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- PDB-7bw6: Varicella-zoster virus capsid -

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Basic information

Entry
Database: PDB / ID: 7bw6
TitleVaricella-zoster virus capsid
Components
  • Major capsid protein
  • Small capsomere-interacting protein
  • Triplex capsid protein 1
  • Triplex capsid protein 2
KeywordsVIRUS / A-capsid
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
Herpesvirus UL35 / Herpesvirus UL35 family / 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
Capsid protein / Major capsid protein / Small capsomere-interacting protein / Capsid protein
Similarity search - Component
Biological speciesHuman herpesvirus 3 (Varicella-zoster virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang, P.Y. / Qi, J.X. / Liu, C.C. / Sun, J.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81673358 China
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structure of the varicella-zoster virus A-capsid.
Authors: Junqing Sun / Congcong Liu / Ruchao Peng / Fu-Kun Zhang / Zhou Tong / Sheng Liu / Yi Shi / Zhennan Zhao / Wen-Bo Zeng / George Fu Gao / Hong-Jie Shen / Xiaoming Yang / Minhua Luo / Jianxun Qi / Peiyi Wang /
Abstract: Varicella-zoster virus (VZV), a member of the Alphaherpesvirinae subfamily, causes severe diseases in humans of all ages. The viral capsids play critical roles in herpesvirus infection, making them ...Varicella-zoster virus (VZV), a member of the Alphaherpesvirinae subfamily, causes severe diseases in humans of all ages. The viral capsids play critical roles in herpesvirus infection, making them potential antiviral targets. Here, we present the 3.7-Å-resolution structure of the VZV A-capsid and define the molecular determinants underpinning the assembly of this complicated viral machinery. Overall, the VZV capsid has a similar architecture to that of other known herpesviruses. The major capsid protein (MCP) assembles into pentons and hexons, forming extensive intra- and inter-capsomer interaction networks that are further secured by the small capsid protein (SCP) and the heterotriplex. The structure reveals a pocket beneath the floor of MCP that could potentially be targeted by antiviral inhibitors. In addition, we identified two alphaherpesvirus-specific structural features in SCP and Tri1 proteins. These observations highlight the divergence of different herpesviruses and provide an important basis for developing antiviral drugs.
History
DepositionApr 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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
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  • Simplified surface model + fitted atomic model
  • EMDB-30228
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  • Superimposition on EM map
  • EMDB-30228
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,463,28846
Polymers3,463,28846
Non-polymers00
Water0
1
A: Major capsid protein
B: Major capsid protein
C: Small capsomere-interacting protein
D: Major capsid protein
E: Small capsomere-interacting protein
F: Major capsid protein
G: Small capsomere-interacting protein
H: Major capsid protein
I: Small capsomere-interacting protein
J: Major capsid protein
K: Small capsomere-interacting protein
L: Major capsid protein
M: Small capsomere-interacting protein
N: Major capsid protein
O: Small capsomere-interacting protein
P: Major capsid protein
Q: Small capsomere-interacting protein
R: Major capsid protein
S: Small capsomere-interacting protein
T: Major capsid protein
U: Small capsomere-interacting protein
V: Major capsid protein
W: Small capsomere-interacting protein
X: Major capsid protein
Y: Small capsomere-interacting protein
a: Major capsid protein
b: Small capsomere-interacting protein
c: Major capsid protein
d: Small capsomere-interacting protein
e: Major capsid protein
f: Small capsomere-interacting protein
g: Triplex capsid protein 2
h: Triplex capsid protein 2
i: Triplex capsid protein 1
j: Triplex capsid protein 2
k: Triplex capsid protein 2
l: Triplex capsid protein 1
m: Triplex capsid protein 2
n: Triplex capsid protein 2
o: Triplex capsid protein 1
p: Triplex capsid protein 2
q: Triplex capsid protein 2
r: Triplex capsid protein 1
s: Triplex capsid protein 2
t: Triplex capsid protein 2
w: Triplex capsid protein 1
x 60


Theoretical massNumber of molelcules
Total (without water)207,797,2542760
Polymers207,797,2542760
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


