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- PDB-8co6: Subtomogram average of Immature Rotavirus TLP penton -

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Basic information

Entry
Database: PDB / ID: 8co6
TitleSubtomogram average of Immature Rotavirus TLP penton
Components
  • Inner capsid protein VP2
  • Intermediate capsid protein VP6
  • Outer capsid glycoprotein VP7
  • Outer capsid protein VP4
KeywordsVIRAL PROTEIN / Rotavirus / STA
Function / homology
Function and homology information


viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / host cell rough endoplasmic reticulum / viral inner capsid / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / host cell rough endoplasmic reticulum / viral inner capsid / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / RNA binding / membrane / metal ion binding
Similarity search - Function
Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Haemagglutinin outer capsid protein VP4, concanavalin-like domain ...Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Viral capsid/haemagglutinin protein / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Outer capsid protein VP4 / Outer capsid glycoprotein VP7 / Inner capsid protein VP2 / Intermediate capsid protein VP6
Similarity search - Component
Biological speciesRotavirus A
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.7 Å
AuthorsShah, P.N.M. / Stuart, D.I.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Wellcome Trust03141/Z/16/Z United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
CitationJournal: Cell Host Microbe / Year: 2023
Title: Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography.
Authors: Pranav N M Shah / James B Gilchrist / Björn O Forsberg / Alister Burt / Andrew Howe / Shyamal Mosalaganti / William Wan / Julika Radecke / Yuriy Chaban / Geoff Sutton / David I Stuart / Mark Boyce /
Abstract: Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and ...Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and visualization of the assembly process has been hampered by the inaccessibility of unstable intermediates. We characterize the assembly pathway of group A rotaviruses observed in situ within cryo-preserved infected cells through the use of cryoelectron tomography of cellular lamellae. Our findings demonstrate that the viral polymerase VP1 recruits viral genomes during particle assembly, as revealed by infecting with a conditionally lethal mutant. Additionally, pharmacological inhibition to arrest the transiently enveloped stage uncovered a unique conformation of the VP4 spike. Subtomogram averaging provided atomic models of four intermediate states, including a pre-packaging single-layered intermediate, the double-layered particle, the transiently enveloped double-layered particle, and the fully assembled triple-layered virus particle. In summary, these complementary approaches enable us to elucidate the discrete steps involved in forming an intracellular rotavirus particle.
History
DepositionFeb 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer capsid protein VP4
B: Outer capsid protein VP4
C: Outer capsid protein VP4
D: Outer capsid glycoprotein VP7
E: Outer capsid glycoprotein VP7
F: Outer capsid glycoprotein VP7
G: Outer capsid glycoprotein VP7
H: Outer capsid glycoprotein VP7
I: Outer capsid glycoprotein VP7
J: Outer capsid glycoprotein VP7
K: Outer capsid glycoprotein VP7
L: Outer capsid glycoprotein VP7
M: Outer capsid glycoprotein VP7
N: Outer capsid glycoprotein VP7
O: Outer capsid glycoprotein VP7
d: Intermediate capsid protein VP6
e: Intermediate capsid protein VP6
f: Intermediate capsid protein VP6
g: Intermediate capsid protein VP6
h: Intermediate capsid protein VP6
i: Intermediate capsid protein VP6
j: Intermediate capsid protein VP6
k: Intermediate capsid protein VP6
l: Intermediate capsid protein VP6
m: Intermediate capsid protein VP6
n: Intermediate capsid protein VP6
o: Intermediate capsid protein VP6
q: Inner capsid protein VP2
r: Inner capsid protein VP2


Theoretical massNumber of molelcules
Total (without water)1,450,82729
Polymers1,450,82729
Non-polymers00
Water00
1
A: Outer capsid protein VP4
B: Outer capsid protein VP4
C: Outer capsid protein VP4
D: Outer capsid glycoprotein VP7
E: Outer capsid glycoprotein VP7
F: Outer capsid glycoprotein VP7
G: Outer capsid glycoprotein VP7
H: Outer capsid glycoprotein VP7
I: Outer capsid glycoprotein VP7
J: Outer capsid glycoprotein VP7
K: Outer capsid glycoprotein VP7
L: Outer capsid glycoprotein VP7
M: Outer capsid glycoprotein VP7
N: Outer capsid glycoprotein VP7
O: Outer capsid glycoprotein VP7
d: Intermediate capsid protein VP6
e: Intermediate capsid protein VP6
f: Intermediate capsid protein VP6
g: Intermediate capsid protein VP6
h: Intermediate capsid protein VP6
i: Intermediate capsid protein VP6
j: Intermediate capsid protein VP6
k: Intermediate capsid protein VP6
l: Intermediate capsid protein VP6
m: Intermediate capsid protein VP6
n: Intermediate capsid protein VP6
o: Intermediate capsid protein VP6
q: Inner capsid protein VP2
r: Inner capsid protein VP2
x 5


  • defined by author
  • 7.25 MDa, 145 polymers
Theoretical massNumber of molelcules
Total (without water)7,254,133145
Polymers7,254,133145
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4

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Components

#1: Protein Outer capsid protein VP4


Mass: 86767.953 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rotavirus A / References: UniProt: A0A1Q2TSK9
#2: Protein
Outer capsid glycoprotein VP7


Mass: 37230.664 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Rotavirus A / References: UniProt: A0A1Q2TSM6
#3: Protein
Intermediate capsid protein VP6


Mass: 44910.738 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Rotavirus A / References: UniProt: A2T3S6
#4: Protein Inner capsid protein VP2


Mass: 102412.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rotavirus A / References: UniProt: A2T3R1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Rotavirus A / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Rotavirus A
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Virus shellDiameter: 1000 nm / Triangulation number (T number): 13
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 2.2 e/Å2 / Avg electron dose per subtomogram: 90 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7NAMDmodel fitting
13PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1961 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 85 / Num. of volumes extracted: 1961
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingSource name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00294511
ELECTRON MICROSCOPYf_angle_d0.434128695
ELECTRON MICROSCOPYf_dihedral_angle_d11.86134531
ELECTRON MICROSCOPYf_chiral_restr0.03914775
ELECTRON MICROSCOPYf_plane_restr0.00316645

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