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- PDB-7bsi: Epstein-Barr virus, one asymmetric unit structure of the icosahed... -

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Basic information

Entry
Database: PDB / ID: 7bsi
TitleEpstein-Barr virus, one asymmetric unit structure of the icosahedral tegumented capsid
Components
  • Major capsid protein
  • Small capsomere-interacting protein
  • Triplex capsid protein 1
  • Triplex capsid protein 2
KeywordsVIRUS / tegumented capsid / icosahedral reconstruction
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral capsid assembly / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Gammaherpesvirus capsid / Gammaherpesvirus capsid protein / Herpesvirus capsid protein 2 / Herpesvirus capsid shell protein 1 / Herpesvirus VP23 like capsid protein / Herpesvirus capsid shell protein VP19C / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
Triplex capsid protein 1 / Major capsid protein / 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: 4.1 Å
AuthorsLi, Z. / Yu, X.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900869 China
National Natural Science Foundation of China (NSFC)81830090 China
National Natural Science Foundation of China (NSFC)81702001 China
Ministry of Science and Technology (MoST, China)2017YFA0505600 China
Ministry of Science and Technology (MoST, China)2016YFA0502101 China
CitationJournal: Cell Res / Year: 2020
Title: CryoEM structure of the tegumented capsid of Epstein-Barr virus.
Authors: Zhihai Li / Xiao Zhang / Lili Dong / Jingjing Pang / Miao Xu / Qian Zhong / Mu-Sheng Zeng / Xuekui Yu /
Abstract: Epstein-Barr virus (EBV) is the primary cause of infectious mononucleosis and has been shown to be closely associated with various malignancies. Here, we present a complete atomic model of EBV, ...Epstein-Barr virus (EBV) is the primary cause of infectious mononucleosis and has been shown to be closely associated with various malignancies. Here, we present a complete atomic model of EBV, including the icosahedral capsid, the dodecameric portal and the capsid-associated tegument complex (CATC). Our in situ portal from the tegumented capsid adopts a closed conformation with its channel valve holding the terminal viral DNA and with its crown region firmly engaged by three layers of ring-like dsDNA, which, together with the penton flexibility, effectively alleviates the capsid inner pressure placed on the portal cap. In contrast, the CATCs, through binding to the flexible penton vertices in a stoichiometric manner, accurately increase the inner capsid pressure to facilitate the pressure-driven genome delivery. Together, our results provide important insights into the mechanism by which the EBV capsid, portal, packaged genome and the CATCs coordinately achieve a pressure balance to simultaneously benefit both viral genome retention and ejection.
History
DepositionMar 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-30162
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-30162
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
m: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
l: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
P: Small capsomere-interacting protein
M: Major capsid protein
Q: Small capsomere-interacting protein
N: Major capsid protein
R: Small capsomere-interacting protein
O: Major capsid protein
0: Small capsomere-interacting protein
U: Major capsid protein
1: Small capsomere-interacting protein
V: Major capsid protein
X: Small capsomere-interacting protein
k: Major capsid protein
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
G: Small capsomere-interacting protein
A: Major capsid protein
H: Small capsomere-interacting protein
B: Major capsid protein
I: Small capsomere-interacting protein
C: Major capsid protein
J: Small capsomere-interacting protein
D: Major capsid protein
K: Small capsomere-interacting protein
E: Major capsid protein
L: Small capsomere-interacting protein
F: Major capsid protein
x: Major capsid protein
y: Small capsomere-interacting protein
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2
a: Triplex capsid protein 1
8: Triplex capsid protein 2
9: Triplex capsid protein 2


