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- PDB-4oeo: High resolution crystal structure of the unliganded ZO-1 PDZ1 domain -

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Basic information

Entry
Database: PDB / ID: 4oeo
TitleHigh resolution crystal structure of the unliganded ZO-1 PDZ1 domain
ComponentsTight junction protein ZO-1
KeywordsCELL ADHESION / MAGUK / PDZ1 / SCAFFOLDING / Claudin / tight junction assembly
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
ACETATE ION / Tight junction protein ZO-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNomme, J. / Lavie, A.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis of a Key Factor Regulating the Affinity between the Zonula Occludens First PDZ Domain and Claudins.
Authors: Nomme, J. / Antanasijevic, A. / Caffrey, M. / Van Itallie, C.M. / Anderson, J.M. / Fanning, A.S. / Lavie, A.
History
DepositionJan 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Tight junction protein ZO-1
C: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,92310
Polymers34,4613
Non-polymers1,4637
Water1,72996
1
A: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6423
Polymers11,4871
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2485
Polymers11,4871
Non-polymers7614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0342
Polymers11,4871
Non-polymers5471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Tight junction protein ZO-1
hetero molecules

A: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2846
Polymers22,9742
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2070 Å2
ΔGint-52 kcal/mol
Surface area8890 Å2
MethodPISA
5
B: Tight junction protein ZO-1
hetero molecules

C: Tight junction protein ZO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2817
Polymers22,9742
Non-polymers1,3075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444-x-1/2,y-1/2,-z-11
Buried area1820 Å2
ΔGint-31 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.993, 60.473, 62.217
Angle α, β, γ (deg.)90.00, 124.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-201-

12P

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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: 11486.908 Da / Num. of mol.: 3 / Fragment: PDZ1 domain, UNP residues 18-110
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 DE3 C41 / References: UniProt: Q07157
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG2K MME, 0.1 M NaAc pH4.6, 0.2 M AmSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2013
RadiationMonochromator: c111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.89→30 Å / Num. all: 24585 / Num. obs: 24585 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.028 / Net I/σ(I): 17.46
Reflection shellResolution: 1.89→2.01 Å / Mean I/σ(I) obs: 2.71 / Num. unique all: 3900 / Rsym value: 0.448 / % possible all: 94.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.248 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24282 1145 5.2 %RANDOM
Rwork0.1953 ---
obs0.19779 21085 87.09 %-
all-21085 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.904 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å2-0.9 Å2
2--2.55 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 85 96 2218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192150
X-RAY DIFFRACTIONr_bond_other_d0.0060.022056
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9322892
X-RAY DIFFRACTIONr_angle_other_deg1.2093.0154672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67423.43896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.13215288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.2721518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02528
X-RAY DIFFRACTIONr_mcbond_it2.2513.4131128
X-RAY DIFFRACTIONr_mcbond_other2.2523.4061124
X-RAY DIFFRACTIONr_mcangle_it3.1975.0931401
X-RAY DIFFRACTIONr_mcangle_other3.1965.0961402
X-RAY DIFFRACTIONr_scbond_it3.2953.9251022
X-RAY DIFFRACTIONr_scbond_other3.2983.9291015
X-RAY DIFFRACTIONr_scangle_other5.0525.7251480
X-RAY DIFFRACTIONr_long_range_B_refined6.63927.6972285
X-RAY DIFFRACTIONr_long_range_B_other6.55727.6462272
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 74 -
Rwork0.343 1280 -
obs--71.34 %

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