[English] 日本語
Yorodumi
- PDB-5vku: An atomic structure of the human cytomegalovirus (HCMV) capsid wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vku
TitleAn atomic structure of the human cytomegalovirus (HCMV) capsid with its securing layer of pp150 tegument protein
Components
  • Major capsid protein
  • Small capsomere-interacting protein
  • Tegument protein pp150
  • Triplex capsid protein 1
  • Triplex capsid protein 2
KeywordsVIRUS / icosahedral / capsid / tegument / Herpesvirus
Function / homology
Function and homology information


host cell viral assembly compartment / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / host cell cytoplasmic vesicle / viral capsid / host cell perinuclear region of cytoplasm / host cell nucleus / structural molecule activity / viral process / DNA binding
Similarity search - Function
Herpesvirus large structural phosphoprotein UL32 / Small capsid protein of Herpesviridae / Small capsid protein, Herpesviridae / Herpesvirus UL11/UL32 / Herpesvirus VP23 like capsid protein / Herpesvirus capsid protein 2 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid shell protein 1 / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
Large structural phosphoprotein / Triplex capsid protein 2 / Major capsid protein / Triplex capsid protein 1 / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman cytomegalovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsYu, X. / Jih, J. / Jiang, J. / Zhou, H.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR23057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
CitationJournal: Science / Year: 2017
Title: Atomic structure of the human cytomegalovirus capsid with its securing tegument layer of pp150.
Authors: Xuekui Yu / Jonathan Jih / Jiansen Jiang / Z Hong Zhou /
Abstract: Herpesviruses possess a genome-pressurized capsid. The 235-kilobase genome of human cytomegalovirus (HCMV) is by far the largest of any herpesvirus, yet it has been unclear how its capsid, which is ...Herpesviruses possess a genome-pressurized capsid. The 235-kilobase genome of human cytomegalovirus (HCMV) is by far the largest of any herpesvirus, yet it has been unclear how its capsid, which is similar in size to those of other herpesviruses, is stabilized. Here we report a HCMV atomic structure consisting of the herpesvirus-conserved capsid proteins MCP, Tri1, Tri2, and SCP and the HCMV-specific tegument protein pp150-totaling ~4000 molecules and 62 different conformers. MCPs manifest as a complex of insertions around a bacteriophage HK97 gp5-like domain, which gives rise to three classes of capsid floor-defining interactions; triplexes, composed of two "embracing" Tri2 conformers and a "third-wheeling" Tri1, fasten the capsid floor. HCMV-specific strategies include using hexon channels to accommodate the genome and pp150 helix bundles to secure the capsid via cysteine tetrad-to-SCP interactions. Our structure should inform rational design of countermeasures against HCMV, other herpesviruses, and even HIV/AIDS.
History
DepositionApr 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Structure summary / Category: em_entity_assembly / pdbx_audit_support
Item: _em_entity_assembly.entity_id_list / _pdbx_audit_support.funding_organization

-
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-8703
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8703
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: Tegument protein pp150
1: Tegument protein pp150
2: Tegument protein pp150
3: Tegument protein pp150
4: Tegument protein pp150
5: Tegument protein pp150
6: Tegument protein pp150
7: Tegument protein pp150
8: Tegument protein pp150
9: Tegument protein pp150
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: 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: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
T: Small capsomere-interacting protein
U: Small capsomere-interacting protein
V: Small capsomere-interacting protein
W: Small capsomere-interacting protein
X: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
a: Small capsomere-interacting protein
b: Small capsomere-interacting protein
c: Small capsomere-interacting protein
d: Small capsomere-interacting protein
e: Small capsomere-interacting protein
f: Small capsomere-interacting protein
g: Triplex capsid protein 1
h: Triplex capsid protein 2
i: Triplex capsid protein 2
j: Triplex capsid protein 1
k: Triplex capsid protein 2
l: Triplex capsid protein 2
m: Triplex capsid protein 1
n: Triplex capsid protein 2
o: Triplex capsid protein 2
p: Triplex capsid protein 1
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: Tegument protein pp150
w: Tegument protein pp150
x: Tegument protein pp150
y: Tegument protein pp150
z: Tegument protein pp150


Theoretical massNumber of molelcules
Total (without water)3,610,91762
Polymers3,610,91762
Non-polymers00
Water0
1
0: Tegument protein pp150
1: Tegument protein pp150
2: Tegument protein pp150
3: Tegument protein pp150
4: Tegument protein pp150
5: Tegument protein pp150
6: Tegument protein pp150
7: Tegument protein pp150
8: Tegument protein pp150
9: Tegument protein pp150
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: 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: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
T: Small capsomere-interacting protein
U: Small capsomere-interacting protein
V: Small capsomere-interacting protein
W: Small capsomere-interacting protein
X: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
a: Small capsomere-interacting protein
b: Small capsomere-interacting protein
c: Small capsomere-interacting protein
d: Small capsomere-interacting protein
e: Small capsomere-interacting protein
f: Small capsomere-interacting protein
g: Triplex capsid protein 1
h: Triplex capsid protein 2
i: Triplex capsid protein 2
j: Triplex capsid protein 1
k: Triplex capsid protein 2
l: Triplex capsid protein 2
m: Triplex capsid protein 1
n: Triplex capsid protein 2
o: Triplex capsid protein 2
p: Triplex capsid protein 1
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: Tegument protein pp150
w: Tegument protein pp150
x: Tegument protein pp150
y: Tegument protein pp150
z: Tegument protein pp150
x 60


