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- PDB-3shu: Crystal structure of ZO-1 PDZ3 -

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Basic information

Entry
Database: PDB / ID: 3shu
TitleCrystal structure of ZO-1 PDZ3
ComponentsTight junction protein ZO-1
KeywordsCELL ADHESION / PDZ
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: 2.75 Å
AuthorsYu, J. / Pan, L. / Chen, J. / Yu, H. / Zhang, M.
CitationJournal: To be Published
Title: The Structure of the PDZ3-SH3-GuK Tandem of ZO-1 Suggests a Supramodular Organization of the Conserved MAGUK Family Scaffold Core
Authors: Pan, L. / Chen, J. / Yu, J. / Yu, H. / Zhang, M.
History
DepositionJun 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Tight junction protein ZO-1


Theoretical massNumber of molelcules
Total (without water)20,7622
Polymers20,7622
Non-polymers00
Water90150
1
A: Tight junction protein ZO-1


Theoretical massNumber of molelcules
Total (without water)10,3811
Polymers10,3811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tight junction protein ZO-1


Theoretical massNumber of molelcules
Total (without water)10,3811
Polymers10,3811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.030, 76.840, 39.110
Angle α, β, γ (deg.)90.00, 113.04, 90.00
Int Tables number4
Space group name H-MP1211

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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: 10380.932 Da / Num. of mol.: 2 / Fragment: PDZ3 domain, UNP residues 421-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q07157
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 4000, 10% (v/v) 2-Propanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2009
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→76.84 Å / Num. all: 4871 / Num. obs: 4871 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 6
Reflection shellHighest resolution: 2.75 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→38.42 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.862 / SU B: 35.63 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26385 489 9.8 %RANDOM
Rwork0.21493 ---
obs0.21991 4504 99.84 %-
all-4871 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.157 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å2-0.52 Å2
2---1.66 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.75→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 0 50 1500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221464
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2542.0031966
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.10124.76965
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14415280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5351512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211080
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1971.5928
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17721486
X-RAY DIFFRACTIONr_scbond_it1.8973536
X-RAY DIFFRACTIONr_scangle_it3.4694.5480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 35 -
Rwork0.267 324 -
obs--99.72 %
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)
15.20141.1960.13192.0190.77631.1643-0.0513-0.1942-0.0947-0.09230.0592-0.0486-0.1705-0.1316-0.00790.17210.0153-0.05680.15180.02420.0299.544-13.5515.203
21.3933-0.0709-1.23161.8771.74085.1141-0.00610.0271-0.0290.0572-0.002-0.07620.1555-0.15350.00810.14050.0169-0.10330.11080.01860.09862.0557.6371.974
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 96
2X-RAY DIFFRACTION2B3 - 97

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