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- PDB-6b9q: Single particle cryo-EM structure determination of the LuIII caps... -

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Basic information

Entry
Database: PDB / ID: 6b9q
TitleSingle particle cryo-EM structure determination of the LuIII capsid protein
ComponentsCapsid protein VP2
KeywordsVIRUS LIKE PARTICLE / Parvoviridae / VP2 capsid protein
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / structural molecule activity / virion attachment to host cell / metal ion binding
Similarity search - Function
Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesParvovirus LuIII
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsPittman, N.C. / Agbandje-McKenna, M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946-07S1, 229 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5T32AI007110-34 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA029303 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
CitationJournal: Viruses / Year: 2017
Title: Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction.
Authors: Nikéa Pittman / Adam Misseldine / Lorena Geilen / Sujata Halder / J Kennon Smith / Justin Kurian / Paul Chipman / Mandy Janssen / Robert Mckenna / Timothy S Baker / Anthony D'Abramo / Susan ...Authors: Nikéa Pittman / Adam Misseldine / Lorena Geilen / Sujata Halder / J Kennon Smith / Justin Kurian / Paul Chipman / Mandy Janssen / Robert Mckenna / Timothy S Baker / Anthony D'Abramo / Susan Cotmore / Peter Tattersall / Mavis Agbandje-McKenna /
Abstract: LuIII, a protoparvovirus pathogenic to rodents, replicates in human mitotic cells, making it applicable for use to kill cancer cells. This virus group includes H-1 parvovirus (H-1PV) and minute virus ...LuIII, a protoparvovirus pathogenic to rodents, replicates in human mitotic cells, making it applicable for use to kill cancer cells. This virus group includes H-1 parvovirus (H-1PV) and minute virus of mice (MVM). However, LuIII displays enhanced oncolysis compared to H-1PV and MVM, a phenotype mapped to the major capsid viral protein 2 (VP2). This suggests that within LuIII VP2 are determinants for improved tumor lysis. To investigate this, the structure of the LuIII virus-like-particle was determined using single particle cryo-electron microscopy and image reconstruction to 3.17 Å resolution, and compared to the H-1PV and MVM structures. The LuIII VP2 structure, ordered from residue 37 to 587 (C-terminal), had the conserved VP topology and capsid morphology previously reported for other protoparvoviruses. This includes a core β-barrel and α-helix A, a depression at the icosahedral 2-fold and surrounding the 5-fold axes, and a single protrusion at the 3-fold axes. Comparative analysis identified surface loop differences among LuIII, H-1PV, and MVM at or close to the capsid 2- and 5-fold symmetry axes, and the shoulder of the 3-fold protrusions. The 2-fold differences cluster near the previously identified MVM sialic acid receptor binding pocket, and revealed potential determinants of protoparvovirus tumor tropism.
History
DepositionOct 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein VP2
B: Capsid protein VP2
C: Capsid protein VP2
D: Capsid protein VP2
E: Capsid protein VP2
F: Capsid protein VP2
G: Capsid protein VP2
H: Capsid protein VP2
I: Capsid protein VP2
J: Capsid protein VP2
K: Capsid protein VP2
L: Capsid protein VP2
M: Capsid protein VP2
N: Capsid protein VP2
O: Capsid protein VP2
P: Capsid protein VP2
Q: Capsid protein VP2
R: Capsid protein VP2
S: Capsid protein VP2
T: Capsid protein VP2
U: Capsid protein VP2
V: Capsid protein VP2
W: Capsid protein VP2
X: Capsid protein VP2
Y: Capsid protein VP2
Z: Capsid protein VP2
1: Capsid protein VP2
2: Capsid protein VP2
3: Capsid protein VP2
4: Capsid protein VP2
5: Capsid protein VP2
6: Capsid protein VP2
a: Capsid protein VP2
b: Capsid protein VP2
c: Capsid protein VP2
d: Capsid protein VP2
e: Capsid protein VP2
f: Capsid protein VP2
g: Capsid protein VP2
h: Capsid protein VP2
i: Capsid protein VP2
j: Capsid protein VP2
k: Capsid protein VP2
l: Capsid protein VP2
m: Capsid protein VP2
n: Capsid protein VP2
o: Capsid protein VP2
p: Capsid protein VP2
q: Capsid protein VP2
r: Capsid protein VP2
s: Capsid protein VP2
t: Capsid protein VP2
u: Capsid protein VP2
v: Capsid protein VP2
w: Capsid protein VP2
x: Capsid protein VP2
y: Capsid protein VP2
z: Capsid protein VP2
7: Capsid protein VP2
8: Capsid protein VP2


Theoretical massNumber of molelcules
Total (without water)3,929,39760
Polymers3,929,39760
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, Fully assembled particles were visualized by transmission electron microscopy after VLP purification from sf9 cell extracts.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1008690 Å2
ΔGint-4183 kcal/mol
Surface area872310 Å2

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Components

#1: Protein ...
Capsid protein VP2 / / Isoform VP2 of capsid protein VP1


Mass: 65489.953 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parvovirus LuIII / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P36310

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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: LuIII virus / Type: VIRUS / Details: Overexpression of VP2 in Sf9 cells / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 3.9 MDa / Experimental value: NO
Source (natural)Organism: LuIII virus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: unidentified
Virus shellName: VP / Diameter: 280 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
10.1 MTrisC4H11NO31
20.5 Msodium chlorideNaClSodium chloride1
30.002 Mmagnesium chlorideMgCl21
40.008 Mcalcium chlorideCaCl21
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/4
VitrificationCryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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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 / Cs: 2.7 mm
Image recordingElectron dose: 1.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF post-column filter
Image scansMovie frames/image: 50 / Used frames/image: 2-30

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Processing

SoftwareName: PHENIX / Version: 1.10-2155_2155: / Classification: refinement
EM software
IDNameCategory
1AUTOPP Mparticle selection
13Auto3DEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 20142
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18134 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009271560
ELECTRON MICROSCOPYf_angle_d0.798371640
ELECTRON MICROSCOPYf_dihedral_angle_d6.029272700
ELECTRON MICROSCOPYf_chiral_restr0.05539960
ELECTRON MICROSCOPYf_plane_restr0.00649140

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