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- PDB-6lgn: The atomic structure of varicella zoster virus C-capsid -

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Basic information

Entry
Database: PDB / ID: 6lgn
TitleThe atomic structure of varicella zoster virus C-capsid
Components
  • Major capsid protein
  • Small capsomere-interacting protein
  • Triplex capsid protein 1
  • Triplex capsid protein 2
KeywordsVIRUS / Herpesvirus / Varicella zoster virus / C-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: 5.3 Å
AuthorsLi, S. / Zheng, Q.
CitationJournal: Nat Microbiol / Year: 2020
Title: Near-atomic cryo-electron microscopy structures of varicella-zoster virus capsids.
Authors: Wei Wang / Qingbing Zheng / Dequan Pan / Hai Yu / Wenkun Fu / Jian Liu / Maozhou He / Rui Zhu / Yuze Cai / Yang Huang / Zhenghui Zha / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Yuqiong Que ...Authors: Wei Wang / Qingbing Zheng / Dequan Pan / Hai Yu / Wenkun Fu / Jian Liu / Maozhou He / Rui Zhu / Yuze Cai / Yang Huang / Zhenghui Zha / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Yuqiong Que / Ting Wu / Jun Zhang / Shaowei Li / Hua Zhu / Z Hong Zhou / Tong Cheng / Ningshao Xia /
Abstract: Varicella-zoster virus (VZV) is a medically important human herpesvirus that causes chickenpox and shingles, but its cell-associated nature has hindered structure studies. Here we report the cryo- ...Varicella-zoster virus (VZV) is a medically important human herpesvirus that causes chickenpox and shingles, but its cell-associated nature has hindered structure studies. Here we report the cryo-electron microscopy structures of purified VZV A-capsid and C-capsid, as well as of the DNA-containing capsid inside the virion. Atomic models derived from these structures show that, despite enclosing a genome that is substantially smaller than those of other human herpesviruses, VZV has a similarly sized capsid, consisting of 955 major capsid protein (MCP), 900 small capsid protein (SCP), 640 triplex dimer (Tri2) and 320 triplex monomer (Tri1) subunits. The VZV capsid has high thermal stability, although with relatively fewer intra- and inter-capsid protein interactions and less stably associated tegument proteins compared with other human herpesviruses. Analysis with antibodies targeting the N and C termini of the VZV SCP indicates that the hexon-capping SCP-the largest among human herpesviruses-uses its N-terminal half to bridge hexon MCP subunits and possesses a C-terminal flexible half emanating from the inner rim of the upper hexon channel into the tegument layer. Correlation of these structural features and functional observations provide insights into VZV assembly and pathogenesis and should help efforts to engineer gene delivery and anticancer vectors based on the currently available VZV vaccine.
History
DepositionDec 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Movie
  • 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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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

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


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


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


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 1


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
#4: Protein
Triplex capsid protein 2


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

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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: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2838 / Symmetry type: POINT

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