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- PDB-6q1f: Atomic structure of the Human Herpesvirus 6B Capsid and Capsid-As... -

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Basic information

Entry
Database: PDB / ID: 6q1f
TitleAtomic structure of the Human Herpesvirus 6B Capsid and Capsid-Associated Tegument Complexes
Components
  • Large structural phosphoprotein
  • Major capsid protein
  • Small capsomere-interacting protein
  • Triplex capsid protein 1
  • Triplex capsid protein 2
KeywordsVIRUS / beta-herpesvirus / HHV-6B / murine cytomegalovirus / human cytomegalovirus / pp150 / pU11 / pUL32 / pM32 / pU14
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Herpesvirus UL11/UL32 / Small capsid protein, Herpesviridae / Herpesvirus large structural phosphoprotein UL32 / Small capsid protein of Herpesviridae / 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
Large structural phosphoprotein / Major capsid protein / Triplex capsid protein 2 / Small capsomere-interacting protein / Triplex capsid protein 1
Similarity search - Component
Biological speciesHuman herpesvirus 6B
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsZhang, Y.B. / Liu, W. / Li, Z.H. / Kumar, V. / Alvarez-Cabrera, A.L. / Leibovitch, E. / Cui, Y.X. / Mei, Y. / Bi, G.Q. / Jacobson, S. / Zhou, Z.H.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583, DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1S10RR23057, 1S10OD018111, and 1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 and DMR-1548924 United States
CitationJournal: Nat Commun / Year: 2019
Title: Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes.
Authors: Yibo Zhang / Wei Liu / Zihang Li / Vinay Kumar / Ana L Alvarez-Cabrera / Emily C Leibovitch / Yanxiang Cui / Ye Mei / Guo-Qiang Bi / Steve Jacobson / Z Hong Zhou /
Abstract: Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B ...Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B capsid and capsid-associated tegument complex (CATC) obtained by cryoEM and sub-particle reconstruction. Compared to other β-herpesviruses, HHV-6B exhibits high similarity in capsid structure but organizational differences in its CATC (pU11 tetramer). 180 "VΛ"-shaped CATCs are observed in HHV-6B, distinguishing from the 255 "Λ"-shaped dimeric CATCs observed in murine cytomegalovirus and the 310 "Δ"-shaped CATCs in human cytomegalovirus. This trend in CATC quantity correlates with the increasing genomes sizes of these β-herpesviruses. Incompatible distances revealed by the atomic structures rationalize the lack of CATC's binding to triplexes Ta, Tc, and Tf in HHV-6B. Our results offer insights into HHV-6B capsid assembly and the roles of its tegument proteins, including not only the β-herpesvirus-specific pU11 and pU14, but also those conserved across all subfamilies of Herpesviridae.
History
DepositionAug 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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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
q: Major capsid protein
r: Major capsid protein
s: Major capsid protein
t: Major capsid protein
u: Major capsid protein
v: Major capsid protein
w: Major capsid protein
e: Large structural phosphoprotein
f: Large structural phosphoprotein
g: Large structural phosphoprotein
h: Large structural phosphoprotein
i: Large structural phosphoprotein
j: Large structural phosphoprotein
k: Large structural phosphoprotein
l: Large structural phosphoprotein
m: Large structural phosphoprotein
n: Large structural phosphoprotein
o: Large structural phosphoprotein
p: Large structural phosphoprotein
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
x: Small capsomere-interacting protein
y: Small capsomere-interacting protein
z: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Small capsomere-interacting protein
5: Triplex capsid protein 1
S: Triplex capsid protein 1
T: Triplex capsid protein 1
U: Triplex capsid protein 1
V: Triplex capsid protein 1
6: Triplex capsid protein 2
W: Triplex capsid protein 2
X: Triplex capsid protein 2
Y: Triplex capsid protein 2
Z: Triplex capsid protein 2
7: 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)4,248,21159
Polymers4,248,21159
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
q: Major capsid protein
r: Major capsid protein
s: Major capsid protein
t: Major capsid protein
u: Major capsid protein
v: Major capsid protein
w: Major capsid protein
e: Large structural phosphoprotein
f: Large structural phosphoprotein
g: Large structural phosphoprotein
h: Large structural phosphoprotein
i: Large structural phosphoprotein
j: Large structural phosphoprotein
k: Large structural phosphoprotein
l: Large structural phosphoprotein
m: Large structural phosphoprotein
n: Large structural phosphoprotein
o: Large structural phosphoprotein
p: Large structural phosphoprotein
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
x: Small capsomere-interacting protein
y: Small capsomere-interacting protein
z: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Small capsomere-interacting protein
5: Triplex capsid protein 1
S: Triplex capsid protein 1
T: Triplex capsid protein 1
U: Triplex capsid protein 1
V: Triplex capsid protein 1
6: Triplex capsid protein 2
W: Triplex capsid protein 2
X: Triplex capsid protein 2
Y: Triplex capsid protein 2
Z: Triplex capsid protein 2
7: 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
  • 255 MDa, 3540 polymers
Theoretical massNumber of molelcules
Total (without water)254,892,6833540
Polymers254,892,6833540
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
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
q: Major capsid protein
r: Major capsid protein
s: Major capsid protein
t: Major capsid protein
u: Major capsid protein
v: Major capsid protein
w: Major capsid protein
e: Large structural phosphoprotein
f: Large structural phosphoprotein
g: Large structural phosphoprotein
h: Large structural phosphoprotein
i: Large structural phosphoprotein
j: Large structural phosphoprotein
k: Large structural phosphoprotein
l: Large structural phosphoprotein
m: Large structural phosphoprotein
n: Large structural phosphoprotein
o: Large structural phosphoprotein
p: Large structural phosphoprotein
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
x: Small capsomere-interacting protein
y: Small capsomere-interacting protein
z: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Small capsomere-interacting protein
5: Triplex capsid protein 1
S: Triplex capsid protein 1
T: Triplex capsid protein 1
U: Triplex capsid protein 1
V: Triplex capsid protein 1
6: Triplex capsid protein 2
W: Triplex capsid protein 2
X: Triplex capsid protein 2
Y: Triplex capsid protein 2
Z: Triplex capsid protein 2
7: 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
  • 21.2 MDa, 295 polymers
Theoretical massNumber of molelcules
Total (without water)21,241,057295
Polymers21,241,057295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
q: Major capsid protein
r: Major capsid protein
s: Major capsid protein
t: Major capsid protein
u: Major capsid protein
v: Major capsid protein
w: Major capsid protein
e: Large structural phosphoprotein
f: Large structural phosphoprotein
g: Large structural phosphoprotein
h: Large structural phosphoprotein
i: Large structural phosphoprotein
j: Large structural phosphoprotein
k: Large structural phosphoprotein
l: Large structural phosphoprotein
m: Large structural phosphoprotein
n: Large structural phosphoprotein
o: Large structural phosphoprotein
p: Large structural phosphoprotein
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
x: Small capsomere-interacting protein
y: Small capsomere-interacting protein
z: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Small capsomere-interacting protein
5: Triplex capsid protein 1
S: Triplex capsid protein 1
T: Triplex capsid protein 1
U: Triplex capsid protein 1
V: Triplex capsid protein 1
6: Triplex capsid protein 2
W: Triplex capsid protein 2
X: Triplex capsid protein 2
Y: Triplex capsid protein 2
Z: Triplex capsid protein 2
7: 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
  • 25.5 MDa, 354 polymers
Theoretical massNumber of molelcules
Total (without water)25,489,268354
Polymers25,489,268354
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))

