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- PDB-7rk2: Crystal structure of the human astrovirus serotype 8 capsid spike... -

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Basic information

Entry
Database: PDB / ID: 7rk2
TitleCrystal structure of the human astrovirus serotype 8 capsid spike in complex with scFv 2D9, an astrovirus-neutralizing antibody, at 2.65-A resolution
Components
  • Capsid protein VP25
  • scFv 2D9
KeywordsVIRAL PROTEIN / Capsid protein / Icosahedral virus / Single chain variable fragment
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 / identical protein binding / Capsid polyprotein VP90
Function and homology information
Biological speciesHuman astrovirus-8
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMeyer, L. / Cuellar, C. / 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: J.Virol. / Year: 2022
Title: Structures of Two Human Astrovirus Capsid/Neutralizing Antibody Complexes Reveal Distinct Epitopes and Inhibition of Virus Attachment to Cells.
Authors: Ricemeyer, L. / Aguilar-Hernandez, N. / Lopez, T. / Espinosa, R. / Lanning, S. / Mukherjee, S. / Cuellar, C. / Lopez, S. / Arias, C.F. / DuBois, R.M.
History
DepositionJul 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP25
B: Capsid protein VP25
C: scFv 2D9
D: scFv 2D9


Theoretical massNumber of molelcules
Total (without water)104,9574
Polymers104,9574
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, scFv 2D9 and Spike 8 co-elute in a 2:2 ratio
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.592, 97.340, 208.307
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Capsid protein VP25


Mass: 25886.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human astrovirus-8 / Gene: ORF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9IFX1
#2: Antibody scFv 2D9


Mass: 26592.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 16 % PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 9, 2018
RadiationMonochromator: Si(111) Khozu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.65→208.31 Å / Num. obs: 30304 / % possible obs: 100 % / Redundancy: 76.5 % / Biso Wilson estimate: 42.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.451 / Rpim(I) all: 0.051 / Rrim(I) all: 0.454 / Net I/σ(I): 16 / Num. measured all: 2317578 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.65-2.7866.63.87726431139680.6920.4713.907299.8
8.79-208.3169.20.0886692696710.0110.08943100

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimless0.7.4data scaling
PHENIXphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QSQ

3qsq


Resolution: 2.65→104.15 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 1998 6.61 %
Rwork0.2182 28213 -
obs0.2201 30211 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.99 Å2 / Biso mean: 40.0268 Å2 / Biso min: 15.4 Å2
Refinement stepCycle: final / Resolution: 2.65→104.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6922 0 0 150 7072
Biso mean---35.52 -
Num. residues----883
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.720.38621390.34351965210499
2.72-2.790.3171420.304819832125100
2.79-2.870.28591400.271919882128100
2.87-2.960.30381390.244919712110100
2.96-3.070.24611400.247819802120100
3.07-3.190.28221400.250419812121100
3.19-3.340.31031430.249820132156100
3.34-3.510.26141410.223619982139100
3.51-3.740.21961420.203319942136100
3.74-4.020.24291430.205820172160100
4.02-4.430.20311440.185520272171100
4.43-5.070.18191440.162220342178100
5.07-6.390.23621470.199820812228100
6.39-104.150.24991540.21921812335100

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