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- PDB-2h3m: Crystal Structure of ZO-1 PDZ1 -

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Basic information

Entry
Database: PDB / ID: 2h3m
TitleCrystal Structure of ZO-1 PDZ1
ComponentsTight junction protein ZO-1
KeywordsCELL ADHESION / PDZ Domain
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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 22, 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 / 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 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
A: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7583
Polymers10,5661
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.789, 62.789, 153.531
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-111-

SO4

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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: 10565.941 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M Sodium Acetate, 0.2 M Ammonium Sulfate, 30% PEG 2000 Monomethyl Ether, pH 4.6, vapor diffusion, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 3037 / % possible obs: 99.8 % / Redundancy: 9.4 % / Rsym value: 0.076 / Χ2: 1.213 / Net I/σ(I): 34.2
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueΧ2% possible allRmerge(I) obs
2.8-2.92.62890.5440.7898
2.9-3.023000.8491000.369
3.02-3.152920.9051000.312
3.15-3.323020.9151000.219
3.32-3.532980.9671000.146
3.53-3.82901.1081000.115
3.8-4.183231.2891000.077
4.18-4.782951.5841000.062
4.78-6.023091.8931000.051
6.02-303391.57399.70.034

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2H3L

2h3l


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9 / SU B: 21.328 / SU ML: 0.366 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.294 123 4.4 %RANDOM
Rwork0.227 ---
all0.23 3058 --
obs0.23 2769 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.572 Å2
Baniso -1Baniso -2Baniso -3
1-4.18 Å22.09 Å20 Å2
2--4.18 Å20 Å2
3----6.27 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms722 0 10 0 732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021742
X-RAY DIFFRACTIONr_angle_refined_deg1.151.937997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.077593
X-RAY DIFFRACTIONr_chiral_restr0.0740.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02560
X-RAY DIFFRACTIONr_nbd_refined0.2060.2320
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.22
X-RAY DIFFRACTIONr_mcbond_it0.2641.5462
X-RAY DIFFRACTIONr_mcangle_it0.5142738
X-RAY DIFFRACTIONr_scbond_it0.8083280
X-RAY DIFFRACTIONr_scangle_it1.4054.5259
LS refinement shellResolution: 2.9→3.001 Å / Total num. of bins used: 15
RfactorNum. reflection
Rfree0.449 11
Rwork0.308 255
obs-266
Refinement TLS params.Method: refined / Origin x: 12.729 Å / Origin y: 23.2005 Å / Origin z: 12.9854 Å
111213212223313233
T0.1059 Å20.1425 Å2-0.0023 Å2-0.2042 Å20.0235 Å2--0.0563 Å2
L3.1682 °2-0.8957 °2-3.6386 °2-4.0096 °20.0181 °2--12.9972 °2
S-0.349 Å °-0.367 Å °-0.3217 Å °0.2999 Å °0.158 Å °-0.1468 Å °0.8941 Å °0.5302 Å °0.1909 Å °
Refinement TLS groupSelection: ALL

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