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- PDB-1f97: SOLUBLE PART OF THE JUNCTION ADHESION MOLECULE FROM MOUSE -

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Basic information

Entry
Database: PDB / ID: 1f97
TitleSOLUBLE PART OF THE JUNCTION ADHESION MOLECULE FROM MOUSE
ComponentsJUNCTION ADHESION MOLECULE
KeywordsCELL ADHESION / immunoglobulin superfamily / beta-sandwich fold
Function / homology
Function and homology information


Tight junction interactions / positive regulation of establishment of endothelial barrier / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / memory T cell extravasation / Integrin cell surface interactions / regulation of membrane permeability / establishment of endothelial intestinal barrier / Cell surface interactions at the vascular wall / protein localization to bicellular tight junction / actomyosin structure organization ...Tight junction interactions / positive regulation of establishment of endothelial barrier / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / memory T cell extravasation / Integrin cell surface interactions / regulation of membrane permeability / establishment of endothelial intestinal barrier / Cell surface interactions at the vascular wall / protein localization to bicellular tight junction / actomyosin structure organization / positive regulation of platelet aggregation / 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 / bicellular tight junction / epithelial cell differentiation / regulation of cytokine production / protein localization to plasma membrane / PDZ domain binding / cellular response to mechanical stimulus / integrin binding / regulation of cell shape / cell adhesion / protein homodimerization activity / protein-containing complex / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsKostrewa, D. / Brockhaus, M. / D'Arcy, A. / Dale, G. / Bazzoni, G. / Dejana, E. / Winkler, F. / Hennig, M.
CitationJournal: EMBO J. / Year: 2001
Title: X-ray structure of junctional adhesion molecule: structural basis for homophilic adhesion via a novel dimerization motif.
Authors: Kostrewa, D. / Brockhaus, M. / D'Arcy, A. / Dale, G.E. / Nelboeck, P. / Schmid, G. / Mueller, F. / Bazzoni, G. / Dejana, E. / Bartfai, T. / Winkler, F.K. / Hennig, M.
History
DepositionJul 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JUNCTION ADHESION MOLECULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8762
Polymers22,8511
Non-polymers241
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.540, 83.280, 130.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Detailshomodimer, under certain conditions a fraction of tetramer

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Components

#1: Protein JUNCTION ADHESION MOLECULE


Mass: 22851.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O88792
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% Peg 3350, 200 mM MgCl2, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
225 %PEG33501reservoir
3200 mM1reservoirMgCl2
4100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Aug 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 18966 / Num. obs: 18966 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.032 / Num. unique all: 7497 / % possible all: 68.3
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 7497 / Num. measured all: 18966
Reflection shell
*PLUS
% possible obs: 68.3 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
SHARPphasing
X-PLOR98refinement
RefinementResolution: 2.5→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 750 -10% of data
Rwork0.15 ---
all0.15 7497 --
obs0.15 7497 89.5 %-
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 1 70 1637
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
Software
*PLUS
Name: X-PLOR / Version: 98 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.15 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.3

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