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- PDB-7rk1: Crystal structure of the human astrovirus serotype 8 capsid spike... -

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Basic information

Entry
Database: PDB / ID: 7rk1
TitleCrystal structure of the human astrovirus serotype 8 capsid spike in complex with scFv 3E8, an astrovirus-neutralizing antibody, at 2.05-A resolution
Components
  • Capsid polyprotein VP70
  • scFv 3E8
KeywordsVIRAL PROTEIN / capsid protein / icosahedral virus / single chain variable fragment
Function / homology
Function and homology information


T=3 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / host extracellular space / identical protein binding
Similarity search - Function
Turkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / Viral coat protein subunit
Similarity search - Domain/homology
Capsid polyprotein VP90
Similarity search - Component
Biological speciesHuman astrovirus-8
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMeyer, L. / 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid polyprotein VP70
C: scFv 3E8
B: Capsid polyprotein VP70
D: scFv 3E8


Theoretical massNumber of molelcules
Total (without water)105,5294
Polymers105,5294
Non-polymers00
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, scFv 3E8 and Spike 8 co-elute in a 2:2 ratio
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.829, 80.429, 117.208
Angle α, β, γ (deg.)90.000, 90.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid polyprotein VP70


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 3E8


Mass: 26878.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium citrate tribasic, 18 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033184 Å / Relative weight: 1
ReflectionResolution: 2.05→80.43 Å / Num. obs: 55739 / % possible obs: 97.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 25.28 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.081 / Rrim(I) all: 0.202 / Net I/σ(I): 7.2 / Num. measured all: 337857 / Scaling rejects: 795
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
2.05-2.115.31.2682188441590.6020.6141.4152.294.8
8.94-80.436.30.07646017340.9960.0320.08217.199.8

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Processing

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

3qsq


Resolution: 2.05→66.32 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2377 1992 3.58 %
Rwork0.223 53638 -
obs0.2235 55630 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.06 Å2 / Biso mean: 32.1572 Å2 / Biso min: 13.8 Å2
Refinement stepCycle: final / Resolution: 2.05→66.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7001 0 0 335 7336
Biso mean---33.32 -
Num. residues----882
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 (%)
2.05-2.10.32361260.30753630375694
2.1-2.160.29911400.27353848398898
2.16-2.220.31231450.26963887403298
2.22-2.290.28991460.26883824397098
2.29-2.380.26921390.26023825396499
2.38-2.470.29971450.2633871401699
2.47-2.580.26931410.26463822396397
2.58-2.720.30351480.27663688383695
2.72-2.890.27031460.25283881402799
2.89-3.110.25221460.22993860400699
3.11-3.430.25761400.21853890403099
3.43-3.920.20141360.19153777391396
3.92-4.940.17031440.16363926407099
4.94-66.320.19531500.1973909405997

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