6B9Q image
Deposition Date 2017-10-11
Release Date 2017-11-15
Last Version Date 2025-05-21
Entry Detail
PDB ID:
6B9Q
Title:
Single particle cryo-EM structure determination of the LuIII capsid protein
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.17 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Capsid protein VP2
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, AA (auth: 1), BA (auth: 2), CA (auth: 3), DA (auth: 4), EA (auth: 5), FA (auth: 6), GA (auth: a), HA (auth: b), IA (auth: c), JA (auth: d), KA (auth: e), LA (auth: f), MA (auth: g), NA (auth: h), OA (auth: i), PA (auth: j), QA (auth: k), RA (auth: l), SA (auth: m), TA (auth: n), UA (auth: o), VA (auth: p), WA (auth: q), XA (auth: r), YA (auth: s), ZA (auth: t), AB (auth: u), BB (auth: v), CB (auth: w), DB (auth: x), EB (auth: y), FB (auth: z), GB (auth: 7), HB (auth: 8)
Chain Length:587
Number of Molecules:60
Biological Source:Parvovirus LuIII
Ligand Molecules
Primary Citation
Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction.
Viruses 9 ? ? (2017)
PMID: 29084163 DOI: 10.3390/v9110321

Abstact

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.

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Primary Citation of related structures