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- PDB-8ep9: The capsid structure of Human Parvovirus 4 -

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Basic information

Entry
Database: PDB / ID: 8ep9
TitleThe capsid structure of Human Parvovirus 4
ComponentsHuman Parvovirus 4
KeywordsVIRUS LIKE PARTICLE / Parvovirus / Capsid / PARV4 / Tetraparvovirus / Pathogen
Function / homologyPhospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / ORF2
Function and homology information
Biological speciesHuman parvovirus 4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsMietzsch, M. / 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: Viruses / Year: 2022
Title: Capsid Structure of Aleutian Mink Disease Virus and Human Parvovirus 4: New Faces in the Parvovirus Family Portrait.
Authors: Renuk Lakshmanan / Mario Mietzsch / Alberto Jimenez Ybargollin / Paul Chipman / Xiaofeng Fu / Jianming Qiu / Maria Söderlund-Venermo / Robert McKenna /
Abstract: Parvoviruses are small, single-stranded DNA viruses with non-enveloped capsids. Determining the capsid structures provides a framework for annotating regions important to the viral life cycle. ...Parvoviruses are small, single-stranded DNA viruses with non-enveloped capsids. Determining the capsid structures provides a framework for annotating regions important to the viral life cycle. Aleutian mink disease virus (AMDV), a pathogen in minks, and human parvovirus 4 (PARV4), infecting humans, are parvoviruses belonging to the genera and , respectively. While Aleutian mink disease caused by AMDV is a major threat to mink farming, no clear clinical manifestations have been established following infection with PARV4 in humans. Here, the capsid structures of AMDV and PARV4 were determined via cryo-electron microscopy at 2.37 and 3.12 Å resolutions, respectively. Despite low amino acid sequence identities (10-30%) both viruses share the icosahedral nature of parvovirus capsids, with 60 viral proteins (VPs) assembling the capsid via two-, three-, and five-fold symmetry VP-related interactions, but display major structural variabilities in the surface loops when the capsid structures are superposed onto other parvoviruses. The capsid structures of AMDV and PARV4 will add to current knowledge of the structural platform for parvoviruses and permit future functional annotation of these viruses, which will help in understanding their infection mechanisms at a molecular level for the development of diagnostics and therapeutics.
History
DepositionOct 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,701,45060
Polymers3,701,45060
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Human Parvovirus 4


Mass: 61690.828 Da / Num. of mol.: 60 / Fragment: UNP residues 363-914
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parvovirus 4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A7J3Q7

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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: Human parvovirus 4 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human parvovirus 4
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Virus shellTriangulation number (T number): 1
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k)

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Processing

SoftwareName: PHENIX / Version: 1.10-2155_2155: / Classification: refinement
EM softwareName: cisTEM / Category: CTF correction
CTF correctionType: NONE
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5248 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.015264720
ELECTRON MICROSCOPYf_angle_d1.05362400
ELECTRON MICROSCOPYf_dihedral_angle_d14.706211380
ELECTRON MICROSCOPYf_chiral_restr0.05938580
ELECTRON MICROSCOPYf_plane_restr0.00747880

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