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- PDB-2h2b: Crystal Structure of ZO-1 PDZ1 Bound to a Phage-Derived Ligand (W... -

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Basic information

Entry
Database: PDB / ID: 2h2b
TitleCrystal Structure of ZO-1 PDZ1 Bound to a Phage-Derived Ligand (WRRTTYL)
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 / protein localization to cell-cell junction / establishment of endothelial intestinal barrier / regulation of cell junction assembly / protein localization to bicellular tight 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 / protein localization to cell-cell junction / establishment of endothelial intestinal barrier / regulation of cell junction assembly / protein localization to bicellular tight junction / Regulation of gap junction activity / 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 / cell-cell junction assembly / regulation of bicellular tight junction assembly / negative regulation of stress fiber assembly / apical junction complex / regulation of cytoskeleton organization / maintenance of blood-brain barrier / positive regulation of sprouting angiogenesis / 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
ACETIC ACID / Tight junction protein ZO-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7762
Polymers11,7161
Non-polymers601
Water1,964109
1
A: Tight junction protein ZO-1
hetero molecules

A: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5534
Polymers23,4322
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3170 Å2
ΔGint-12 kcal/mol
Surface area12130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.425, 52.425, 92.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-201-

ACY

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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: 11716.234 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: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium Acetate, 0.2 M Ammonium Sulfate, 30% PEG 2000 Monomethyl Ether, pH 4.6, VAPOR DIFFUSION, SITTING DROP, 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: 1.61→50 Å / Num. obs: 17606 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rsym value: 0.052 / Χ2: 1.024 / Net I/σ(I): 31.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueΧ2% possible allRmerge(I) obs
1.61-1.675.83.716900.4010.8898.4
1.67-1.736.717251.0031000.292
1.73-1.817.717281.0861000.217
1.81-1.917.717331.0721000.166
1.91-2.037.717421.0581000.114
2.03-2.197.617421.0841000.085
2.19-2.47.517611.021000.074
2.4-2.757.517691.01599.80.058
2.75-3.477.318081.0061000.046
3.47-506.919080.97197.90.034

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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: 1.6→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.734 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 898 5.1 %RANDOM
Rwork0.203 ---
all0.205 17664 --
obs0.205 17538 99.35 %-
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: 27.636 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms824 0 4 109 937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021843
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9231132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9835106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.2762340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45815145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.697158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02650
X-RAY DIFFRACTIONr_nbd_refined0.1880.2321
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.210
X-RAY DIFFRACTIONr_mcbond_it1.1811.5542
X-RAY DIFFRACTIONr_mcangle_it1.6422835
X-RAY DIFFRACTIONr_scbond_it2.5033339
X-RAY DIFFRACTIONr_scangle_it4.0494.5297
LS refinement shellResolution: 1.604→1.646 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 73 -
Rwork0.184 1143 -
obs-1216 95 %
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)
12.29780.28080.68070.84910.31620.97090.0854-0.0184-0.0397-0.02140.030.00710.0058-0.0033-0.1154-0.0549-0.0066-0.0058-0.0146-0.0123-0.05116.558514.4032-13.6384
28.30751.9776-0.27193.8073-0.72742.56220.0292-0.15770.29060.0510.20.4187-0.2339-0.2365-0.22920.00910.02150.0216-0.02140.03510.0168.358315.855214.5225
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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