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- PDB-3cyy: The crystal structure of ZO-1 PDZ2 in complex with the Cx43 peptide -

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Basic information

Entry
Database: PDB / ID: 3cyy
TitleThe crystal structure of ZO-1 PDZ2 in complex with the Cx43 peptide
Components
  • Tight junction protein ZO-1
  • peptide from Gap junction alpha-1 protein
KeywordsPEPTIDE BINDING PROTEIN / Protein-ligand complex / Cell junction / Membrane / Phosphoprotein / SH3 domain / Tight junction / Gap junction / Transmembrane
Function / homology
Function and homology information


vascular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Regulation of gap junction activity / positive regulation of cell communication by chemical coupling / Gap junction assembly / positive regulation of glomerular filtration / RHOQ GTPase cycle / positive regulation of blood-brain barrier permeability / negative regulation of gonadotropin secretion / positive regulation of striated muscle tissue development ...vascular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Regulation of gap junction activity / positive regulation of cell communication by chemical coupling / Gap junction assembly / positive regulation of glomerular filtration / RHOQ GTPase cycle / positive regulation of blood-brain barrier permeability / negative regulation of gonadotropin secretion / positive regulation of striated muscle tissue development / milk ejection reflex / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / atrial ventricular junction remodeling / cell communication by chemical coupling / cell communication by electrical coupling / adherens junction maintenance / positive regulation of cell-cell adhesion mediated by cadherin / positive regulation of behavioral fear response / neuroblast migration / chronic inflammatory response / Gap junction degradation / Formation of annular gap junctions / columnar/cuboidal epithelial cell maturation / maintenance of protein localization in endoplasmic reticulum / RUNX1 regulates expression of components of tight junctions / regulation of cell communication by electrical coupling / gap junction hemi-channel activity / positive regulation of establishment of Sertoli cell barrier / negative regulation of trophoblast cell migration / positive regulation of meiotic nuclear division / regulation of bone remodeling / microtubule-based transport / monoatomic ion transmembrane transporter activity / ATP transport / SARS-CoV-2 targets PDZ proteins in cell-cell junction / regulation of ventricular cardiac muscle cell membrane depolarization / epididymis development / gap junction channel activity involved in cell communication by electrical coupling / establishment of endothelial intestinal barrier / protein localization to cell-cell junction / glutathione transmembrane transporter activity / contractile muscle fiber / regulation of cell junction assembly / gap junction assembly / negative regulation of cardiac muscle cell proliferation / protein localization to adherens junction / cellular response to pH / endothelium development / Regulation of gap junction activity / protein localization to bicellular tight junction / skeletal muscle tissue regeneration / response to fluid shear stress / connexin complex / regulation of atrial cardiac muscle cell membrane depolarization / cardiac conduction / regulation of actin filament organization / Golgi-associated vesicle membrane / fascia adherens / cell-cell contact zone / gap junction / gap junction channel activity / bone remodeling / export across plasma membrane / cell-cell junction organization / xenobiotic transport / negative regulation of DNA biosynthetic process / adult heart development / connexin binding / regulation of bone mineralization / embryonic heart tube development / glutamate secretion / Apoptotic cleavage of cell adhesion proteins / regulation of ventricular cardiac muscle cell membrane repolarization / tight junction / actomyosin structure organization / podosome / response to pH / Signaling by Hippo / regulation of bicellular tight junction assembly / cell-cell junction assembly / cellular response to parathyroid hormone stimulus / blood vessel morphogenesis / lens development in camera-type eye / negative regulation of stress fiber assembly / apical junction complex / intermediate filament / regulation of heart contraction / embryonic digit morphogenesis / maintenance of blood-brain barrier / beta-tubulin binding / positive regulation of sprouting angiogenesis / regulation of cytoskeleton organization / positive regulation of stem cell proliferation / heart looping / efflux transmembrane transporter activity / negative regulation of endothelial cell proliferation / establishment of mitotic spindle orientation / regulation of calcium ion transport / decidualization
Similarity search - Function
Tight junction protein ZO-1 / ZO-1, SH3 domain / Tight junction protein ZO / Gap junction alpha-1 protein (Cx43) / Gap junction alpha-1 protein (Cx43), C-terminal / Gap junction alpha-1 protein (Cx43), alpha helix domain superfamily / Gap junction alpha-1 protein (Cx43) / Connexin, C-terminal / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain ...Tight junction protein ZO-1 / ZO-1, SH3 domain / Tight junction protein ZO / Gap junction alpha-1 protein (Cx43) / Gap junction alpha-1 protein (Cx43), C-terminal / Gap junction alpha-1 protein (Cx43), alpha helix domain superfamily / Gap junction alpha-1 protein (Cx43) / Connexin, C-terminal / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin / Connexins signature 1. / Connexins signature 2. / Connexin homologues / Gap junction channel protein cysteine-rich domain / 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
Gap junction alpha-1 protein / Tight junction protein ZO-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPan, L. / Zhang, M.
CitationJournal: Embo J. / Year: 2008
Title: Domain-swapped dimerization of ZO-1 PDZ2 generates specific and regulatory connexin43-binding sites
Authors: Chen, J. / Pan, L. / Wei, Z. / Zhao, Y. / Zhang, M.
History
DepositionApr 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: peptide from Gap junction alpha-1 protein
D: peptide from Gap junction alpha-1 protein