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


  • icosahedral pentamer
  • 17.3 MDa, 230 polymers
Theoretical massNumber of molelcules
Total (without water)17,316,438230
Polymers17,316,438230
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Major capsid protein
B: Major capsid protein
C: Small capsomere-interacting protein
D: Major capsid protein
E: Small capsomere-interacting protein
F: Major capsid protein
G: Small capsomere-interacting protein
H: Major capsid protein
I: Small capsomere-interacting protein
J: Major capsid protein
K: Small capsomere-interacting protein
L: Major capsid protein
M: Small capsomere-interacting protein
N: Major capsid protein
O: Small capsomere-interacting protein
P: Major capsid protein
Q: Small capsomere-interacting protein
R: Major capsid protein
S: Small capsomere-interacting protein
T: Major capsid protein
U: Small capsomere-interacting protein
V: Major capsid protein
W: Small capsomere-interacting protein
X: Major capsid protein
Y: Small capsomere-interacting protein
a: Major capsid protein
b: Small capsomere-interacting protein
c: Major capsid protein
d: Small capsomere-interacting protein
e: Major capsid protein
f: Small capsomere-interacting protein
g: Triplex capsid protein 2
h: Triplex capsid protein 2
i: Triplex capsid protein 1
j: Triplex capsid protein 2
k: Triplex capsid protein 2
l: Triplex capsid protein 1
m: Triplex capsid protein 2
n: Triplex capsid protein 2
o: Triplex capsid protein 1
p: Triplex capsid protein 2
q: Triplex capsid protein 2
r: Triplex capsid protein 1
s: Triplex capsid protein 2
t: Triplex capsid protein 2
w: Triplex capsid protein 1
x 6


  • icosahedral 23 hexamer
  • 20.8 MDa, 276 polymers
Theoretical massNumber of molelcules
Total (without water)20,779,725276
Polymers20,779,725276
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
Major capsid protein / MCP / VP5


Mass: 155145.359 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 3 (Varicella-zoster virus)
References: UniProt: Q6QCL5
#2: Protein
Small capsomere-interacting protein / VP26


Mass: 24440.119 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 3 (Varicella-zoster virus)
References: UniProt: Q6QCN2
#3: Protein
Triplex capsid protein 2 / VP23


Mass: 34421.914 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 3 (Varicella-zoster virus)
References: UniProt: Q6QCL4
#4: Protein
Triplex capsid protein 1 / VP19c


Mass: 54028.180 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 3 (Varicella-zoster virus)
References: UniProt: Q6QCN5

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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 alphaherpesvirus 3Varicella zoster virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 2 seconds before plunging

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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: 59000 X / Calibrated magnification: 59000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 386.3 nm / Calibrated defocus max: 5116 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 93 K / Temperature (min): 81 K
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 26979
Image scansWidth: 4096 / Height: 4096

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.16_3549refinement
PHENIX1.16_3549refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4CTFFIND4.1CTF correctionminimum defocus 0.5um,maximnum defocous 5um
7UCSF Chimera1.13.1model fitting
9PHENIX1.17model refinementrealspace refinement and validation
10Coot0.8.9.2model refinementmodel validation
11RELION3.0.8initial Euler assignment
12RELION3.0.8final Euler assignment
13RELION3.0.8classificationlocal angular search range 3,sampling interval:0.5degree, +-4 pixel offset search.
14RELION3.0.83D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 94640
Details: Images were low-pass to 15 angstrom to facilitated particle picking.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 311236 / Num. of class averages: 5 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-IDPdb chain residue range
15ZZ8

5zz8

1174-482
25ZZ8

5zz8

218-316
35ZZ8

5zz8

A119-1393
45ZZ8

5zz8

b18-107
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 101.55 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0031213696
ELECTRON MICROSCOPYf_angle_d0.5756291528
ELECTRON MICROSCOPYf_chiral_restr0.041333619
ELECTRON MICROSCOPYf_plane_restr0.003338095
ELECTRON MICROSCOPYf_dihedral_angle_d15.9956127825

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