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- PDB-1nbq: Crystal Structure of Human Junctional Adhesion Molecule Type 1 -

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Basic information

Entry
Database: PDB / ID: 1nbq
TitleCrystal Structure of Human Junctional Adhesion Molecule Type 1
ComponentsJunctional adhesion molecule 1
KeywordsIMMUNE SYSTEM / reovirus receptor / adhesion molecule / tight junction formation / immunoglobulin superfamily
Function / homology
Function and homology information


positive regulation of establishment of endothelial barrier / memory T cell extravasation / Tight junction interactions / regulation of membrane permeability / establishment of endothelial intestinal barrier / protein localization to bicellular tight junction / actomyosin structure organization / positive regulation of platelet aggregation / tight junction / intestinal absorption ...positive regulation of establishment of endothelial barrier / memory T cell extravasation / Tight junction interactions / regulation of membrane permeability / establishment of endothelial intestinal barrier / protein localization to bicellular tight junction / actomyosin structure organization / positive regulation of platelet aggregation / tight junction / intestinal absorption / negative regulation of stress fiber assembly / 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 / protein localization to plasma membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / PDZ domain binding / Cell surface interactions at the vascular wall / regulation of actin cytoskeleton organization / cell-cell adhesion / cellular response to mechanical stimulus / integrin binding / cell junction / cell-cell junction / regulation of cell shape / virus receptor activity / cadherin binding / inflammatory response / protein homodimerization activity / protein-containing complex / extracellular exosome / plasma membrane
Similarity search - Function
Junctional adhesion molecule A / 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. ...Junctional adhesion molecule A / 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
Junctional adhesion molecule A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsProta, A.E. / Campbell, J.A. / Schelling, P. / Forrest, J.C. / Watson, M.J. / Peters, T.R. / Aurrand-Lions, M. / Imhof, B.A. / Dermody, T.S. / Stehle, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of human junctional adhesion molecule 1: Implications for reovirus binding
Authors: Prota, A.E. / Campbell, J.A. / Schelling, P. / Forrest, J.C. / Watson, M.J. / Peters, T.R. / Aurrand-Lions, M. / Imhof, B.A. / Dermody, T.S. / Stehle, T.
History
DepositionDec 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / refine / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Junctional adhesion molecule 1
B: Junctional adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)45,4062
Polymers45,4062
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.8, 61.8, 82.9
Angle α, β, γ (deg.)90.0, 120.01, 90.0
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein Junctional adhesion molecule 1 / JAM / Platelet adhesion molecule 1 / PAM-1 / Platelet F11 receptor


Mass: 22703.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y624
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, isopropanol, sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
216 %PEG60001reservoir
318 %isopropanol1reservoir
40.1 Msodium citrate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONNSLS X2521.1
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 2, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1monochromator at X25SINGLE WAVELENGTHMx-ray1
2monochromator at X25SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 11454 / Num. obs: 9736 / % possible obs: 85.1 % / Observed criterion σ(I): 3
Reflection shellResolution: 2.9→3.1 Å / % possible all: 51
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / Num. measured all: 27850 / Rmerge(I) obs: 0.114
Reflection shell
*PLUS
% possible obs: 51 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.305 970 -random
Rwork0.22 ---
obs0.2201 9736 10 %-
all-11454 --
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 0 124 3299
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg2.7
Refinement
*PLUS
Highest resolution: 2.9 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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