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- PDB-6nhj: Atomic structures and deletion mutant reveal different capsid-bin... -

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Basic information

Entry
Database: PDB / ID: 6nhj
TitleAtomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development
Components
  • Major capsid protein
  • Minor capsid protein
  • Small capsomere-interacting protein
  • Tegument protein
  • Triplex capsid protein 2
KeywordsVIRUS / cryoEM / beta-herpesvirus / murine cytomegalovirus / human cytomegalovirus / pp150 / pUL32 / pM32 / bacterial artificial chromosome-based mutagenesis
Function / homologyHerpesvirus major capsid protein, upper domain superfamily / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpes virus major capsid protein / Herpesvirus VP23 like capsid protein / Small capsid protein, Herpesviridae / Herpesvirus UL11/UL32 / Herpesvirus capsid protein 2 / Small capsid protein of Herpesviridae / Herpesvirus major capsid protein ...Herpesvirus major capsid protein, upper domain superfamily / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpes virus major capsid protein / Herpesvirus VP23 like capsid protein / Small capsid protein, Herpesviridae / Herpesvirus UL11/UL32 / Herpesvirus capsid protein 2 / Small capsid protein of Herpesviridae / Herpesvirus major capsid protein / Herpesvirus large structural phosphoprotein UL32 / T=16 icosahedral viral capsid / viral capsid assembly / viral capsid / host cell nucleus / viral process / structural molecule activity / DNA binding / Major capsid protein / Tegument protein / Minor capsid protein / Small capsomere-interacting protein / Triplex capsid protein 2
Function and homology information
Specimen sourceMurine cytomegalovirus (Murine cytomegalovirus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5 Å resolution
AuthorsLiu, W. / Dai, X.H. / Jih, J. / Chan, K. / Trang, P. / Yu, X.K. / Balogun, R. / Mei, Y. / Liu, F.Y. / Zhou, Z.H.
CitationJournal: PLoS Pathog. / Year: 2019
Title: Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development.
Authors: Wei Liu / Xinghong Dai / Jonathan Jih / Karen Chan / Phong Trang / Xuekui Yu / Rilwan Balogun / Ye Mei / Fenyong Liu / Z Hong Zhou
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 22, 2018 / Release: Mar 6, 2019

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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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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  • Simplified surface model + fitted atomic model
  • EMDB-9366
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  • Superimposition on EM map
  • EMDB-9366
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Structure viewerMolecule:
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Assembly

Deposited unit
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
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: Major capsid protein
2: Tegument protein
3: Tegument protein
e: Tegument protein
h: Tegument protein
f: Tegument protein
i: Tegument protein
g: Tegument protein
j: Tegument 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
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: Minor capsid protein
S: Minor capsid protein
T: Minor capsid protein
U: Minor capsid protein
V: Minor capsid protein
z: Triplex capsid protein 2
W: Triplex capsid protein 2
X: Triplex capsid protein 2
Y: Triplex capsid protein 2
Z: Triplex capsid protein 2
1: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 2
c: Triplex capsid protein 2
d: Triplex capsid protein 2


Theoretical massNumber of molelcules
Total (without water)3,727,30055
Polyers3,727,30055
Non-polymers00
Water0
1
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
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: Major capsid protein
2: Tegument protein
3: Tegument protein
e: Tegument protein
h: Tegument protein
f: Tegument protein
i: Tegument protein
g: Tegument protein
j: Tegument 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
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: Minor capsid protein
S: Minor capsid protein
T: Minor capsid protein
U: Minor capsid protein
V: Minor capsid protein
z: Triplex capsid protein 2
W: Triplex capsid protein 2
X: Triplex capsid protein 2
Y: Triplex capsid protein 2
Z: Triplex capsid protein 2
1: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 2
c: Triplex capsid protein 2
d: Triplex capsid protein 2
x 60


  • complete icosahedral assembly
  • Evidence: none
  • 224 MDa, 3300 polymers
Theoretical massNumber of molelcules
Total (without water)223,638,0253300
Polyers223,638,0253300
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
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
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: Major capsid protein
2: Tegument protein
3: Tegument protein
e: Tegument protein
h: Tegument protein
f: Tegument protein
i: Tegument protein
g: Tegument protein
j: Tegument 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
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: Minor capsid protein
S: Minor capsid protein
T: Minor capsid protein
U: Minor capsid protein
V: Minor capsid protein
z: Triplex capsid protein 2
W: Triplex capsid protein 2
X: Triplex capsid protein 2
Y: Triplex capsid protein 2
Z: Triplex capsid protein 2
1: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 2
c: Triplex capsid protein 2
d: Triplex capsid protein 2
x 5


  • icosahedral pentamer
  • 18.6 MDa, 275 polymers
Theoretical massNumber of molelcules
Total (without water)18,636,502275
Polyers18,636,502275
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
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
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: Major capsid protein
2: Tegument protein
3: Tegument protein
e: Tegument protein
h: Tegument protein
f: Tegument protein
i: Tegument protein
g: Tegument protein
j: Tegument 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
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: Minor capsid protein
S: Minor capsid protein
T: Minor capsid protein
U: Minor capsid protein
V: Minor capsid protein
z: Triplex capsid protein 2
W: Triplex capsid protein 2
X: Triplex capsid protein 2
Y: Triplex capsid protein 2
Z: Triplex capsid protein 2
1: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 2
c: Triplex capsid protein 2
d: Triplex capsid protein 2
x 6


  • icosahedral 23 hexamer
  • 22.4 MDa, 330 polymers
Theoretical massNumber of molelcules
Total (without water)22,363,803330
Polyers22,363,803330
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

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Components

#1: Protein/peptide
Major capsid protein / MCP


Mass: 151673.031 Da / Num. of mol.: 16 / Source: (natural) Murine cytomegalovirus (strain Smith) / Strain: Smith / References: UniProt: A0A1S5YGR4
#2: Protein/peptide
Tegument protein


Mass: 78749.961 Da / Num. of mol.: 8 / Source: (natural) Murine cytomegalovirus (strain Smith) / Strain: Smith / References: UniProt: D3XDM2
#3: Protein/peptide
Small capsomere-interacting protein


Mass: 9845.198 Da / Num. of mol.: 16 / Source: (natural) Murine cytomegalovirus (strain Smith) / Strain: Smith / References: UniProt: D3XDN6
#4: Protein/peptide
Minor capsid protein


Mass: 33281.289 Da / Num. of mol.: 5 / Source: (natural) Murine cytomegalovirus (strain Smith) / Strain: Smith / References: UniProt: D3XDN4
#5: Protein/peptide
Triplex capsid protein 2


Mass: 34660.262 Da / Num. of mol.: 10 / Source: (natural) Murine cytomegalovirus (strain Smith) / Strain: Smith / References: UniProt: D3XDR2

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Murid herpesvirus 1 (strain Smith) / Type: VIRUS / Entity ID: 1, 2, 3, 4, 5 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Murid herpesvirus 1 (strain Smith)
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Buffer solutionDetails: PBS buffer, PH=7.4 / pH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: The grids were manually plunged into the Ethane.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 47000 / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25 e/Å2 / Film or detector model: AGFA SCIENTA FILM / Number of real images: 2200
Image scansScanner model: NIKON SUPER COOLSCAN 9000

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Processing

EM software
IDNameCategory
4CTFFINDCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 58254
SymmetryPoint symmetry: I
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 47982 / Symmetry type: POINT
Atomic model buildingOverall b value: 200 / Ref protocol: OTHER / Ref space: REAL

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