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- EMDB-7071: Single particle cryo-EM structure determination of the LuIII caps... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7071 | ||||||||||||||||||
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Title | Single particle cryo-EM structure determination of the LuIII capsid protein | ||||||||||||||||||
![]() | The capsid structure for the oncolytic parvovirus LuIII determined by single-particle electron microscopy to 3.17 Angstrom resolution | ||||||||||||||||||
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![]() | Parvoviridae / VP2 capsid protein / VIRUS LIKE PARTICLE | ||||||||||||||||||
Function / homology | ![]() 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 / virion attachment to host cell / structural molecule activity / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | ||||||||||||||||||
![]() | Pittman NC / Agbandje-McKenna M | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 60.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.3 KB 14.3 KB | Display Display | ![]() |
Images | ![]() | 298.6 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6b9qMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The capsid structure for the oncolytic parvovirus LuIII determined by single-particle electron microscopy to 3.17 Angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : LuIII virus
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: LuIII virus
Supramolecule | Name: 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 |
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Host (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 3.9 MDa |
Virus shell | Shell ID: 1 / Name: VP / Diameter: 280.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Capsid protein VP2
Macromolecule | Name: Capsid protein VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 65.489953 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.75 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/4 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K | |||||||||||||||
Details | This sample was monodisperse. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF post-column filter |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |