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- PDB-3tsw: crystal structure of the PDZ3-SH3-GUK core module of Human ZO-1 -

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Basic information

Entry
Database: PDB / ID: 3tsw
Titlecrystal structure of the PDZ3-SH3-GUK core module of Human ZO-1
ComponentsTight junction protein ZO-1
KeywordsCELL ADHESION / PDZ3-SH3-GUK domains / 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 / 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 / SH3 Domains / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tight junction protein ZO-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.847 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 ...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
B: Tight junction protein ZO-1
C: Tight junction protein ZO-1
D: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,31611
Polymers178,6444
Non-polymers6727
Water1,26170
1
A: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8533
Polymers44,6611
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8533
Polymers44,6611
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7572
Polymers44,6611
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8533
Polymers44,6611
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-25 kcal/mol
Surface area52440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.634, 100.634, 182.516
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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: 44660.914 Da / Num. of mol.: 4 / Fragment: PDZ3-SH3-GUK (UNP Residues 417-803)
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.2M AmSO4, 0.1M NaAc pH 5.0, 60mM NaF, VAPOR DIFFUSION, HANGING 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: Nov 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
111.000H, 1.000K, L10.508
11-1.000H, 1.000H+1.000K, -L20.492
ReflectionResolution: 2.83→87.17 Å / Num. all: 47918 / Num. obs: 47918 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.08
Reflection shellResolution: 2.83→3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 1.87 / Num. unique all: 6860 / % possible all: 86.9

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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: 2.847→87.17 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.882 / SU B: 8.787 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28972 4709 10.1 %RANDOM
Rwork0.21054 ---
all0.21848 41930 --
obs0.21848 41930 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.427 Å2
Baniso -1Baniso -2Baniso -3
1-25.4 Å20 Å20 Å2
2--25.4 Å20 Å2
3----50.79 Å2
Refinement stepCycle: LAST / Resolution: 2.847→87.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8532 0 35 70 8637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228710
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.96811745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.90851052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.94823.888427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.344151592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6971576
X-RAY DIFFRACTIONr_chiral_restr0.1040.21290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216540
X-RAY DIFFRACTIONr_mcbond_it0.4851.55275
X-RAY DIFFRACTIONr_mcangle_it0.90628502
X-RAY DIFFRACTIONr_scbond_it1.19533435
X-RAY DIFFRACTIONr_scangle_it2.0034.53243
LS refinement shellResolution: 2.847→2.921 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 246 -
Rwork0.243 2064 -
obs--64.2 %

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