[English] 日本語
Yorodumi
- PDB-7fj1: Cryo-EM structure of pseudorabies virus C-capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fj1
TitleCryo-EM structure of pseudorabies virus C-capsid
Components
  • (Triplex capsid protein ...) x 2
  • Capsid vertex component 1
  • DNA packaging tegument protein UL25
  • Major capsid protein
  • Small capsomere-interacting protein
  • VP1/2
KeywordsVIRUS / Pseudorabies virus / C-capsid / Cryo-EM
Function / homology
Function and homology information


viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / viral DNA genome replication / viral process / chromosome organization / cysteine-type peptidase activity / viral penetration into host nucleus ...viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / viral DNA genome replication / viral process / chromosome organization / cysteine-type peptidase activity / viral penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis / DNA binding / membrane
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus UL25 ...Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus UL25 / Herpesvirus UL25 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 / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Small capsomere-interacting protein / Major capsid protein / Capsid triplex subunit 2 / UL17 protein / VP1/2 / UL25 / Capsid triplex subunit 1
Similarity search - Component
Biological speciesSuid alphaherpesvirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.43 Å
AuthorsZheng, Q. / Li, S. / Zha, Z. / Sun, H.
CitationJournal: Nat Commun / Year: 2022
Title: Structures of pseudorabies virus capsids.
Authors: Guosong Wang / Zhenghui Zha / Pengfei Huang / Hui Sun / Yang Huang / Maozhou He / Tian Chen / Lina Lin / Zhenqin Chen / Zhibo Kong / Yuqiong Que / Tingting Li / Ying Gu / Hai Yu / Jun Zhang ...Authors: Guosong Wang / Zhenghui Zha / Pengfei Huang / Hui Sun / Yang Huang / Maozhou He / Tian Chen / Lina Lin / Zhenqin Chen / Zhibo Kong / Yuqiong Que / Tingting Li / Ying Gu / Hai Yu / Jun Zhang / Qingbing Zheng / Yixin Chen / Shaowei Li / Ningshao Xia /
Abstract: Pseudorabies virus (PRV) is a major etiological agent of swine infectious diseases and is responsible for significant economic losses in the swine industry. Recent data points to human viral ...Pseudorabies virus (PRV) is a major etiological agent of swine infectious diseases and is responsible for significant economic losses in the swine industry. Recent data points to human viral encephalitis caused by PRV infection, suggesting that PRV may be able to overcome the species barrier to infect humans. To date, there is no available therapeutic for PRV infection. Here, we report the near-atomic structures of the PRV A-capsid and C-capsid, and illustrate the interaction that occurs between these subunits. We show that the C-capsid portal complex is decorated with capsid-associated tegument complexes. The PRV capsid structure is highly reminiscent of other α-herpesviruses, with some additional structural features of β- and γ-herpesviruses. These results illustrate the structure of the PRV capsid and elucidate the underlying assembly mechanism at the molecular level. This knowledge may be useful for the development of oncolytic agents or specific therapeutics against this arm of the herpesvirus family.
History
DepositionAug 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: Major capsid protein
1: Triplex capsid protein 2
2: Triplex capsid protein 2
3: Triplex capsid protein 2
A: Major capsid protein
B: Capsid vertex component 1
E: Small capsomere-interacting protein
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: Major capsid protein
T: Triplex capsid protein 1
U: Major capsid protein
V: Small capsomere-interacting protein
X: DNA packaging tegument protein UL25
Y: VP1/2
Z: VP1/2
a: Major capsid protein
c: DNA packaging tegument protein UL25
e: Major capsid protein
f: Major capsid protein
g: Major capsid protein
h: Triplex capsid protein 1
i: Triplex capsid protein 1
j: Triplex capsid protein 2
k: Triplex capsid protein 2
l: Major capsid protein
m: Major capsid protein
n: Major capsid protein
o: Triplex capsid protein 2
p: Major capsid protein
q: Major capsid protein
r: Triplex capsid protein 1
s: Triplex capsid protein 2
t: Triplex capsid protein 1
u: Major capsid protein
v: Triplex capsid protein 2
w: Major capsid protein
x: Triplex capsid protein 2
y: Major capsid protein
z: Triplex capsid protein 2


Theoretical massNumber of molelcules
Total (without water)3,221,21951
Polymers3,221,21951
Non-polymers00
Water00
1
0: Major capsid protein
1: Triplex capsid protein 2
2: Triplex capsid protein 2
3: Triplex capsid protein 2
A: Major capsid protein
B: Capsid vertex component 1
E: Small capsomere-interacting protein
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: Major capsid protein
T: Triplex capsid protein 1
U: Major capsid protein
V: Small capsomere-interacting protein
X: DNA packaging tegument protein UL25
Y: VP1/2
Z: VP1/2
a: Major capsid protein
c: DNA packaging tegument protein UL25
e: Major capsid protein
f: Major capsid protein
g: Major capsid protein
h: Triplex capsid protein 1
i: Triplex capsid protein 1
j: Triplex capsid protein 2
k: Triplex capsid protein 2
l: Major capsid protein
m: Major capsid protein
n: Major capsid protein
o: Triplex capsid protein 2
p: Major capsid protein
q: Major capsid protein
r: Triplex capsid protein 1
s: Triplex capsid protein 2
t: Triplex capsid protein 1
u: Major capsid protein
v: Triplex capsid protein 2
w: Major capsid protein
x: Triplex capsid protein 2
y: Major capsid protein
z: Triplex capsid protein 2
x 60


