[English] 日本語
Yorodumi
- PDB-5zap: Atomic structure of the herpes simplex virus type 2 B-capsid -

+
Open data


ID or keywords:

Loading...

-
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 / 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
Triplex capsid protein 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

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-6907
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6907
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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
point symmetry operation5
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
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))

-
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

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Human herpesvirus 2Herpesviridae / 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

-
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: 1.1 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

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