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- PDB-5zz8: Structure of the Herpes simplex virus type 2 C-capsid with capsid... -

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Basic information

Entry
Database: PDB / ID: 5zz8
TitleStructure of the Herpes simplex virus type 2 C-capsid with capsid-vertex-specific component
Components
  • Major capsid protein
  • UL17
  • UL25
  • UL36
  • VP19C
  • VP23
  • VP26
KeywordsSTRUCTURAL PROTEIN / Herpes simplex virus 2 / capsid / capsid-vertex-specific component
Function / homology
Function and homology information


chromosome organization => GO:0051276 / T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / viral release from host cell / viral process / viral penetration into host nucleus ...chromosome organization => GO:0051276 / T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / viral release from host cell / viral process / viral penetration into host nucleus / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont entry into host cell / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein ...Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus UL25 / Herpesvirus UL25 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 / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Major capsid protein / Large tegument protein deneddylase / Capsid vertex component 2 / Capsid vertex component 1 / Capsid triplex subunit 1 / Triplex capsid protein 2 / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman herpesvirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsWang, J.L. / Yuan, S. / Zhu, D.J. / Tang, H. / Wang, N. / Chen, W.Y. / Gao, Q. / Li, Y.H. / Wang, J.Z. / Liu, H.R. ...Wang, J.L. / Yuan, S. / Zhu, D.J. / Tang, H. / Wang, N. / Chen, W.Y. / Gao, Q. / Li, Y.H. / Wang, J.Z. / Liu, H.R. / Zhang, X.Z. / Rao, Z.H. / Wang, X.X.
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the herpes simplex virus type 2 C-capsid with capsid-vertex-specific component.
Authors: Jialing Wang / Shuai Yuan / Dongjie Zhu / Hao Tang / Nan Wang / Wenyuan Chen / Qiang Gao / Yuhua Li / Junzhi Wang / Hongrong Liu / Xinzheng Zhang / Zihe Rao / Xiangxi Wang /
Abstract: Herpes simplex viruses (HSVs) cause human oral and genital ulcer diseases. Patients with HSV-2 have a higher risk of acquiring a human immunodeficiency virus infection. HSV-2 is a member of the α- ...Herpes simplex viruses (HSVs) cause human oral and genital ulcer diseases. Patients with HSV-2 have a higher risk of acquiring a human immunodeficiency virus infection. HSV-2 is a member of the α-herpesvirinae subfamily that together with the β- and γ-herpesvirinae subfamilies forms the Herpesviridae family. Here, we report the cryo-electron microscopy structure of the HSV-2 C-capsid with capsid-vertex-specific component (CVSC) that was determined at 3.75 Å using a block-based reconstruction strategy. We present atomic models of multiple conformers for the capsid proteins (VP5, VP23, VP19C, and VP26) and CVSC. Comparison of the HSV-2 homologs yields information about structural similarities and differences between the three herpesviruses sub-families and we identify α-herpesvirus-specific structural features. The hetero-pentameric CVSC, consisting of a UL17 monomer, a UL25 dimer and a UL36 dimer, is bound tightly by a five-helix bundle that forms extensive networks of subunit contacts with surrounding capsid proteins, which reinforce capsid stability.
History
DepositionMay 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: atom_sites / cell ...atom_sites / cell / entity / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _entity.formula_weight

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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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  • Superimposition on EM map
  • EMDB-6976
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Structure viewerMolecule:
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Assembly

Deposited unit
Q: VP19C
R: VP23
S: VP23
T: VP19C
U: VP23
V: VP23
W: VP19C
X: VP23
Y: VP23
1: VP19C
3: VP23
2: VP23
w: VP19C
x: VP23
y: VP23
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
A: Major capsid protein
H: Major capsid protein
h: VP26
i: VP26
j: VP26
k: VP26
l: VP26
m: VP26
n: VP26
o: VP26
p: VP26
N: Major capsid protein
O: Major capsid protein
P: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
q: UL17
E: Major capsid protein
r: UL25
F: Major capsid protein
s: UL25
G: Major capsid protein
t: UL36
b: VP26
c: VP26
d: VP26
e: VP26
f: VP26
g: VP26
u: UL36