Theoretical massNumber of molelcules
Total (without water)216,655,0443720
Polymers216,655,0443720
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
0: Tegument protein pp150
1: Tegument protein pp150
2: Tegument protein pp150
3: Tegument protein pp150
4: Tegument protein pp150
5: Tegument protein pp150
6: Tegument protein pp150
7: Tegument protein pp150
8: Tegument protein pp150
9: Tegument protein pp150
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: 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: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
T: Small capsomere-interacting protein
U: Small capsomere-interacting protein
V: Small capsomere-interacting protein
W: Small capsomere-interacting protein
X: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
a: Small capsomere-interacting protein
b: Small capsomere-interacting protein
c: Small capsomere-interacting protein
d: Small capsomere-interacting protein
e: Small capsomere-interacting protein
f: Small capsomere-interacting protein
g: Triplex capsid protein 1
h: Triplex capsid protein 2
i: Triplex capsid protein 2
j: Triplex capsid protein 1
k: Triplex capsid protein 2
l: Triplex capsid protein 2
m: Triplex capsid protein 1
n: Triplex capsid protein 2
o: Triplex capsid protein 2
p: Triplex capsid protein 1
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: Tegument protein pp150
w: Tegument protein pp150
x: Tegument protein pp150
y: Tegument protein pp150
z: Tegument protein pp150
x 5


  • icosahedral pentamer
  • 18.1 MDa, 310 polymers
Theoretical massNumber of molelcules
Total (without water)18,054,587310
Polymers18,054,587310
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
0: Tegument protein pp150
1: Tegument protein pp150
2: Tegument protein pp150
3: Tegument protein pp150
4: Tegument protein pp150
5: Tegument protein pp150
6: Tegument protein pp150
7: Tegument protein pp150
8: Tegument protein pp150
9: Tegument protein pp150
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: 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: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
T: Small capsomere-interacting protein
U: Small capsomere-interacting protein
V: Small capsomere-interacting protein
W: Small capsomere-interacting protein
X: Small capsomere-interacting protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
a: Small capsomere-interacting protein
b: Small capsomere-interacting protein
c: Small capsomere-interacting protein
d: Small capsomere-interacting protein
e: Small capsomere-interacting protein
f: Small capsomere-interacting protein
g: Triplex capsid protein 1
h: Triplex capsid protein 2
i: Triplex capsid protein 2
j: Triplex capsid protein 1
k: Triplex capsid protein 2
l: Triplex capsid protein 2
m: Triplex capsid protein 1
n: Triplex capsid protein 2
o: Triplex capsid protein 2
p: Triplex capsid protein 1
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: Tegument protein pp150
w: Tegument protein pp150
x: Tegument protein pp150
y: Tegument protein pp150
z: Tegument protein pp150
x 6


  • icosahedral 23 hexamer
  • 21.7 MDa, 372 polymers
Theoretical massNumber of molelcules
Total (without water)21,665,504372
Polymers21,665,504372
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 (正20面体型対称))

-
Components

#1: Protein
Tegument protein pp150 / 150 kDa matrix phosphoprotein / 150 kDa phosphoprotein / pp150 / Basic phosphoprotein / BPP / ...150 kDa matrix phosphoprotein / 150 kDa phosphoprotein / pp150 / Basic phosphoprotein / BPP / Phosphoprotein UL32 / Tegument protein UL32


Mass: 33232.418 Da / Num. of mol.: 15 / Fragment: UNP residues 1-285 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus (strain AD169) / Strain: AD169 / References: UniProt: P08318
#2: Protein
Major capsid protein / MCP


Mass: 154048.906 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus (strain AD169) / Strain: AD169 / References: UniProt: P16729
#3: Protein
Small capsomere-interacting protein / Smallest capsid protein / SCP


Mass: 8495.924 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus (strain AD169) / Strain: AD169 / References: UniProt: Q7M6N6
#4: Protein
Triplex capsid protein 1 / Triplex monomer protein / Tri1


Mass: 33071.270 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus (strain AD169) / Strain: AD169 / References: UniProt: P16783
#5: Protein
Triplex capsid protein 2 / Triplex dimer protein / Tri2


Mass: 34635.750 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus (strain AD169) / Strain: AD169 / References: UniProt: P16728

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Human herpesvirus 5 strain AD169 / Type: VIRUS / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Human cytomegalovirus (strain AD169)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Virus shellDiameter: 1320 nm / Triangulation number (T number): 16
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: 2.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (正20面体型対称)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39600 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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