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- PDB-3eoy: Structure of Reovirus sigma1 in Complex with Its Receptor Junctio... -

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Basic information

Entry
Database: PDB / ID: 3eoy
TitleStructure of Reovirus sigma1 in Complex with Its Receptor Junctional Adhesion Molecule-A
Components
  • Junctional adhesion molecule A
  • Outer capsid protein sigma-1
KeywordsVIRAL PROTEIN/CELL ADHESION / protein complex / virus receptor complex / beta-barrel / beta-spiral repeat / greek key motif / trimer / immunoglobulin superfamily / VIRAL PROTEIN-CELL ADHESION COMPLEX
Function / homology
Function and homology information


positive regulation of establishment of endothelial barrier / memory T cell extravasation / Tight junction interactions / establishment of endothelial intestinal barrier / regulation of membrane permeability / viral outer capsid / protein localization to bicellular tight junction / actomyosin structure organization / positive regulation of platelet aggregation / tight junction ...positive regulation of establishment of endothelial barrier / memory T cell extravasation / Tight junction interactions / establishment of endothelial intestinal barrier / regulation of membrane permeability / viral outer capsid / protein localization to bicellular tight junction / actomyosin structure organization / positive regulation of platelet aggregation / tight junction / regulation of bicellular tight junction assembly / intestinal absorption / negative regulation of stress fiber assembly / regulation of cytoskeleton organization / positive regulation of Rho protein signal transduction / leukocyte cell-cell adhesion / maintenance of blood-brain barrier / bicellular tight junction / Integrin cell surface interactions / regulation of cytokine production / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / PDZ domain binding / protein localization to plasma membrane / regulation of actin cytoskeleton organization / Cell surface interactions at the vascular wall / cell-cell adhesion / cellular response to mechanical stimulus / cell-cell junction / integrin binding / virus receptor activity / cell junction / regulation of cell shape / cell adhesion / cadherin binding / inflammatory response / symbiont entry into host cell / virion attachment to host cell / protein homodimerization activity / protein-containing complex / extracellular exosome / plasma membrane
Similarity search - Function
Junctional adhesion molecule A / 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 / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...Junctional adhesion molecule A / 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 / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein sigma-1 / Junctional adhesion molecule A
Similarity search - Component
Biological speciesreovirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsKirchner, E. / Guglielmi, K.M. / Dermody, T.S. / Stehle, T.
CitationJournal: Plos Pathog. / Year: 2008
Title: Structure of reovirus sigma1 in complex with its receptor junctional adhesion molecule-A
Authors: Kirchner, E. / Guglielmi, K.M. / Strauss, H.M. / Dermody, T.S. / Stehle, T.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer capsid protein sigma-1
B: Outer capsid protein sigma-1
C: Outer capsid protein sigma-1
D: Outer capsid protein sigma-1
E: Outer capsid protein sigma-1
F: Outer capsid protein sigma-1
G: Junctional adhesion molecule A
H: Junctional adhesion molecule A
I: Junctional adhesion molecule A
J: Junctional adhesion molecule A
K: Junctional adhesion molecule A
L: Junctional adhesion molecule A


Theoretical massNumber of molelcules
Total (without water)176,63912
Polymers176,63912
Non-polymers00
Water0
1
A: Outer capsid protein sigma-1
B: Outer capsid protein sigma-1
C: Outer capsid protein sigma-1
G: Junctional adhesion molecule A
H: Junctional adhesion molecule A
I: Junctional adhesion molecule A


Theoretical massNumber of molelcules
Total (without water)88,3206
Polymers88,3206
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Outer capsid protein sigma-1
E: Outer capsid protein sigma-1
F: Outer capsid protein sigma-1
J: Junctional adhesion molecule A
K: Junctional adhesion molecule A
L: Junctional adhesion molecule A


Theoretical massNumber of molelcules
Total (without water)88,3206
Polymers88,3206
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.940, 124.340, 130.659
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Outer capsid protein sigma-1 / Sigma1 / Hemagglutinin / Cell attachment protein


Mass: 17921.033 Da / Num. of mol.: 6 / Fragment: head domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) reovirus / Strain: TYPE 3/STRAIN DEARING / Gene: S1 / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P03528
#2: Protein
Junctional adhesion molecule A / JAM-A / Junctional adhesion molecule 1 / JAM-1 / Platelet adhesion molecule 1 / PAM-1 / Platelet F11 receptor


Mass: 11518.841 Da / Num. of mol.: 6 / Fragment: D1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q9Y624
Sequence detailsTHIS SEQUENCE IS BASED ON REFERENCE 8 IN UNP DATABASE, P03528.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.51 % / Mosaicity: 1.39 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1 M CHES, 30% PEG 3350, streak seeding, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91988 Å
DetectorType: MAR225 CCD / Detector: CCD / Date: Mar 26, 2007
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91988 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. all: 21974 / Num. obs: 21974 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.163 / Χ2: 0.988 / Net I/σ(I): 6.933
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1669 / Χ2: 0.488 / % possible all: 69.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2OJ5 and 1NBQ

2oj5

1nbq


Resolution: 3.4→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2187 9 %random
Rwork0.21 ---
all0.21 21954 --
obs0.21 21954 90.2 %-
Solvent computationBsol: 28.443 Å2
Displacement parametersBiso max: 120.71 Å2 / Biso mean: 62.229 Å2 / Biso min: 29.54 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12227 0 0 0 12227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.543
LS refinement shellResolution: 3.4→3.52 Å
RfactorNum. reflection% reflection
Rfree0.328 178 -
Rwork0.284 --
obs-1668 69.7 %
Xplor fileSerial no: 1 / Param file: protein_rep.param

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