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- PDB-3tsv: crystal structure of the third PDZ domain of the human ZO-1 MAGUK... -

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Basic information

Entry
Database: PDB / ID: 3tsv
Titlecrystal structure of the third PDZ domain of the human ZO-1 MAGUK protein
ComponentsTight junction protein ZO-1
KeywordsCELL ADHESION / PDZ / Scaffolding / JAM / Tight junction
Function / homology
Function and homology information


positive regulation of blood-brain barrier permeability / adherens junction maintenance / positive regulation of cell-cell adhesion mediated by cadherin / RUNX1 regulates expression of components of tight junctions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of endothelial intestinal barrier / protein localization to cell-cell junction / regulation of cell junction assembly / Regulation of gap junction activity / protein localization to bicellular tight junction ...positive regulation of blood-brain barrier permeability / adherens junction maintenance / positive regulation of cell-cell adhesion mediated by cadherin / RUNX1 regulates expression of components of tight junctions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of endothelial intestinal barrier / protein localization to cell-cell junction / regulation of cell junction assembly / Regulation of gap junction activity / protein localization to bicellular tight junction / protein localization to adherens junction / gap junction / cell-cell junction organization / actomyosin structure organization / Apoptotic cleavage of cell adhesion proteins / podosome / Signaling by Hippo / tight junction / regulation of bicellular tight junction assembly / cell-cell junction assembly / negative regulation of stress fiber assembly / apical junction complex / maintenance of blood-brain barrier / positive regulation of sprouting angiogenesis / regulation of cytoskeleton organization / bicellular tight junction / cell adhesion molecule binding / cell projection / adherens junction / cell-cell adhesion / apical part of cell / cell junction / actin cytoskeleton organization / basolateral plasma membrane / calmodulin binding / positive regulation of cell migration / cadherin binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein-containing complex / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tight junction protein ZO-1 / ZO-1, SH3 domain / Tight junction protein ZO / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain ...Tight junction protein ZO-1 / ZO-1, SH3 domain / Tight junction protein ZO / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / 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-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.989 Å
AuthorsNomme, J. / Lavie, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Src Homology 3 Domain Is Required for Junctional Adhesion Molecule Binding to the Third PDZ Domain of the Scaffolding Protein ZO-1.
Authors: Nomme, J. / Fanning, A.S. / Caffrey, M. / Lye, M.F. / Anderson, J.M. / Lavie, A.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Sep 13, 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

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Assembly

Deposited unit
A: Tight junction protein ZO-1


Theoretical massNumber of molelcules
Total (without water)13,7111
Polymers13,7111
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.497, 45.117, 59.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13710.578 Da / Num. of mol.: 1 / Fragment: PDZ3 domain (UNP Residues 417-516)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TJP1, ZO1 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(C41) / References: UniProt: Q07157
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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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: 1.69 Å3/Da / Density % sol: 27.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 25% PEG 1500, 0.1M MMT, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.989→35.98 Å / Num. all: 6649 / Num. obs: 6649 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.1
Reflection shellResolution: 1.989→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.1 / Num. unique all: 995 / % possible all: 93.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LH5

3lh5


Resolution: 1.989→35.98 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.19 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31526 663 10 %RANDOM
Rwork0.26858 ---
all0.27326 5970 --
obs0.27326 5970 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.873 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20 Å2
2--1.18 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.989→35.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms721 0 0 32 753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022728
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.997977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.928592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91424.84833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29115141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.73156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02530
X-RAY DIFFRACTIONr_mcbond_it0.6061.5458
X-RAY DIFFRACTIONr_mcangle_it1.1222735
X-RAY DIFFRACTIONr_scbond_it1.3473270
X-RAY DIFFRACTIONr_scangle_it2.3674.5242
LS refinement shellResolution: 1.989→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 46 -
Rwork0.398 384 -
obs--85.83 %

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