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- PDB-3lh5: Crystal Structure of the SH3-Guanylate kinase core domain of ZO-1 -

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Basic information

Entry
Database: PDB / ID: 3lh5
TitleCrystal Structure of the SH3-Guanylate kinase core domain of ZO-1
ComponentsTight junction protein ZO-1
KeywordsPROTEIN BINDING / ZO-1 / SH3-Guanylate kinase / Intramolecular fold / Cell junction / Cell membrane / Membrane / Phosphoprotein / SH3 domain / 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 / regulation of bicellular tight junction assembly / cell-cell junction assembly / negative regulation of stress fiber assembly / regulation of cytoskeleton organization / apical junction complex / 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. / 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 / MIRAS / Resolution: 2.6 Å
AuthorsLye, M.F. / Lavie, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Insights into regulated ligand binding sites from the structure of ZO-1 Src homology 3-guanylate kinase module.
Authors: Lye, M.F. / Fanning, A.S. / Su, Y. / Anderson, J.M. / Lavie, A.
History
DepositionJan 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)29,0471
Polymers29,0471
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.800, 125.800, 35.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Tight junction protein ZO-1 / / Zonula occludens protein 1 / Zona occludens protein 1 / Tight junction protein 1


Mass: 29047.043 Da / Num. of mol.: 1 / Fragment: UNP residues 516-588, 626-803
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q07157
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 7% isopropanol, 15-20% PEG3350, 1-5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 25, 2008
RadiationProtocol: MIRAS / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 10199 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rsym value: 0.085 / Net I/σ(I): 15.5
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.085 / % possible all: 58.8

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Phasing

PhasingMethod: MIRAS

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MIRAS / Resolution: 2.6→27.24 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.036 / SU ML: 0.252 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.901 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28545 1010 9.9 %RANDOM
Rwork0.20528 ---
obs0.21288 9187 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.391 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å20 Å2
2---0.3 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.6→27.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 0 73 2099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222070
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9462795
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.325246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1423.551107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.94315372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1121519
X-RAY DIFFRACTIONr_chiral_restr0.0810.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021584
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2892
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21375
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5431.51273
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87921995
X-RAY DIFFRACTIONr_scbond_it1.3713909
X-RAY DIFFRACTIONr_scangle_it2.2424.5800
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 71 -
Rwork0.271 694 -
obs--100 %
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)
110.09872.7294-1.50554.3760.16024.1607-0.36760.54290.3308-0.35380.39960.247-0.0318-0.4065-0.0320.0081-0.2946-0.1350.04460.1523-0.018617.05348.77715.59
22.94810.66060.46092.7049-0.15674.05140.00630.01740.1992-0.0927-0.07960.0316-0.1650.06290.0733-0.2507-0.0156-0.0403-0.12980.0903-0.1186-5.50833.29816.392
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 89
2X-RAY DIFFRACTION2A90 - 251

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