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- PDB-5zap: Atomic structure of the herpes simplex virus type 2 B-capsid -

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Basic information

Entry
Database: PDB / ID: 5zap
TitleAtomic structure of the herpes simplex virus type 2 B-capsid
Components
  • Major capsid protein
  • Small capsomere-interacting protein
  • Triplex capsid protein 1
  • Triplex capsid protein 2
KeywordsVIRUS / herpesvirus / capsid / cryo-em / atomic structure
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral capsid assembly / viral process / virion component / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Herpesvirus UL35 / Herpesvirus UL35 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
Similarity search - Domain/homology
Capsid triplex subunit 1 / Capsid triplex subunit 2 / Major capsid protein / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman herpesvirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYuan, S. / Wang, J.L. / Zhu, D.J. / Wang, N. / Gao, Q. / Chen, W.Y. / Tang, H. / Wang, J.Z. / Zhang, X.Z. / Liu, H.R. ...Yuan, S. / Wang, J.L. / Zhu, D.J. / Wang, N. / Gao, Q. / Chen, W.Y. / Tang, H. / Wang, J.Z. / Zhang, X.Z. / Liu, H.R. / Rao, Z.H. / Wang, X.X.
Citation
Journal: Science / Year: 2018
Title: Cryo-EM structure of a herpesvirus capsid at 3.1 Å.
Authors: Shuai Yuan / Jialing Wang / Dongjie Zhu / Nan Wang / Qiang Gao / Wenyuan Chen / Hao Tang / Junzhi Wang / Xinzheng Zhang / Hongrong Liu / Zihe Rao / Xiangxi Wang /
Abstract: Structurally and genetically, human herpesviruses are among the largest and most complex of viruses. Using cryo-electron microscopy (cryo-EM) with an optimized image reconstruction strategy, we ...Structurally and genetically, human herpesviruses are among the largest and most complex of viruses. Using cryo-electron microscopy (cryo-EM) with an optimized image reconstruction strategy, we report the herpes simplex virus type 2 (HSV-2) capsid structure at 3.1 angstroms, which is built up of about 3000 proteins organized into three types of hexons (central, peripentonal, and edge), pentons, and triplexes. Both hexons and pentons contain the major capsid protein, VP5; hexons also contain a small capsid protein, VP26; and triplexes comprise VP23 and VP19C. Acting as core organizers, VP5 proteins form extensive intermolecular networks, involving multiple disulfide bonds (about 1500 in total) and noncovalent interactions, with VP26 proteins and triplexes that underpin capsid stability and assembly. Conformational adaptations of these proteins induced by their microenvironments lead to 46 different conformers that assemble into a massive quasisymmetric shell, exemplifying the structural and functional complexity of HSV.
#1: Journal: Nat Commun / Year: 2018
Title: Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions.
Authors: Dongjie Zhu / Xiangxi Wang / Qianglin Fang / James L Van Etten / Michael G Rossmann / Zihe Rao / Xinzheng Zhang /
Abstract: The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a ...The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a reconstruction. Here we estimate the attainable resolution and report a "block-based" reconstruction method for extending the resolution limit. We find the Ewald sphere effect limits the resolution of large objects, especially large viruses. After processing two real datasets of large viruses, we show that our procedure can extend the resolution for both datasets and can accommodate the flexibility associated with large protein complexes.
History
DepositionFeb 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Sep 5, 2018Group: Data collection / Structure summary / Category: audit_author
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _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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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,168,59246
Polymers3,168,59246
Non-polymers00
Water00
1
G: Major capsid protein
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: 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: Triplex capsid protein 2
R: Triplex capsid protein 2
S: Triplex capsid protein 1
T: Triplex capsid protein 2
U: Triplex capsid protein 2
V: Triplex capsid protein 1
W: Triplex capsid protein 2
X: Triplex capsid protein 2
Y: Triplex capsid protein 1
Z: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
e: Triplex capsid protein 1
f: Small capsomere-interacting protein
g: Small capsomere-interacting protein
h: Small capsomere-interacting protein
i: Small capsomere-interacting protein
j: Small capsomere-interacting protein
k: Small capsomere-interacting protein
l: Small capsomere-interacting protein
m: Small capsomere-interacting protein
n: Small capsomere-interacting protein
o: Small capsomere-interacting protein
p: Small capsomere-interacting protein
q: Small capsomere-interacting protein
r: Small capsomere-interacting protein
s: Small capsomere-interacting protein
t: Small capsomere-interacting protein
x 60


Theoretical massNumber of molelcules
Total (without water)190,115,5372760
Polymers190,115,5372760
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
G: Major capsid protein
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: 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: Triplex capsid protein 2
R: Triplex capsid protein 2
S: Triplex capsid protein 1
T: Triplex capsid protein 2
U: Triplex capsid protein 2
V: Triplex capsid protein 1
W: Triplex capsid protein 2
X: Triplex capsid protein 2
Y: Triplex capsid protein 1
Z: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
e: Triplex capsid protein 1
f: Small capsomere-interacting protein
g: Small capsomere-interacting protein
h: Small capsomere-interacting protein
i: Small capsomere-interacting protein
j: Small capsomere-interacting protein
k: Small capsomere-interacting protein
l: Small capsomere-interacting protein
m: Small capsomere-interacting protein
n: Small capsomere-interacting protein
o: Small capsomere-interacting protein
p: Small capsomere-interacting protein
q: Small capsomere-interacting protein
r: Small capsomere-interacting protein
s: Small capsomere-interacting protein
t: Small capsomere-interacting protein
x 5


  • icosahedral pentamer
  • 15.8 MDa, 230 polymers
Theoretical massNumber of molelcules
Total (without water)15,842,961230
Polymers15,842,961230
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
G: Major capsid protein
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: 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: Triplex capsid protein 2
R: Triplex capsid protein 2
S: Triplex capsid protein 1
T: Triplex capsid protein 2
U: Triplex capsid protein 2
V: Triplex capsid protein 1
W: Triplex capsid protein 2
X: Triplex capsid protein 2
Y: Triplex capsid protein 1
Z: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
e: Triplex capsid protein 1
f: Small capsomere-interacting protein
g: Small capsomere-interacting protein
h: Small capsomere-interacting protein
i: Small capsomere-interacting protein
j: Small capsomere-interacting protein
k: Small capsomere-interacting protein
l: Small capsomere-interacting protein
m: Small capsomere-interacting protein
n: Small capsomere-interacting protein
o: Small capsomere-interacting protein
p: Small capsomere-interacting protein
q: Small capsomere-interacting protein
r: Small capsomere-interacting protein
s: Small capsomere-interacting protein
t: Small capsomere-interacting protein
x 6


  • icosahedral 23 hexamer
  • 19 MDa, 276 polymers
Theoretical massNumber of molelcules
Total (without water)19,011,554276
Polymers19,011,554276
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: 149370.359 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I240
#2: Protein
Triplex capsid protein 2


Mass: 34373.785 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I239
#3: Protein
Triplex capsid protein 1


Mass: 50542.617 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: A0A1U9ZFW1
#4: Protein
Small capsomere-interacting protein


Mass: 12147.707 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I257
Has protein modificationY

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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 2 / Type: VIRUS / Entity ID: #1, #4, #2-#3 / Source: NATURAL
Source (natural)Organism: Human herpesvirus 2
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Human herpesvirus 2
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 FIELD
Image recordingElectron dose: 1.1 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45000 / Symmetry type: POINT

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