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- PDB-5ewn: Crystal structure of the human astrovirus 1 capsid protein core d... -

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Basic information

Entry
Database: PDB / ID: 5ewn
TitleCrystal structure of the human astrovirus 1 capsid protein core domain at 2.6 A resolution
ComponentsStructural proteinProtein
KeywordsVIRAL PROTEIN / virus protein / capsid protein / icosahedral virus / jelly-roll
Function / homologyTurkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, 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 speciesHuman astrovirus-1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.602 Å
AuthorsYork, R.L. / Yousefi, P.A. / Bogdanoff, W. / Haile, S. / Tripathi, S. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095369 United States
CitationJournal: J.Virol. / Year: 2015
Title: Structural, Mechanistic, and Antigenic Characterization of the Human Astrovirus Capsid.
Authors: York, R.L. / Yousefi, P.A. / Bogdanoff, W. / Haile, S. / Tripathi, S. / DuBois, R.M.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structural protein
B: Structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0626
Polymers79,9202
Non-polymers1424
Water1,53185
1
A: Structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0313
Polymers39,9601
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0313
Polymers39,9601
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.243, 71.098, 158.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsHuman astrovirus 1 capsid protein core domain forms a monomer in solution, however its biological assembly in the virus is 180 molecules in a T=3 icosahedral virus particle

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Components

#1: Protein Structural protein / Protein


Mass: 39959.922 Da / Num. of mol.: 2 / Fragment: UNP residues 80-429
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human astrovirus-1 / Plasmid: pET52b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q82452
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: PEG 6000, sodium acetate, lithium chloride

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.110.977
SYNCHROTRONALS 5.0.220.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9771
20.9791
ReflectionResolution: 2.6→48.47 Å / Num. obs: 23541 / % possible obs: 99.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 19.66
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.41 / % possible all: 98.4

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.602→48.466 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2341 1209 5.15 %
Rwork0.1919 --
obs0.1941 23493 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.602→48.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 4 85 4883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174904
X-RAY DIFFRACTIONf_angle_d1.6016696
X-RAY DIFFRACTIONf_dihedral_angle_d15.7121716
X-RAY DIFFRACTIONf_chiral_restr0.095792
X-RAY DIFFRACTIONf_plane_restr0.008844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6024-2.70650.3151280.24922319X-RAY DIFFRACTION94
2.7065-2.82970.33041230.2412437X-RAY DIFFRACTION99
2.8297-2.97890.281180.23782458X-RAY DIFFRACTION99
2.9789-3.16550.31341500.22742424X-RAY DIFFRACTION99
3.1655-3.40980.22181380.21232454X-RAY DIFFRACTION99
3.4098-3.75290.22091380.18652491X-RAY DIFFRACTION100
3.7529-4.29560.20441240.16632504X-RAY DIFFRACTION100
4.2956-5.41090.19331590.15412525X-RAY DIFFRACTION100
5.4109-48.47480.22221310.18052672X-RAY DIFFRACTION100

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