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- PDB-4yg3: Structural basis of glycan recognition in neonate-specific rotaviruses -

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Basic information

Entry
Database: PDB / ID: 4yg3
TitleStructural basis of glycan recognition in neonate-specific rotaviruses
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / rotavirus / structural biology / glycan
Function / homology
Function and homology information


host cell rough endoplasmic reticulum / permeabilization of host organelle membrane involved in viral entry into host cell / host cytoskeleton / viral outer capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein VP4 / Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.285 Å
AuthorsHu, L. / Prasad, B.V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI36040 United States
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis of glycan specificity in neonate-specific bovine-human reassortant rotavirus.
Authors: Hu, L. / Ramani, S. / Czako, R. / Sankaran, B. / Yu, Y. / Smith, D.F. / Cummings, R.D. / Estes, M.K. / Venkataram Prasad, B.V.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3524
Polymers18,0641
Non-polymers2883
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-23 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.812, 64.734, 36.752
Angle α, β, γ (deg.)90.00, 114.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer capsid protein VP4 / Hemagglutinin


Mass: 18063.570 Da / Num. of mol.: 1 / Fragment: UNP residues 65-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35746, UniProt: A2T3T2*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.72 Å3/Da / Density % sol: 28.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris, 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2014
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / Num. obs: 5508 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 10.8
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 5.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YFW

4yfw


Resolution: 2.285→29.643 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 250 4.54 %
Rwork0.184 --
obs0.1866 5504 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.285→29.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 15 81 1369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031316
X-RAY DIFFRACTIONf_angle_d0.7011806
X-RAY DIFFRACTIONf_dihedral_angle_d11.809455
X-RAY DIFFRACTIONf_chiral_restr0.028197
X-RAY DIFFRACTIONf_plane_restr0.002238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.285-2.87820.28681220.2162614X-RAY DIFFRACTION98
2.8782-29.6450.22031280.16892640X-RAY DIFFRACTION98

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