILWDCDAL IYRDEAARDR LPAIRVSGRN GYQALHFVDM AGHNFQRRDN VLIHGRPVRG DTGQAIPI T PHHDREWGIL SKIYYYIVIP AFSRGSCCTM GVRYDRLYPA LQAVIVPEIP ADEEAPTTPE DPRHPLHAHQ LVPNSLNVY FHNAHLTVDG DALLTLQELM GDMAERTTAI LVSSAPDAGA ATATTRNMRI YDGALYHGLI MMAYQAYDET IATGTFFYPV PVNPLFACP EHLASLRGMT NARRVLAKMV PPIPPFLGAN HHATIRQPVA YHVTHSKSDF NTLTYSLLGG YFKFTPISLT H QLRTGFHP GIAFTVVRQD RFATEQLLYA ERASESYFVG QIQVHHHDAI GGVNFTLTQP RAHVDLGVGY TAVCATAALR CP LTDMGNT AQNLFFSRGG VPMLHDNVTE SLRRITASGG RLNPTEPLPI FGGLRPATSA GIARGQASVC EFVAMPVSTD LQY FRTACN PRGRASGMLY MGDRDADIEA IMFDHTQSDV AYTDRATLNP WASQKHSYGD RLYNGTYNLT GASPIYSPCF KFFT PAEVN TNCNTLDRLL MEAKAVASQS STDTEYQFKR PPGSTEMTQD PCGLFQEAYP PLCSSDAAML RTAHAGETGA DEVHL AQYL IRDASPLRGC LPL

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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: 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: 2 / 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 38.719105 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAIVI NRMNNIQINP TSIGNPQTIR LPLNNFKSTT QLIQQVSLTD FFRPDIEHA GSTVLILRHP TDLPHLARHR APPGRQTERL AEAWGQLLEA SESGCARAYV TSLSFIAACR AEEYTDKQAA E ANRTAIVS ...String:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAIVI NRMNNIQINP TSIGNPQTIR LPLNNFKSTT QLIQQVSLTD FFRPDIEHA GSTVLILRHP TDLPHLARHR APPGRQTERL AEAWGQLLEA SESGCARAYV TSLSFIAACR AEEYTDKQAA E ANRTAIVS AYGCSRMGAR LIRFSECLRA MVQCHVFPHR FISFFGSLLE YTIQDNLCNI TAVAKGPQEA ARTDKTSTRR VT ANIPACV FWDVDKDLHL SADGLKHVFL VFVYTQRRQR EGVRLHLALS QLNEQCFGRG IGFLLGARIC MYAAYTLIGT IPS ESVRYT RRMERFGGYN VPTIWLEGVV WGGTNTWNEC Y

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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: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25531
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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