9NBG | pdb_00009nbg

H-1 Parvovirus VLP - Glycan [s(Lex)2]


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mapping the sialic acid-binding sites of LuIII and H-1 parvovirus.

Busuttil, K.Pittman, N.Zachary, J.Halder, S.Geilen, L.Singh, A.Misseldine, A.Kaplonek, P.Chipman, P.Heimburg-Molinaro, J.Seeberger, P.H.Mietzsch, M.Bennett, A.D.McKenna, R.

(2025) J Virol 99: e0029725-e0029725

  • DOI: https://doi.org/10.1128/jvi.00297-25
  • Primary Citation of Related Structures:  
    9NBG

  • PubMed 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 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. 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.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein559H-1 parvovirusMutation(s): 0 
UniProt
Find proteins for P03136 (Hamster parvovirus H1)
Explore P03136 
Go to UniProtKB:  P03136
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03136
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AC [auth aA],
AD [auth DB],
BC [auth bA],
BD [auth EB],
CC [auth dA],
AC [auth aA],
AD [auth DB],
BC [auth bA],
BD [auth EB],
CC [auth dA],
CD [auth GB],
DC [auth eA],
DD [auth HB],
EC [auth gA],
ED [auth JB],
FC [auth hA],
FD [auth KB],
GC [auth jA],
GD [auth MB],
HC [auth kA],
HD [auth NB],
IB [auth 9],
IC [auth mA],
ID [auth PB],
JB [auth AA],
JC [auth nA],
JD [auth QB],
KB [auth CA],
KC [auth pA],
KD [auth SB],
LB [auth DA],
LC [auth qA],
LD [auth TB],
MB [auth FA],
MC [auth sA],
MD [auth VB],
NB [auth GA],
NC [auth tA],
ND [auth WB],
OB [auth IA],
OC [auth vA],
OD [auth YB],
PB [auth JA],
PC [auth wA],
PD [auth ZB],
QB [auth LA],
QC [auth yA],
RB [auth MA],
RC [auth zA],
SB [auth OA],
SC [auth 1A],
TB [auth PA],
TC [auth 2A],
UB [auth RA],
UC [auth 4A],
VB [auth SA],
VC [auth 5A],
WB [auth UA],
WC [auth 7A],
XB [auth VA],
XC [auth 8A],
YB [auth XA],
YC [auth AB],
ZB [auth YA],
ZC [auth BB]
3N/A
Glycosylation Resources
GlyTouCan:  G57474XD
GlyCosmos:  G57474XD
GlyGen:  G57474XD
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_900067
Query on PRD_900067
AC [auth 1A]
AD [auth 2A]
BC [auth 4A]
BD [auth 5A]
CC [auth 7A]
AC [auth 1A],
AD [auth 2A],
BC [auth 4A],
BD [auth 5A],
CC [auth 7A],
CD [auth 8A],
DC [auth 9],
DD [auth AA],
EC [auth AB],
ED [auth BB],
FC [auth CA],
FD [auth DA],
GC [auth DB],
GD [auth EB],
HC [auth FA],
HD [auth GA],
IB [auth GB],
IC [auth HB],
ID [auth IA],
JB [auth JA],
JC [auth JB],
JD [auth KB],
KB [auth LA],
KC [auth MA],
KD [auth MB],
LB [auth NB],
LC [auth OA],
LD [auth PA],
MB [auth PB],
MC [auth QB],
MD [auth RA],
NB [auth SA],
NC [auth SB],
ND [auth TB],
OB [auth UA],
OC [auth VA],
OD [auth VB],
PB [auth WB],
PC [auth XA],
PD [auth YA],
QB [auth YB],
QC [auth ZB],
RB [auth aA],
RC [auth bA],
SB [auth dA],
SC [auth eA],
TB [auth gA],
TC [auth hA],
UB [auth jA],
UC [auth kA],
VB [auth mA],
VC [auth nA],
WB [auth pA],
WC [auth qA],
XB [auth sA],
XC [auth tA],
YB [auth vA],
YC [auth wA],
ZB [auth yA],
ZC [auth zA]
3'-sialyl-N-acetyllactosamineOligosaccharide / Substrate analog
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.10-2155_2155
RECONSTRUCTIONcisTEM

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM082946

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release
  • Version 1.1: 2026-02-25
    Changes: Data collection, Database references