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- PDB-2h2c: Crystal Structure of ZO-1 PDZ1 Bound to a Phage-Derived Ligand (W... -

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Basic information

Entry
Database: PDB / ID: 2h2c
TitleCrystal Structure of ZO-1 PDZ1 Bound to a Phage-Derived Ligand (WRRTTWV)
ComponentsTight junction protein ZO-1
KeywordsCELL ADHESION / PDZ Domain / Phage Derived High Affinity Ligand
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 / protein localization to adherens junction / 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 / 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 / protein localization to adherens junction / Regulation of gap junction activity / protein localization to bicellular tight junction / gap junction / cell-cell junction organization / Apoptotic cleavage of cell adhesion proteins / tight junction / actomyosin structure organization / podosome / Signaling by Hippo / 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 / cytoplasm / cytosol
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: 2 Å
AuthorsAppleton, B.A. / Zhang, Y. / Wu, P. / Yin, J.P. / Hunziker, W. / Skelton, N.J. / Sidhu, S.S. / Wiesmann, C.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity.
Authors: Appleton, B.A. / Zhang, Y. / Wu, P. / Yin, J.P. / Hunziker, W. / Skelton, N.J. / Sidhu, S.S. / Wiesmann, C.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: Convergent and Divergent Ligand Specificity Amongst the PDZ Domains of the LAP and ZO Families
Authors: Zhang, Y. / Yeh, S. / Appleton, B.A. / Held, H.A. / Kausalya, J.P. / Phua, D.C.Y. / Wong, W.L. / Lasky, L.A. / Wiesmann, C. / Hunziker, W. / Sidhu, S.S.
History
DepositionMay 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 30, 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)11,7251
Polymers11,7251
Non-polymers00
Water77543
1
A: Tight junction protein ZO-1

A: Tight junction protein ZO-1


Theoretical massNumber of molelcules
Total (without water)23,4502
Polymers23,4502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3290 Å2
ΔGint-18 kcal/mol
Surface area11580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)51.591, 51.591, 88.262
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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: 11725.243 Da / Num. of mol.: 1 / Fragment: First PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZO1 (TJP1) / Plasmid: pET22d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07157
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M Sodium Acetate, 2 M sodium formate, pH 4.6, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9658 / % possible obs: 99.8 % / Redundancy: 5.8 % / Rsym value: 0.059 / Χ2: 1.03 / Net I/σ(I): 29.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueΧ2% possible allRmerge(I) obs
2-2.075.54.79300.310.895100
2.07-2.155.99471.0441000.242
2.15-2.2569461.0661000.207
2.25-2.3769531.0581000.163
2.37-2.5269471.0411000.132
2.52-2.7169711.0421000.107
2.71-2.995.99541.041000.081
2.99-3.425.99811.041000.063
3.42-4.315.89791.0571000.047
4.31-505.410501.00198.50.034

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2H3M

2h3m


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.325 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 458 4.8 %RANDOM
Rwork0.209 ---
all0.21 9647 --
obs0.21 9629 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.385 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.89 Å20 Å2
2--1.79 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 0 0 43 868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021842
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9091133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6245106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.872340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04515144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.162158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02648
X-RAY DIFFRACTIONr_nbd_refined0.1920.2304
X-RAY DIFFRACTIONr_nbtor_refined0.2970.2562
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.27
X-RAY DIFFRACTIONr_mcbond_it0.6841.5539
X-RAY DIFFRACTIONr_mcangle_it1.0332834
X-RAY DIFFRACTIONr_scbond_it1.9283345
X-RAY DIFFRACTIONr_scangle_it3.1124.5299
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 36 -
Rwork0.244 654 -
obs-690 100 %
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)
10.59580.32410.03526.77653.45886.99060.1062-0.08440.07020.4034-0.1248-0.15740.4198-0.04630.0186-0.1358-0.15270.0072-0.15140.0227-0.119925.0013-0.75172.1293
27.2082-0.9299-10.00058.838-1.216524.0014-0.06480.2767-0.13060.21660.16610.37890.9173-0.593-0.1013-0.13550.0584-0.0172-0.21370.0002-0.170124.8388-9.9539-28.3692
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1114 - 1121 - 99
22113 - 120100 - 107

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