[English] 日本語
Yorodumi
- EMDB-38190: penton capsomer of the VZV C-capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38190
Titlepenton capsomer of the VZV C-capsid
Map data
Sample
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
    • Protein or peptide: Large tegument protein deneddylase
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Tri2A
    • Protein or peptide: Tri2B
    • Protein or peptide: Tri1
KeywordsVZV / capsid structure / VIRUS
Function / homology
Function and homology information


nuclear capsid assembly / viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / chromosome organization / viral penetration into host nucleus ...nuclear capsid assembly / viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / chromosome organization / viral penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / 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 capsid vertex component 1 / Herpesvirus UL17 protein / 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 large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Large tegument protein deneddylase / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / 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
Capsid vertex component 1 / Capsid vertex component 2 / Large tegument protein deneddylase / Major capsid protein
Similarity search - Component
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

-
Structure visualization

Supplemental images

emd_38190.png

Downloads & links

-
Map

FileDownload / File: emd_38190.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: 0.004
Minimum - Maximum-0.02875249 - 0.049944904
Average (Standard dev.)0.00039342363 (±0.0043911273)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_38190_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_38190_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human alphaherpesvirus 3

EntireName: Human alphaherpesvirus 3 (Varicella-zoster virus)
Components
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
    • Protein or peptide: Large tegument protein deneddylase
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Tri2A
    • Protein or peptide: Tri2B
    • Protein or peptide: Tri1

-
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

-
Macromolecule #1: Large tegument protein deneddylase

MacromoleculeName: Large tegument protein deneddylase / type: protein_or_peptide / ID: 1 / 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

-
Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / 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

-
Macromolecule #3: Capsid vertex component 1

MacromoleculeName: Capsid vertex component 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 73.998547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNAHLANEVQ YDLGHARVGP SSLVHVIISS ECLAAAGIPL AALMRGRPGL GTAANFQVEI QTRAHATGDC TPWCTAFAAY VPADAVGEL LAPVVPAHPG LLPRASSAGG LFVSLPVVCD AQGVYDPYAV AALRLAWGSG ASCARVILFS YDELVPPNTR Y AADSTRIM ...String:
MNAHLANEVQ YDLGHARVGP SSLVHVIISS ECLAAAGIPL AALMRGRPGL GTAANFQVEI QTRAHATGDC TPWCTAFAAY VPADAVGEL LAPVVPAHPG LLPRASSAGG LFVSLPVVCD AQGVYDPYAV AALRLAWGSG ASCARVILFS YDELVPPNTR Y AADSTRIM RVCRHLCRYV ALLGAAAPPA AKEAAAHLSM GLGESASPRP QPLARPHAGA PADPPIVGAS DPPISPEEQL TA PGGDTTA AQDVSIAQEN EEILALVQRA VQDVTRRHPV RARTGRAACG VASGLRQGAL VHQAVSGGAM GAADADAVLA GLE PPGGGR FVAPAPHGPG GEDILNDVLT LTPGTAKPRS LVEWLDRGWE ALAGGDRPDW LWSRRSISVV LRHHYGTKQR FVVV SYENS VAWGGRRARP PLLSSALATA LTEACAAERV VRPHQLSPAG QAELLLRFPA LEVPLRHPRP VLPPFDIAAE VAFTA RIHL ACLRALGQAI RAALQGGPRI SQRLRYDFGP DQRAWLGEVT RRFPILLENL MRAVEGTAPD AFFHTAYALA VLAHLG GRG GRGRRVVPLG DDLPARFADS DGHYVFDYYS TSGDTLRLNN RPIAVAMDGD VSKREQSKCR FMEAVPSTAP RRVCEQY LP GESYAYLCLG FNRRLCGIVV FPGGFAFTIN IAAYLSLSDP VARAAVLRFC RKVS

UniProtKB: Capsid vertex component 1

-
Macromolecule #4: Capsid vertex component 2

MacromoleculeName: Capsid vertex component 2 / type: protein_or_peptide / ID: 4 / 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

-
Macromolecule #5: Tri2A

MacromoleculeName: Tri2A / type: protein_or_peptide / ID: 5 / 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

-
Macromolecule #6: Tri2B

MacromoleculeName: Tri2B / type: protein_or_peptide / ID: 6 / 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

-
Macromolecule #7: Tri1

MacromoleculeName: Tri1 / type: protein_or_peptide / ID: 7 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

-
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

-
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: 417864
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more