Theoretical massNumber of molelcules
Total (without water)3,288,79347
Polymers3,288,79347
Non-polymers00
Water0
1
m: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
l: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
P: Small capsomere-interacting protein
M: Major capsid protein
Q: Small capsomere-interacting protein
N: Major capsid protein
R: Small capsomere-interacting protein
O: Major capsid protein
0: Small capsomere-interacting protein
U: Major capsid protein
1: Small capsomere-interacting protein
V: Major capsid protein
X: Small capsomere-interacting protein
k: Major capsid protein
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
G: Small capsomere-interacting protein
A: Major capsid protein
H: Small capsomere-interacting protein
B: Major capsid protein
I: Small capsomere-interacting protein
C: Major capsid protein
J: Small capsomere-interacting protein
D: Major capsid protein
K: Small capsomere-interacting protein
E: Major capsid protein
L: Small capsomere-interacting protein
F: Major capsid protein
x: Major capsid protein
y: Small capsomere-interacting protein
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2
a: Triplex capsid protein 1
8: Triplex capsid protein 2
9: Triplex capsid protein 2
x 60


Theoretical massNumber of molelcules
Total (without water)197,327,5762820
Polymers197,327,5762820
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area370050 Å2
ΔGint-1904 kcal/mol
Surface area903640 Å2
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
m: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
l: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
P: Small capsomere-interacting protein
M: Major capsid protein
Q: Small capsomere-interacting protein
N: Major capsid protein
R: Small capsomere-interacting protein
O: Major capsid protein
0: Small capsomere-interacting protein
U: Major capsid protein
1: Small capsomere-interacting protein
V: Major capsid protein
X: Small capsomere-interacting protein
k: Major capsid protein
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
G: Small capsomere-interacting protein
A: Major capsid protein
H: Small capsomere-interacting protein
B: Major capsid protein
I: Small capsomere-interacting protein
C: Major capsid protein
J: Small capsomere-interacting protein
D: Major capsid protein
K: Small capsomere-interacting protein
E: Major capsid protein
L: Small capsomere-interacting protein
F: Major capsid protein
x: Major capsid protein
y: Small capsomere-interacting protein
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2
a: Triplex capsid protein 1
8: Triplex capsid protein 2
9: Triplex capsid protein 2
x 5


  • icosahedral pentamer
  • 16.4 MDa, 235 polymers
Theoretical massNumber of molelcules
Total (without water)16,443,965235
Polymers16,443,965235
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
m: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
l: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
P: Small capsomere-interacting protein
M: Major capsid protein
Q: Small capsomere-interacting protein
N: Major capsid protein
R: Small capsomere-interacting protein
O: Major capsid protein
0: Small capsomere-interacting protein
U: Major capsid protein
1: Small capsomere-interacting protein
V: Major capsid protein
X: Small capsomere-interacting protein
k: Major capsid protein
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
G: Small capsomere-interacting protein
A: Major capsid protein
H: Small capsomere-interacting protein
B: Major capsid protein
I: Small capsomere-interacting protein
C: Major capsid protein
J: Small capsomere-interacting protein
D: Major capsid protein
K: Small capsomere-interacting protein
E: Major capsid protein
L: Small capsomere-interacting protein
F: Major capsid protein
x: Major capsid protein
y: Small capsomere-interacting protein
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2
a: Triplex capsid protein 1
8: Triplex capsid protein 2
9: Triplex capsid protein 2
x 6


  • icosahedral 23 hexamer
  • 19.7 MDa, 282 polymers
Theoretical massNumber of molelcules
Total (without water)19,732,758282
Polymers19,732,758282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Small capsomere-interacting protein


Mass: 18169.100 Da / Num. of mol.: 16 / 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
#2: Protein
Major capsid protein / MCP


Mass: 154086.828 Da / Num. of mol.: 16 / 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
#3: Protein
Triplex capsid protein 1


Mass: 39231.539 Da / Num. of mol.: 5 / 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
#4: Protein
Triplex capsid protein 2


Mass: 33654.039 Da / Num. of mol.: 10 / 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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Human gammaherpesvirus 4Epstein–Barr virus / Type: VIRUS / Source: NATURAL
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2RELION3image acquisition
4RELION3CTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32721 / Symmetry type: POINT

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