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- PDB-8ufn: Crystal Structure of neuronal HAstV VA1 capsid spike domain at 2.... -

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Basic information

Entry
Database: PDB / ID: 8ufn
TitleCrystal Structure of neuronal HAstV VA1 capsid spike domain at 2.73 A resolution
ComponentsCapsid polyprotein VP90
KeywordsVIRAL PROTEIN / Human Astrovirus / Capsid spike domain / Antigenicity
Function / homologyCapsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=3 icosahedral viral capsid / Viral coat protein subunit / clathrin-dependent endocytosis of virus by host cell / Capsid polyprotein VP90
Function and homology information
Biological speciesAstrovirus VA1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsGhosh, A. / Delgado-Cunningham, K. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI144090 United States
CitationJournal: Plos Pathog. / Year: 2024
Title: Structure and antigenicity of the divergent human astrovirus VA1 capsid spike.
Authors: Ghosh, A. / Delgado-Cunningham, K. / Lopez, T. / Green, K. / Arias, C.F. / DuBois, R.M.
History
DepositionOct 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid polyprotein VP90
B: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)69,0012
Polymers69,0012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-40 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.203, 86.315, 108.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Capsid polyprotein VP90


Mass: 34500.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Astrovirus VA1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D7P3D4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 27.5% PEG3350 / PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.73→46.04 Å / Num. obs: 15883 / % possible obs: 99.93 % / Redundancy: 13 % / Biso Wilson estimate: 44.17 Å2 / CC1/2: 0.989 / Net I/σ(I): 7.6
Reflection shellResolution: 2.73→2.86 Å / Num. unique obs: 1541 / CC1/2: 0.616

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→46.04 Å / SU ML: 0.4613 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.7654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3123 1595 9.99 %
Rwork0.2692 14363 -
obs0.2737 15876 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.92 Å2
Refinement stepCycle: LAST / Resolution: 2.73→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 0 0 0 4265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324389
X-RAY DIFFRACTIONf_angle_d0.5975985
X-RAY DIFFRACTIONf_chiral_restr0.0437652
X-RAY DIFFRACTIONf_plane_restr0.0041756
X-RAY DIFFRACTIONf_dihedral_angle_d17.77411539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.810.43621390.38471262X-RAY DIFFRACTION99.57
2.81-2.910.39891450.35871295X-RAY DIFFRACTION100
2.91-3.030.41631420.32581281X-RAY DIFFRACTION100
3.03-3.170.42081410.30161276X-RAY DIFFRACTION100
3.17-3.330.34251440.28441289X-RAY DIFFRACTION100
3.34-3.540.34441430.2731293X-RAY DIFFRACTION99.93
3.54-3.820.30241450.26361306X-RAY DIFFRACTION100
3.82-4.20.29771450.24661305X-RAY DIFFRACTION99.93
4.2-4.810.26841470.2351316X-RAY DIFFRACTION99.93
4.81-6.060.23271480.23521333X-RAY DIFFRACTION99.93
6.06-46.040.28431560.25381407X-RAY DIFFRACTION99.94

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