[English] 日本語
Yorodumi
- PDB-9nbg: H-1 Parvovirus VLP - Glycan [s(Lex)2] -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nbg
TitleH-1 Parvovirus VLP - Glycan [s(Lex)2]
ComponentsMajor capsid protein
KeywordsVIRUS LIKE PARTICLE / Icosahedron / Virus / Glycan / Complex / Receptor
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
3'-sialyl-N-acetyllactosamine / Major capsid protein
Similarity search - Component
Biological speciesH-1 parvovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsBusuttil, K.B. / Bennett, A.B. / McKenna, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: J Virol / Year: 2025
Title: Mapping the sialic acid-binding sites of LuIII and H-1 parvovirus.
Authors: Kevin Busuttil / Nikéa Pittman / Jon Zachary / Sujata Halder / Lorena Geilen / Amriti Singh / Adam Misseldine / Paulina Kaplonek / Paul Chipman / Jaime Heimburg-Molinaro / Peter H Seeberger ...Authors: Kevin 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 /
Abstract: 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 ...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 ...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.
History
DepositionFeb 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,785,273120
Polymers3,744,79760
Non-polymers40,47660
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
Major capsid protein


Mass: 62413.285 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) H-1 parvovirus / Production host: Baculoviridae sp. (virus) / References: UniProt: J9RQD1
#2: Polysaccharide...
N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpa1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][a-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: H-1 parvovirus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: H-1 parvovirus
Source (recombinant)Organism: Baculoviridae sp. (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1120 nm
Image recordingElectron dose: 75 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cisTEMparticle selection
2PHENIX1.10-2155_2155model refinement
5cisTEMCTF correction
13cisTEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30120 / Symmetry type: POINT

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more