Theoretical massNumber of molelcules
Total (without water)22,5304
Polymers22,5304
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-38 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.040, 68.140, 149.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-11-

HOH

21A-29-

HOH

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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: 10152.662 Da / Num. of mol.: 2 / Fragment: pdz2 domain / Mutation: R193A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07157
#2: Protein/peptide peptide from Gap junction alpha-1 protein / peptide from Connexin-43 / Cx43 / Gap junction 43 kDa heart protein


Mass: 1112.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptides / References: UniProt: P08050
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M CaCl2, 0.1M HEPES, 14%(w/v) polyethylene glycol 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→35.16 Å / Num. obs: 8265 / Rmerge(I) obs: 0.051

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: synaptojanin-2 binding protein (PDB id: 2JIN) and PICK1 (PDB id: 2GZV)

2jin

2gzv


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 16.951 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25366 388 4.7 %RANDOM
Rwork0.21535 ---
obs0.21715 7860 96.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.945 Å2
Baniso -1Baniso -2Baniso -3
1-3.97 Å20 Å20 Å2
2---0.82 Å20 Å2
3----3.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 0 77 1457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221408
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9931897
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2735179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98324.75461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0515277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8351512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2553
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.2919
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0131.5933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31621449
X-RAY DIFFRACTIONr_scbond_it1.6413523
X-RAY DIFFRACTIONr_scangle_it2.8174.5446
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 29 -
Rwork0.298 568 -
obs--94.91 %
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)
10.9630.6213-0.78561.0797-1.1151.4345-0.03260.0852-0.10920.0028-0.0711-0.1077-0.0092-0.00160.10370.0369-0.0523-0.0304-0.0749-0.034-0.0743-1.7612-9.466716.5901
21.54460.9601-1.26370.9974-1.06341.56340.1368-0.0485-0.07780.1178-0.1182-0.0431-0.1840.0175-0.01860.0461-0.0388-0.0166-0.0721-0.0323-0.0823-6.5127-12.118423.8233
31.57840.2836-2.0883.94841.91244.1050.28590.19970.09840.4302-0.26860.1492-0.0584-0.0654-0.01740.0872-0.0956-0.0525-0.0532-0.0012-0.08563.7577-1.270424.2706
40.76461.6242-0.00143.4974-0.65629.0748-0.3763-0.0026-0.6956-0.09420.2273-0.2611-0.3786-0.13240.14890.0654-0.00220.0003-0.0416-0.0936-0.0294-7.0067-23.25318.0003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA183 - 2622 - 81
2X-RAY DIFFRACTION2BB183 - 2632 - 82
3X-RAY DIFFRACTION3CC1 - 91 - 9
4X-RAY DIFFRACTION4DD1 - 91 - 9

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