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

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ID or keywords:

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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: To Be Published
Title: Mapping the Sialic Acid Binding Sites of LuIII and H-1 Parvovirus
Authors: Busuttil, K.B. / Bennett, A.B.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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)

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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

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