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- PDB-4odb: Crystal structure of the T1L reovirus attachment protein sigma1 i... -

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Basic information

Entry
Database: PDB / ID: 4odb
TitleCrystal structure of the T1L reovirus attachment protein sigma1 in complex with Junctional Adhesion Molecule-A
Components
  • Junctional adhesion molecule A
  • Outer capsid protein sigma-1
KeywordsVIRAL PROTEIN / immunoglobulin fold / greek key motif / beta spiral / viral attachment protein / capsid protein / viral receptor / cell adhesion molecule
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 / positive regulation of platelet aggregation / actomyosin structure organization / negative regulation of stress fiber assembly ...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 / positive regulation of platelet aggregation / actomyosin structure organization / negative regulation of stress fiber assembly / intestinal absorption / tight junction / regulation of bicellular tight junction assembly / leukocyte cell-cell adhesion / positive regulation of Rho protein signal transduction / maintenance of blood-brain barrier / regulation of cytoskeleton organization / bicellular tight junction / Integrin cell surface interactions / regulation of cytokine production / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Cell surface interactions at the vascular wall / protein localization to plasma membrane / regulation of actin cytoskeleton organization / PDZ domain binding / cellular response to mechanical stimulus / cell-cell adhesion / integrin binding / cell-cell junction / cell junction / viral capsid / regulation of cell shape / virus receptor activity / 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) / Adenovirus pIV-like, attachment domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-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) / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein sigma-1 / Junctional adhesion molecule A
Similarity search - Component
Biological speciesMammalian orthoreovirus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsStettner, E. / Stehle, T.
CitationJournal: To be Published
Title: The JAM-A binding site is conserved in reovirus sigma1: Structure of the T1L sigma1-JAM-A complex
Authors: Stettner, E. / Reiss, K. / Dietrich, M. / Stehle, T.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: Junctional adhesion molecule A
E: Junctional adhesion molecule A
F: Junctional adhesion molecule A


Theoretical massNumber of molelcules
Total (without water)90,9306
Polymers90,9306
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-59 kcal/mol
Surface area31920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.770, 156.770, 96.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 18791.027 Da / Num. of mol.: 3 / Fragment: Type 1 Lang sigma 1 head domain, residues 308-47
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalian orthoreovirus 1 / Strain: Lang / Gene: S1 / Plasmid: pET15-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P04506
#2: Protein Junctional adhesion molecule A / JAM-A / Junctional adhesion molecule 1 / JAM-1 / Platelet F11 receptor / Platelet adhesion molecule 1 / PAM-1


Mass: 11518.841 Da / Num. of mol.: 3 / Fragment: Ig-like V-type 1 domain, residues 28-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11R, JAM1, JCAM, UNQ264/PRO301 / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9Y624
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: 3.77 Å3/Da / Density % sol: 67.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.1 M MES, 17.1% PEG 20000, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2009
RadiationMonochromator: double-channel cut fixed-exit monochromator for X-rays in the range from 6 to 17.5 keV; vertical collimation and focussing is achieved by mirrors.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 22879 / Num. obs: 22673 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 70.01 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.8
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1643 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EOY (modified with chainsaw)

3eoy


Resolution: 3.2→40.98 Å / Cor.coef. Fo:Fc: 0.8614 / Cor.coef. Fo:Fc free: 0.8261 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 2267 10 %RANDOM
Rwork0.2109 ---
all0.2141 22861 --
obs0.2141 22669 99.16 %-
Displacement parametersBiso mean: 81.61 Å2
Refine analyzeLuzzati coordinate error obs: 0.5616 Å
Refinement stepCycle: LAST / Resolution: 3.2→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 0 0 6276
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2142SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes162HARMONIC2
X-RAY DIFFRACTIONt_gen_planes924HARMONIC5
X-RAY DIFFRACTIONt_it6435HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion852SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7194SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6435HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg8775HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion21.72
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3 -9.99 %
Rwork0.2592 2675 -
all0.2632 2972 -

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