[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleMapping the sialic acid-binding sites of LuIII and H-1 parvovirus.
Journal, issue, pagesJ Virol, Vol. 99, Issue 8, Page e0029725, Year 2025
Publish dateAug 19, 2025
AuthorsKevin Busuttil / Nikéa Pittman / Jon Zachary / Sujata Halder / Lorena Geilen / Amriti Singh / Adam Misseldine / Paulina Kaplonek / Paul Chipman / Jaime Heimburg-Molinaro / Peter H Seeberger / Mario Mietzsch / Antonette D Bennett / Robert McKenna /
PubMed AbstractOncolytic protoparvoviruses, including LuIII, H-1 parvovirus (H-1PV), and the prototypic strain of minute virus of mice (MVMp), can target and destroy cancer cells. Host cell targeting is based ...Oncolytic protoparvoviruses, including LuIII, H-1 parvovirus (H-1PV), and the prototypic strain of minute virus of mice (MVMp), can target and destroy cancer cells. Host cell targeting is based largely on the identification and interaction of the virus with the primary receptor. Previously, it has been shown that MVMp and H-1PV bind to sialic acid (SIA), which is the primary glycan receptor. This study investigates whether LuIII also utilizes a similar glycan for host cell attachment. Microarray analysis confirmed that α2-3-linked SIA is a shared receptor requirement for cell binding for all three viruses. Three glycans were identified in the array, namely, Neu5Acα2-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAc, Neu5Acα2-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAc, and Neu5Acα2-3Galβ1-4(Fucα1-3)-GlcNAcβ1-3-Galβ1-4(Fucα1-3)-GlcNAc. The cryo-EM structures of the LuIII and H-1PV glycan complexes were determined to resolutions ranging from 2.57 to 2.88 Å. Small structural perturbations were observed between the cryo-EM map and the previous X-ray crystallographic maps for H-1PV, including several histidine residues within the HI loop. Overall, LuIII and H-1PV utilize a shared SIA recognition pocket near the icosahedral twofold axis adjacent to (but not overlapping with) the known MVMp SIA binding site. In addition, structural differences between the major capsid protein (VP2) of LuIII, H-1PV, and MVMp all clustered around these glycan-binding pockets. This structural phenotype may contribute to the differences observed in tumor cell killing efficiency among the rodent protoparvoviruses.
IMPORTANCE: Oncolytic viruses could provide a safe alternative for targeting aggressive tumors that evade standard therapies. While rodent protoparvoviruses are innocuous in non-cancerous cells, they carry out efficient cell killing in tumors. Differences in cell tropism and killing efficiency are determined by the viral capsid proteins; thus, structural studies provide insight into understanding the protoparvovirus infection in both wild-type and cancerous cells. Binding to extracellular sialic acid (SIA) initiates cell entry for protoparvoviruses H-1PV, MVMp, and this is also hypothesized for LuIII. This study investigates the structures of LuIII and H-1PV in the presence of their glycan receptors to identify and map the capsid loci that are responsible for this interaction. This knowledge may aid future capsid engineering to improve oncolytic targeting efficiency.
External linksJ Virol / PubMed:40704809 / PubMed Central
MethodsEM (single particle)
Resolution2.57 Å
Structure data

49228

9nbg

EMDB-49228, PDB-9nbg:
H-1 Parvovirus VLP - Glycan [s(Lex)2]
Method: EM (single particle) / Resolution: 2.57 Å

Source
  • h-1 parvovirus
KeywordsVIRUS LIKE PARTICLE / Icosahedron / Virus / Glycan / Complex / Receptor

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more