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- EMDB-7071: Single particle cryo-EM structure determination of the LuIII caps... -

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Basic information

Entry
Database: EMDB / ID: EMD-7071
TitleSingle particle cryo-EM structure determination of the LuIII capsid protein
Map dataThe capsid structure for the oncolytic parvovirus LuIII determined by single-particle electron microscopy to 3.17 Angstrom resolution
Sample
  • Virus: LuIII virus
    • Protein or peptide: Capsid protein VP2
KeywordsParvoviridae / VP2 capsid protein / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / 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 / LuIII virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsPittman NC / Agbandje-McKenna M
Funding support United States, 5 items
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, 2017-
Header (metadata) releaseNov 15, 2017-
Map releaseNov 15, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
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  • Surface view with fitted model
  • Atomic models: PDB-6b9q
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6b9q
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7071.png

Downloads & links

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Map

FileDownload / File: emd_7071.map.gz / Format: CCP4 / Size: 176.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe capsid structure for the oncolytic parvovirus LuIII determined by single-particle electron microscopy to 3.17 Angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.06 Å/pix.
x 359 pix.
= 381.976 Å		1.06 Å/pix.
x 359 pix.
= 381.976 Å		1.06 Å/pix.
x 359 pix.
= 381.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-7.755486 - 14.711995
Average (Standard dev.)-0.000000002758523 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-179-179-179
Dimensions359359359
Spacing359359359
CellA=B=C: 381.976 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0641.0641.064
M x/y/z359359359
origin x/y/z0.0000.0000.000
length x/y/z381.976381.976381.976
α/β/γ90.00090.00090.000
start NX/NY/NZ-179-179-179
NX/NY/NZ359359359
MAP C/R/S213
start NC/NR/NS-179-179-179
NC/NR/NS359359359
D min/max/mean-7.75514.712-0.000

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Supplemental data

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Sample components

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Entire : LuIII virus

EntireName: LuIII virus
Components
  • Virus: LuIII virus
    • Protein or peptide: Capsid protein VP2

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Supramolecule #1: LuIII virus

SupramoleculeName: LuIII virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Overexpression of VP2 in Sf9 cells / NCBI-ID: 35339 / Sci species name: LuIII virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: unidentified (others)
Molecular weightTheoretical: 3.9 MDa
Virus shellShell ID: 1 / Name: VP / Diameter: 280.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Parvovirus LuIII
Molecular weightTheoretical: 65.489953 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSDGTDQSDS GNAVQSAARV ERAADGPGGS GGGGSGGGGV GVSTGSYDNQ THYKFLGDGW VEITAYSTRM VHLNMPKSEN YCRVRVHNT NDTGTASHMA MDDAHEQIWT PWSLVDANAW GVWFQPSDWQ YISNNMIHIN LHSLDQELFN VVIKTVTEQN T GAEAIKVY ...String:
MSDGTDQSDS GNAVQSAARV ERAADGPGGS GGGGSGGGGV GVSTGSYDNQ THYKFLGDGW VEITAYSTRM VHLNMPKSEN YCRVRVHNT NDTGTASHMA MDDAHEQIWT PWSLVDANAW GVWFQPSDWQ YISNNMIHIN LHSLDQELFN VVIKTVTEQN T GAEAIKVY NNDLTAAMMV ALDSNNILPY TPAIDNQETL GFYPWKPTIP SPYRYYFSCD RNLSVTYKDE AGTITDTMGL AS GLNSQFF TIENTQRINL LRTGDEYATG TYYFDTEPIR LTHTWQTNRH LGQPPQITEL PSSDTANATL TARGYRSGLT QIQ GRNDVT EATRVRPAQV GFCQPHDNFE TSRAGPFKVP VVPADITQGL DHDANGSLRY TYDKQHGQSW ASQNNKDRYT WDAV NYDSG RWTNNCFIQS VPFTSEPNAN QILTNRDNLA GKTDIHFTNA FNSYGPLTAF PHPAPIYPQG QIWDKELDLE HKPRL HTQA PFVCKNNAPG QLLVRLAPNL TDQYDPNSSN LSRIVTYGTF FWKGKLTLKA KMRPNATWNP VFQISATNQG TNDYMS IER WLPTATGNIT NVPLLSRPVA RNTY

UniProtKB: Capsid protein VP1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.1 MC4H11NO3Tris
0.5 MNaClsodium chloride
0.002 MMgCl2magnesium chloride
0.008 MCaCl2calcium chloride
GridModel: Quantifoil R2/4 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF post-column filter
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-30 / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 20142
Startup modelType of model: OTHER / Details: Ab initio random model calculation by AUTO3DEM
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Auto3DEM / Number images used: 18134
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING

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