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- PDB-8tn8: Crystal structure of the murine astrovirus capsid spike at 1.75 A -

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Basic information

Entry
Database: PDB / ID: 8tn8
TitleCrystal structure of the murine astrovirus capsid spike at 1.75 A
ComponentsCapsid polyprotein VP90
KeywordsVIRAL PROTEIN / capsid / spike / attachment / homodimer
Function / homologyCapsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / Viral coat protein subunit / : / Capsid polyprotein VP90
Function and homology information
Biological speciesMurine astrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLanning, S. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI144090 United States
CitationJournal: J.Gen.Virol. / Year: 2023
Title: Structure and immunogenicity of the murine astrovirus capsid spike.
Authors: Lanning, S. / Pedicino, N. / Haley, D.J. / Hernandez, S. / Cortez, V. / DuBois, R.M.
History
DepositionAug 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5934
Polymers58,5152
Non-polymers782
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-15 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.328, 48.872, 65.463
Angle α, β, γ (deg.)93.340, 102.910, 114.700
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Capsid polyprotein VP90


Mass: 29257.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine astrovirus / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): T7 express / References: UniProt: A0A482N9T7
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.11 % / Description: Small rod shaped crystal
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: Potassium formate, PEG 3350 / PH range: 7.3-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→43.76 Å / Num. obs: 46845 / % possible obs: 94.79 % / Redundancy: 1.7 % / Biso Wilson estimate: 19.93 Å2 / CC1/2: 0.995 / Net I/σ(I): 14.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2226 / CC1/2: 0.936 / % possible all: 92.52

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→43.75 Å / SU ML: 0.1755 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.8905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.201 2293 5 %
Rwork0.1706 43571 -
obs0.1721 45864 92.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.11 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4015 0 2 322 4339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00554157
X-RAY DIFFRACTIONf_angle_d0.81895717
X-RAY DIFFRACTIONf_chiral_restr0.052599
X-RAY DIFFRACTIONf_plane_restr0.0079737
X-RAY DIFFRACTIONf_dihedral_angle_d12.45071399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.28531390.22192633X-RAY DIFFRACTION90.8
1.79-1.830.25841400.20882668X-RAY DIFFRACTION90.82
1.83-1.880.27411400.22072670X-RAY DIFFRACTION90.79
1.88-1.930.24251400.19932656X-RAY DIFFRACTION90.69
1.93-1.980.26441410.18352656X-RAY DIFFRACTION89.85
1.98-2.050.21151410.182690X-RAY DIFFRACTION91.8
2.05-2.120.21041420.18222696X-RAY DIFFRACTION91.99
2.12-2.20.22641450.18492758X-RAY DIFFRACTION92.87
2.2-2.310.20911430.18732700X-RAY DIFFRACTION93.67
2.31-2.430.20681450.17782766X-RAY DIFFRACTION93.54
2.43-2.580.22251450.18672767X-RAY DIFFRACTION94
2.58-2.780.21961470.18562772X-RAY DIFFRACTION94.83
2.78-3.060.22821470.16982794X-RAY DIFFRACTION95.05
3.06-3.50.18841450.1492752X-RAY DIFFRACTION93.94
3.5-4.410.15321480.14062818X-RAY DIFFRACTION95.37
4.41-43.750.16741450.16282775X-RAY DIFFRACTION94.99

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