Theoretical massNumber of molelcules
Total (without water)4,032,16451
Polymers4,032,16451
Non-polymers00
Water0
1
Q: VP19C
R: VP23
S: VP23
T: VP19C
U: VP23
V: VP23
W: VP19C
X: VP23
Y: VP23
1: VP19C
3: VP23
2: VP23
w: VP19C
x: VP23
y: VP23
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
A: Major capsid protein
H: Major capsid protein
h: VP26
i: VP26
j: VP26
k: VP26
l: VP26
m: VP26
n: VP26
o: VP26
p: VP26
N: Major capsid protein
O: Major capsid protein
P: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
q: UL17
E: Major capsid protein
r: UL25
F: Major capsid protein
s: UL25
G: Major capsid protein
t: UL36
b: VP26
c: VP26
d: VP26
e: VP26
f: VP26
g: VP26
u: UL36
x 60


  • complete icosahedral assembly
  • Evidence: microscopy
  • 242 MDa, 3060 polymers
Theoretical massNumber of molelcules
Total (without water)241,929,8693060
Polymers241,929,8693060
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
Q: VP19C
R: VP23
S: VP23
T: VP19C
U: VP23
V: VP23
W: VP19C
X: VP23
Y: VP23
1: VP19C
3: VP23
2: VP23
w: VP19C
x: VP23
y: VP23
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
A: Major capsid protein
H: Major capsid protein
h: VP26
i: VP26
j: VP26
k: VP26
l: VP26
m: VP26
n: VP26
o: VP26
p: VP26
N: Major capsid protein
O: Major capsid protein
P: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
q: UL17
E: Major capsid protein
r: UL25
F: Major capsid protein
s: UL25
G: Major capsid protein
t: UL36
b: VP26
c: VP26
d: VP26
e: VP26
f: VP26
g: VP26
u: UL36
x 5


  • icosahedral pentamer
  • 20.2 MDa, 255 polymers
Theoretical massNumber of molelcules
Total (without water)20,160,822255
Polymers20,160,822255
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
Q: VP19C
R: VP23
S: VP23
T: VP19C
U: VP23
V: VP23
W: VP19C
X: VP23
Y: VP23
1: VP19C
3: VP23
2: VP23
w: VP19C
x: VP23
y: VP23
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
A: Major capsid protein
H: Major capsid protein
h: VP26
i: VP26
j: VP26
k: VP26
l: VP26
m: VP26
n: VP26
o: VP26
p: VP26
N: Major capsid protein
O: Major capsid protein
P: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
q: UL17
E: Major capsid protein
r: UL25
F: Major capsid protein
s: UL25
G: Major capsid protein
t: UL36
b: VP26
c: VP26
d: VP26
e: VP26
f: VP26
g: VP26
u: UL36
x 6


  • icosahedral 23 hexamer
  • 24.2 MDa, 306 polymers
Theoretical massNumber of molelcules
Total (without water)24,192,987306
Polymers24,192,987306
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

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Protein , 7 types, 51 molecules QTW1wRSUVXY32xyIJKLMAHNOPBCDEF...

#1: Protein
VP19C


Mass: 50566.648 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 2 / Gene: UL38, TRX1 / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: G9I260
#2: Protein
VP23


Mass: 34373.785 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 2 / Gene: TRX2, UL18 / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: P89441
#3: Protein
Major capsid protein / VP5 / MCP


Mass: 149384.375 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 2 / Gene: UL19, MCP / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: A0A0E3U2U0
#4: Protein
VP26


Mass: 12147.707 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 2 / Gene: SCP, UL35 / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: P89458
#5: Protein UL17


Mass: 74747.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 2 / Gene: UL17, CVC1 / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: G9I238
#6: Protein UL25


Mass: 63623.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 2 / Gene: UL25, CVC2 / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: D6PUY5
#7: Protein UL36


Mass: 330616.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 2 / Gene: UL36 / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: A0A1U9ZLV0

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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 2Herpesviridae / Type: VIRUS / Entity ID: all
Source (natural)Organism: Human herpesvirus 2
Source (recombinant)Organism: Chlorocebus sabaeus (green monkey)
Details of virusEnveloped: NO / 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: OTHER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56901 / Symmetry type: POINT

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