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- PDB-2rcz: Structure of the second PDZ domain of ZO-1 -

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Basic information

Entry
Database: PDB / ID: 2rcz
TitleStructure of the second PDZ domain of ZO-1
ComponentsTight junction protein ZO-1
KeywordsPROTEIN BINDING / PDZ / domain-swapping / Cell junction / Membrane / Phosphorylation / SH3 domain / 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 / ameloblast differentiation / 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 ...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 / ameloblast differentiation / 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 / actomyosin structure organization / cell-cell junction organization / Apoptotic cleavage of cell adhesion proteins / tight junction / Signaling by Hippo / cell-cell junction assembly / regulation of bicellular tight junction assembly / podosome / 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 / cell junction / apical part of cell / 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 / molecular replacement / Resolution: 1.7 Å
AuthorsLavie, A. / Lye, M.F.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Domain swapping within PDZ2 is responsible for dimerization of ZO proteins.
Authors: Fanning, A.S. / Lye, M.F. / Anderson, J.M. / Lavie, A.
History
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Tight junction protein ZO-1
B: Tight junction protein ZO-1


Theoretical massNumber of molelcules
Total (without water)18,0072
Polymers18,0072
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.750, 33.610, 91.040
Angle α, β, γ (deg.)90.000, 103.640, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 9003.305 Da / Num. of mol.: 2 / Fragment: PDZ2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TJP1, ZO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07157
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M Phosphate-citrate, pH 4.2 and 40 % v/v PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→18.8 Å / Num. obs: 15592 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.327 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.80.55848937244099.8
1.8-1.90.3775.47140193799.6
1.9-20.1887.45910160699.5
2-2.50.08710.517230466599.7
2.5-30.09815.513261209699.9
3-40.07619.410539165999.9
4-60.06919.7470588499.3
6-100.0718.1117826189.1
10-150.094161113352.4
150.07613.6211140.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.4 Å
Translation2.5 Å29.4 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→18.8 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.337 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1551 10 %RANDOM
Rwork0.204 ---
obs0.209 15583 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.103 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0.05 Å2
2---0.16 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 0 103 1302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221203
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9811611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.765158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97625.45544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22515246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.681157
X-RAY DIFFRACTIONr_chiral_restr0.1040.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02833
X-RAY DIFFRACTIONr_nbd_refined0.2040.2452
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2816
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.210
X-RAY DIFFRACTIONr_mcbond_it1.2051.5809
X-RAY DIFFRACTIONr_mcangle_it1.80121257
X-RAY DIFFRACTIONr_scbond_it2.853425
X-RAY DIFFRACTIONr_scangle_it4.7434.5354
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 116 -
Rwork0.215 1019 -
all-1135 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6838-1.79620.96766.6214-4.97625.2035-0.00870.15620.20330.12710.20380.135-0.1967-0.1222-0.195-0.05030.0306-0.0075-0.00830.01350.0441-4.88337.18710.965
21.47780.5908-0.39982.4567-1.57174.83310.0175-0.2165-0.12270.0063-0.1122-0.0665-0.0879-0.00030.0947-0.03580.0915-0.00820.0502-0.0058-0.0257-1.22718.45431.706
31.1127-0.05140.14162.2457-2.78324.44280.0656-0.289-0.09610.0953-0.09260.00250.04880.2270.0270.00170.0863-0.00010.04740.01060.00250.63317.1131.981
42.1231-0.41210.19333.6777-1.53262.6721-0.06220.17610.01020.07620.07120.0112-0.00290.0695-0.009-0.07790.04910.0192-0.0248-0.01730.029-2.18734.88211.995
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA184 - 2091 - 26
2X-RAY DIFFRACTION2AA210 - 26227 - 79
3X-RAY DIFFRACTION3BB184 - 2091 - 26
4X-RAY DIFFRACTION4BB210 - 26427 - 81

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