[English] 日本語
Yorodumi
- PDB-6w2e: Structures of Capsid and Capsid-Associated Tegument Complex insid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w2e
TitleStructures of Capsid and Capsid-Associated Tegument Complex inside the Epstein-Barr Virus
Components
  • (Capsid vertex component ...) x 2
  • (Triplex capsid protein ...) x 2
  • Large tegument protein deneddylase
  • Major capsid protein
  • Small capsomere-interacting protein
KeywordsVIRAL PROTEIN / gamma-herpesvirus / EBV / CATC / Structural plasticity
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / chromosome organization / viral process / viral penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification ...T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / chromosome organization / viral process / 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 / DNA binding
Similarity search - Function
Gammaherpesvirus capsid / Gammaherpesvirus capsid 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 capsid vertex component 1 / Herpesvirus UL17 protein / : / Herpesvirus UL25 ...Gammaherpesvirus capsid / Gammaherpesvirus capsid 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 capsid vertex component 1 / Herpesvirus UL17 protein / : / Herpesvirus UL25 / Herpesvirus UL25 family / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein / 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
Large tegument protein deneddylase / Triplex capsid protein 1 / Capsid vertex component 1 / Major capsid protein / Capsid vertex component 2 / Small capsomere-interacting protein / Triplex capsid protein 2
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsLiu, W. / Cui, Y.X. / Wang, C.Y. / Li, Z.H. / Gong, D.Y. / Dai, X.H. / Bi, G.Q. / Sun, R. / Zhou, Z.H.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583, DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1S10RR23057, 1S10OD018111, and 1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 and DMR-1548924 United States
CitationJournal: Nat Microbiol / Year: 2020
Title: Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus.
Authors: Wei Liu / Yanxiang Cui / Caiyan Wang / Zihang Li / Danyang Gong / Xinghong Dai / Guo-Qiang Bi / Ren Sun / Z Hong Zhou /
Abstract: As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been ...As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been hindered by latency-a hallmark of EBV infection-and atomic structures are thus available only for recombinantly expressed EBV proteins. In the present study, by symmetry relaxation and subparticle reconstruction, we have determined near-atomic-resolution structures of the EBV capsid with an asymmetrically attached DNA-translocating portal and capsid-associated tegument complexes from cryogenic electron microscopy images of just 2,048 EBV virions obtained by chemical induction. The resulting atomic models reveal structural plasticity among the 20 conformers of the major capsid protein, 2 conformers of the small capsid protein (SCP), 4 conformers of the triplex monomer proteins and 2 conformers of the triplex dimer proteins. Plasticity reaches the greatest level at the capsid-tegument interfaces involving SCP and capsid-associated tegument complexes (CATC): SCPs crown pentons/hexons and mediate tegument protein binding, and CATCs bind and rotate all five periportal triplexes, but notably only about one peri-penton triplex. These results offer insights into the EBV capsid assembly and a mechanism for recruiting cell-regulating factors into the tegument compartment as 'cargoes', and should inform future anti-EBV strategies.
History
DepositionMar 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-21526
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-21526
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
J: Major capsid protein
K: Major capsid protein
N: Major capsid protein
O: Major capsid protein
v: Capsid vertex component 1
w: Capsid vertex component 2
x: Capsid vertex component 2
y: Large tegument protein deneddylase
z: Large tegument protein deneddylase
Z: Small capsomere-interacting protein
a: Small capsomere-interacting protein
d: Small capsomere-interacting protein
e: Small capsomere-interacting protein
f: Triplex capsid protein 1
h: Triplex capsid protein 1
k: Triplex capsid protein 2
m: Triplex capsid protein 2
p: Triplex capsid protein 2
r: Triplex capsid protein 2


Theoretical massNumber of molelcules
Total (without water)1,758,30319
Polymers1,758,30319
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area93490 Å2
ΔGint-512 kcal/mol
Surface area333840 Å2

-
Components

-
Protein , 3 types, 10 molecules JKNOyzZade

#1: Protein
Major capsid protein / MCP


Mass: 154086.828 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / References: UniProt: P03226
#4: Protein Large tegument protein deneddylase / LTP protein


Mass: 338310.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8
References: UniProt: P03186, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#5: Protein
Small capsomere-interacting protein


Mass: 18169.100 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / References: UniProt: P14348

-
Capsid vertex component ... , 2 types, 3 molecules vwx

#2: Protein Capsid vertex component 1 / CVC1


Mass: 54527.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / References: UniProt: P03222
#3: Protein Capsid vertex component 2 / CVC2


Mass: 62525.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / References: UniProt: P03233

-
Triplex capsid protein ... , 2 types, 6 molecules fhkmpr

#6: Protein Triplex capsid protein 1


Mass: 39231.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / References: UniProt: P03187
#7: Protein
Triplex capsid protein 2


Mass: 33654.039 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / References: UniProt: P25214

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human herpesvirus 4 strain B95-8 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 28 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2305 / Symmetry type: POINT

+
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