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Components

#1: Protein
Major capsid protein / MCP


Mass: 152260.047 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 6B (strain Z29) / Strain: Z29 / References: UniProt: Q9QJ26
#2: Protein
Large structural phosphoprotein / pp150 / 100 kDa phosphoprotein / pp100 / Major antigenic structural protein


Mass: 95738.125 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 6B (strain Z29) / Strain: Z29 / References: UniProt: Q69535
#3: Protein
Small capsomere-interacting protein / Small Capsid Protein


Mass: 9827.329 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 6B (strain Z29) / Strain: Z29 / References: UniProt: Q9WT32
#4: Protein
Triplex capsid protein 1 / Triplex Complex 1


Mass: 34162.508 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 6B (strain Z29) / Strain: Z29 / References: UniProt: Q9WT35
#5: Protein
Triplex capsid protein 2 / Triplex Complex 2


Mass: 33514.332 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 6B (strain Z29) / Strain: Z29 / References: UniProt: Q9QJ27

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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 6 strain Z29 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Human herpesvirus 6 strain Z29 / Strain: Z29
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4 / Details: PBS buffer, pH 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in.
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
MicroscopyModel: 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: 64000 X / Calibrated magnification: 64000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 2200 nm / Calibrated defocus min: 2200 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 23 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4828

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Processing

EM software
IDNameCategory
4CTFFINDCTF correction
7Cootmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7430
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6443 / Details: bin4 reconstrction / Symmetry type: POINT
Atomic model buildingProtocol: OTHER

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