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- PDB-6w19: Structures of Capsid and Capsid-Associated Tegument Complex insid... -

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Basic information

Entry
Database: PDB / ID: 6w19
TitleStructures of Capsid and Capsid-Associated Tegument Complex inside the Epstein-Barr Virus
Components
  • Major capsid protein
  • Small capsomere-interacting protein
  • Triplex capsid protein 1
  • Triplex capsid protein 2
KeywordsVIRUS / gamma-herpesvirus / EBV / CATC / Structural plasticity
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: 5.5 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 3, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Major capsid protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
T: Small capsomere-interacting protein
U: Small capsomere-interacting protein
V: Small capsomere-interacting protein
W: Small capsomere-interacting protein
X: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
a: Small capsomere-interacting protein
b: Small capsomere-interacting protein
c: Small capsomere-interacting protein
d: Small capsomere-interacting protein
e: Small capsomere-interacting protein
u: Small capsomere-interacting protein
f: Triplex capsid protein 1
g: Triplex capsid protein 1
h: Triplex capsid protein 1
i: Triplex capsid protein 1
j: Triplex capsid protein 1
1: Triplex capsid protein 1
k: Triplex capsid protein 2
l: Triplex capsid protein 2
m: Triplex capsid protein 2
n: Triplex capsid protein 2
o: Triplex capsid protein 2
2: Triplex capsid protein 2
p: Triplex capsid protein 2
q: Triplex capsid protein 2
r: Triplex capsid protein 2
s: Triplex capsid protein 2
t: Triplex capsid protein 2
3: Triplex capsid protein 2


Theoretical massNumber of molelcules
Total (without water)3,395,33350
Polymers3,395,33350
Non-polymers00
Water0
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Major capsid protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
T: Small capsomere-interacting protein
U: Small capsomere-interacting protein
V: Small capsomere-interacting protein
W: Small capsomere-interacting protein
X: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
a: Small capsomere-interacting protein
b: Small capsomere-interacting protein
c: Small capsomere-interacting protein
d: Small capsomere-interacting protein
e: Small capsomere-interacting protein
u: Small capsomere-interacting protein
f: Triplex capsid protein 1
g: Triplex capsid protein 1
h: Triplex capsid protein 1
i: Triplex capsid protein 1
j: Triplex capsid protein 1
1: Triplex capsid protein 1
k: Triplex capsid protein 2
l: Triplex capsid protein 2
m: Triplex capsid protein 2
n: Triplex capsid protein 2
o: Triplex capsid protein 2
2: Triplex capsid protein 2
p: Triplex capsid protein 2
q: Triplex capsid protein 2
r: Triplex capsid protein 2
s: Triplex capsid protein 2
t: Triplex capsid protein 2
3: Triplex capsid protein 2
x 60


Theoretical massNumber of molelcules
Total (without water)203,719,9533000
Polymers203,719,9533000
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Major capsid protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
T: Small capsomere-interacting protein
U: Small capsomere-interacting protein
V: Small capsomere-interacting protein
W: Small capsomere-interacting protein
X: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
a: Small capsomere-interacting protein
b: Small capsomere-interacting protein
c: Small capsomere-interacting protein
d: Small capsomere-interacting protein
e: Small capsomere-interacting protein
u: Small capsomere-interacting protein
f: Triplex capsid protein 1
g: Triplex capsid protein 1
h: Triplex capsid protein 1
i: Triplex capsid protein 1
j: Triplex capsid protein 1
1: Triplex capsid protein 1
k: Triplex capsid protein 2
l: Triplex capsid protein 2
m: Triplex capsid protein 2
n: Triplex capsid protein 2
o: Triplex capsid protein 2
2: Triplex capsid protein 2
p: Triplex capsid protein 2
q: Triplex capsid protein 2
r: Triplex capsid protein 2
s: Triplex capsid protein 2
t: Triplex capsid protein 2
3: Triplex capsid protein 2
x 5


  • icosahedral pentamer
  • 17 MDa, 250 polymers
Theoretical massNumber of molelcules
Total (without water)16,976,663250
Polymers16,976,663250
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Major capsid protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
T: Small capsomere-interacting protein
U: Small capsomere-interacting protein
V: Small capsomere-interacting protein
W: Small capsomere-interacting protein
X: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
a: Small capsomere-interacting protein
b: Small capsomere-interacting protein
c: Small capsomere-interacting protein
d: Small capsomere-interacting protein
e: Small capsomere-interacting protein
u: Small capsomere-interacting protein
f: Triplex capsid protein 1
g: Triplex capsid protein 1
h: Triplex capsid protein 1
i: Triplex capsid protein 1
j: Triplex capsid protein 1
1: Triplex capsid protein 1
k: Triplex capsid protein 2
l: Triplex capsid protein 2
m: Triplex capsid protein 2
n: Triplex capsid protein 2
o: Triplex capsid protein 2
2: Triplex capsid protein 2
p: Triplex capsid protein 2
q: Triplex capsid protein 2
r: Triplex capsid protein 2
s: Triplex capsid protein 2
t: Triplex capsid protein 2
3: Triplex capsid protein 2
x 6


  • icosahedral 23 hexamer
  • 20.4 MDa, 300 polymers
Theoretical massNumber of molelcules
Total (without water)20,371,995300
Polymers20,371,995300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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
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
#2: 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
#3: Protein
Triplex capsid protein 1


Mass: 39231.539 Da / Num. of mol.: 6 / 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.: 12 / 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 herpesvirus 4 strain B95-8 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
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 / Details: PBS buffer, pH 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: The grids were manually plunged into the 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 4000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 28 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1833

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Processing

EM softwareName: CTFFIND / Category: CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2801
3D reconstructionResolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2048 / Symmetry type: POINT

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