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- PDB-2osg: Solution Structure and Binding Property of the Domain-swapped Dim... -

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Basic information

Entry
Database: PDB / ID: 2osg
TitleSolution Structure and Binding Property of the Domain-swapped Dimer of ZO2PDZ2
ComponentsTight junction protein ZO-2
KeywordsCELL ADHESION / TIGHT JUNCTION / ZO-2 / PDZ DOMAIN / HOMODIMER / DOMAIN SWAPPING
Function / homology
Function and homology information


positive regulation of blood-brain barrier permeability / homotypic cell-cell adhesion / establishment of endothelial intestinal barrier / protein localization to cell-cell junction / guanylate kinase activity / regulation of membrane permeability / cell-cell contact zone / cell-cell junction organization / Apoptotic cleavage of cell adhesion proteins / Signaling by Hippo ...positive regulation of blood-brain barrier permeability / homotypic cell-cell adhesion / establishment of endothelial intestinal barrier / protein localization to cell-cell junction / guanylate kinase activity / regulation of membrane permeability / cell-cell contact zone / cell-cell junction organization / Apoptotic cleavage of cell adhesion proteins / Signaling by Hippo / intestinal absorption / RHOB GTPase cycle / maintenance of blood-brain barrier / RHOC GTPase cycle / RHOA GTPase cycle / bicellular tight junction / cell adhesion molecule binding / protein tyrosine kinase binding / : / adherens junction / cell-cell adhesion / protein-macromolecule adaptor activity / transmembrane transporter binding / cadherin binding / protein domain specific binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Tight junction protein ZO-2 / ZO-2, SH3 domain / Tight junction protein ZO / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain ...Tight junction protein ZO-2 / ZO-2, SH3 domain / Tight junction protein ZO / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Tight junction protein ZO-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsWu, J.W. / Yang, Y.S. / Zhang, J.H. / Ji, P. / Wu, J.H. / Shi, Y.Y.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Domain-swapped Dimerization of the Second PDZ Domain of ZO2 May Provide a Structural Basis for the Polymerization of Claudins
Authors: Wu, J.W. / Yang, Y.S. / Zhang, J.H. / Ji, P. / Du, W.J. / Jiang, P. / Xie, D.H. / Huang, H.D. / Wu, M. / Zhang, G.Z. / Wu, J.H. / Shi, Y.Y.
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tight junction protein ZO-2
B: Tight junction protein ZO-2


Theoretical massNumber of molelcules
Total (without water)18,5462
Polymers18,5462
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Tight junction protein ZO-2 / Tight junction associated protein / Zonula occludens 2 protein / Zona occludens 2 protein / Tight ...Tight junction associated protein / Zonula occludens 2 protein / Zona occludens 2 protein / Tight junction protein 2


Mass: 9272.841 Da / Num. of mol.: 2 / Fragment: ZO2PDZ2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: brain / Plasmid: pET22b (+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UDY2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1323D 15N-separated NOESY
1433D 13C-separated NOESY
1533D 13C F1-filtered,F3-edited NOESY
NMR detailsText: Intermolecular interactions were identified in a 13C/15N-filtered (F1), 13C-edited(F3) 3D NOESY spectrum

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM ZO2PDZ2 domain, 20mM phosphate buffer (pH 6.5), 50mM NaCl, 1mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
20.8mM 15N, 13C-labeled ZO2PDZ2 domain, 20mM phosphate buffer(pH 6.5), 50mM NaCl, 1mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
30.8mM 15N, 13C-labeled ZO2PDZ2 domain, 20mM phosphate buffer (pH 6.5), 50mM NaCl, 1mM EDTA, 100% D2O100% D2O
Sample conditionsIonic strength: 20mM phosphate buffer, 50mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1A.T. Brungerstructure solution
NMRPipe2.2F. Delaglio and A. Baxprocessing
MOLMOL2k.2Koradidata analysis
TALOSCornilescudata analysis
Sparky3T.D.Goddard and D.G.Knellerdata analysis
CNS1.1A.T. Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
Details: the structures are based on a total of 3076 restraints, 2916 are NOE-derived distance constraints, 160 dihedral angle restraints,76 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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