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- PDB-1kke: Crystal Structure of Reovirus Attachment Protein Sigma1 Trimer -

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Basic information

Entry
Database: PDB / ID: 1kke
TitleCrystal Structure of Reovirus Attachment Protein Sigma1 Trimer
ComponentsSIGMA 1 PROTEIN
KeywordsVIRAL PROTEIN / reovirus / sigma1 / fiber / beta-spiral / beta-barrel / trimer / receptor-binding
Function / homology
Function and homology information


viral outer capsid / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
reovirus attachment protein sigma1; domain 1 / Virus attachment protein , globular domain / Viral attachment sigma 1, reoviral / Reovirus viral attachment protein sigma 1 / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Laminin / Ribbon / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein sigma-1
Similarity search - Component
Biological speciesMammalian orthoreovirus 3
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.6 Å
AuthorsChappell, J.D. / Prota, A.E. / Dermody, T.S. / Stehle, T.
CitationJournal: EMBO J. / Year: 2002
Title: Crystal structure of reovirus attachment protein sigma1 reveals evolutionary relationship to adenovirus fiber.
Authors: Chappell, J.D. / Prota, A.E. / Dermody, T.S. / Stehle, T.
History
DepositionDec 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: SIGMA 1 PROTEIN
B: SIGMA 1 PROTEIN
C: SIGMA 1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)68,0623
Polymers68,0623
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-82 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.7, 89.0, 119.8
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains a biologically active trimer

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Components

#1: Protein SIGMA 1 PROTEIN / HEMAGGLUTININ / CELL ATTACHMENT PROTEIN / MINOR OUTER CAPSID PROTEIN


Mass: 22687.412 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalian orthoreovirus 3 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: type 3 strain dearing / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03528
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, Isopropanol, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
210 %isopropanol1reservoir
320 %PEG40001reservoir
4100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.541789 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2001 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541789 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 17954 / Num. obs: 16338 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.2 / % possible all: 64
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 91 % / Num. measured all: 56260
Reflection shell
*PLUS
% possible obs: 64 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.6→20 Å / σ(F): 1
Stereochemistry target values: xplor parameter set (Engh & Huber)
RfactorNum. reflectionSelection details
Rfree0.232 817 statistical selection
Rwork0.172 --
all-17954 -
obs-16338 -
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4710 0 0 189 4899
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.4
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor all: 0.172 / Rfactor Rfree: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.4

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