Theoretical massNumber of molelcules
Total (without water)193,273,1613060
Polymers193,273,1613060
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
0: Major capsid protein
1: Triplex capsid protein 2
2: Triplex capsid protein 2
3: Triplex capsid protein 2
A: Major capsid protein
B: Capsid vertex component 1
E: Small capsomere-interacting protein
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: Major capsid protein
T: Triplex capsid protein 1
U: Major capsid protein
V: Small capsomere-interacting protein
X: DNA packaging tegument protein UL25
Y: VP1/2
Z: VP1/2
a: Major capsid protein
c: DNA packaging tegument protein UL25
e: Major capsid protein
f: Major capsid protein
g: Major capsid protein
h: Triplex capsid protein 1
i: Triplex capsid protein 1
j: Triplex capsid protein 2
k: Triplex capsid protein 2
l: Major capsid protein
m: Major capsid protein
n: Major capsid protein
o: Triplex capsid protein 2
p: Major capsid protein
q: Major capsid protein
r: Triplex capsid protein 1
s: Triplex capsid protein 2
t: Triplex capsid protein 1
u: Major capsid protein
v: Triplex capsid protein 2
w: Major capsid protein
x: Triplex capsid protein 2
y: Major capsid protein
z: Triplex capsid protein 2
x 5


  • icosahedral pentamer
  • 16.1 MDa, 255 polymers
Theoretical massNumber of molelcules
Total (without water)16,106,097255
Polymers16,106,097255
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
0: Major capsid protein
1: Triplex capsid protein 2
2: Triplex capsid protein 2
3: Triplex capsid protein 2
A: Major capsid protein
B: Capsid vertex component 1
E: Small capsomere-interacting protein
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: Major capsid protein
T: Triplex capsid protein 1
U: Major capsid protein
V: Small capsomere-interacting protein
X: DNA packaging tegument protein UL25
Y: VP1/2
Z: VP1/2
a: Major capsid protein
c: DNA packaging tegument protein UL25
e: Major capsid protein
f: Major capsid protein
g: Major capsid protein
h: Triplex capsid protein 1
i: Triplex capsid protein 1
j: Triplex capsid protein 2
k: Triplex capsid protein 2
l: Major capsid protein
m: Major capsid protein
n: Major capsid protein
o: Triplex capsid protein 2
p: Major capsid protein
q: Major capsid protein
r: Triplex capsid protein 1
s: Triplex capsid protein 2
t: Triplex capsid protein 1
u: Major capsid protein
v: Triplex capsid protein 2
w: Major capsid protein
x: Triplex capsid protein 2
y: Major capsid protein
z: Triplex capsid protein 2
x 6


  • icosahedral 23 hexamer
  • 19.3 MDa, 306 polymers
Theoretical massNumber of molelcules
Total (without water)19,327,316306
Polymers19,327,316306
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))

-
Components

-
Protein , 5 types, 36 molecules 0ASUaefglmnpquwyBEFGHIJKLMNOPQ...

#1: Protein
Major capsid protein / MCP


Mass: 146101.984 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Suid alphaherpesvirus 1 / References: UniProt: G3G8T2
#3: Protein Capsid vertex component 1


Mass: 64304.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Suid alphaherpesvirus 1 / References: UniProt: G3G8T5
#4: Protein
Small capsomere-interacting protein


Mass: 11509.209 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Suid alphaherpesvirus 1 / References: UniProt: G3G8R4
#6: Protein DNA packaging tegument protein UL25 / UL25 / UL25 protein


Mass: 57412.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Suid alphaherpesvirus 1 / References: UniProt: G3G971
#7: Protein VP1/2


Mass: 7069.434 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Suid alphaherpesvirus 1 / References: UniProt: G3G8Y0

-
Triplex capsid protein ... , 2 types, 15 molecules 123jkosvxzThirt

#2: Protein
Triplex capsid protein 2


Mass: 31763.766 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Suid alphaherpesvirus 1 / References: UniProt: G3G8T3
#5: Protein
Triplex capsid protein 1


Mass: 40008.594 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Suid alphaherpesvirus 1 / References: UniProt: Q85211

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Suid alphaherpesvirus 1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Suid alphaherpesvirus 1
Details of virusEmpty: NO / Enveloped: YES / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14252 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more