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- PDB-3shw: Crystal structure of ZO-1 PDZ3-SH3-Guk supramodule complex with C... -

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Basic information

Entry
Database: PDB / ID: 3shw
TitleCrystal structure of ZO-1 PDZ3-SH3-Guk supramodule complex with Connexin-45 peptide
Components
  • Gap junction gamma-1 protein
  • Tight junction protein ZO-1
KeywordsCELL ADHESION / PDZ-SH3-Guk supramodule
Function / homology
Function and homology information


gap junction channel activity involved in SA node cell-atrial cardiac muscle cell electrical coupling / SA node cell to atrial cardiac muscle cell communication by electrical coupling / AV node cell to bundle of His cell communication by electrical coupling / gap junction channel activity involved in AV node cell-bundle of His cell electrical coupling / positive regulation of blood-brain barrier permeability / adherens junction maintenance / RUNX1 regulates expression of components of tight junctions / positive regulation of cell-cell adhesion mediated by cadherin / ameloblast differentiation / SARS-CoV-2 targets PDZ proteins in cell-cell junction ...gap junction channel activity involved in SA node cell-atrial cardiac muscle cell electrical coupling / SA node cell to atrial cardiac muscle cell communication by electrical coupling / AV node cell to bundle of His cell communication by electrical coupling / gap junction channel activity involved in AV node cell-bundle of His cell electrical coupling / positive regulation of blood-brain barrier permeability / adherens junction maintenance / RUNX1 regulates expression of components of tight junctions / positive regulation of cell-cell adhesion mediated by cadherin / ameloblast differentiation / SARS-CoV-2 targets PDZ proteins in cell-cell junction / protein localization to cell-cell junction / cell development / Electric Transmission Across Gap Junctions / regulation of cell junction assembly / establishment of endothelial intestinal barrier / gap junction assembly / atrial cardiac muscle cell action potential / Regulation of gap junction activity / protein localization to bicellular tight junction / connexin complex / protein localization to adherens junction / gap junction / gap junction channel activity / Gap junction assembly / cell-cell junction organization / Apoptotic cleavage of cell adhesion proteins / actomyosin structure organization / cell-cell junction assembly / Signaling by Hippo / tight junction / cardiac muscle tissue development / negative regulation of stress fiber assembly / podosome / regulation of bicellular tight junction assembly / apical junction complex / maintenance of blood-brain barrier / positive regulation of sprouting angiogenesis / regulation of cytoskeleton organization / monoatomic ion channel activity / intercalated disc / bicellular tight junction / vasculogenesis / cell adhesion molecule binding / muscle contraction / visual perception / cell projection / adherens junction / cell-cell adhesion / cell junction / apical part of cell / cell-cell signaling / actin cytoskeleton organization / basolateral plasma membrane / chemical synaptic transmission / calmodulin binding / positive regulation of cell migration / cadherin binding / positive regulation of cell population proliferation / synapse / endoplasmic reticulum membrane / negative regulation of apoptotic process / endoplasmic reticulum / protein-containing complex / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Gap junction alpha-6 protein (Cx45) / 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. / Connexin / Connexin, N-terminal ...Gap junction alpha-6 protein (Cx45) / 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. / 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. / SH3 Domains / PDZ domain / Pdz3 Domain / 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 / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Gap junction gamma-1 protein / Tight junction protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tight junction protein ZO-1
B: Gap junction gamma-1 protein


Theoretical massNumber of molelcules
Total (without water)54,0632
Polymers54,0632
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-7 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.005, 86.955, 141.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 53013.246 Da / Num. of mol.: 1
Fragment: PDZ3 domain, SH3 domain and Guanylate kinase-like domain, UNP residues 421-888
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q07157
#2: Protein/peptide Gap junction gamma-1 protein / Connexin-45 / Cx45 / Gap junction alpha-7 protein


Mass: 1050.144 Da / Num. of mol.: 1 / Fragment: C-terminal, UNP residues 387-396 / Source method: obtained synthetically
Details: The C-terminal Connexin 45 peptide was synthesized.
References: UniProt: P36383
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 16% (w/v) PEG 8000, 0.1M Sodium Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→74.12 Å / Num. all: 13414 / Num. obs: 13414 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.5
Reflection shellHighest resolution: 2.9 Å / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→74.12 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 32.712 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25299 663 5 %RANDOM
Rwork0.20875 ---
obs0.21083 12726 95.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.654 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--1.12 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 2.9→74.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2746 0 0 13 2759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0061.9583776
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9635338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21723.942137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86515506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5251523
X-RAY DIFFRACTIONr_chiral_restr0.0690.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022110
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.21139
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21894
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2271.51740
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.39922741
X-RAY DIFFRACTIONr_scbond_it0.60231184
X-RAY DIFFRACTIONr_scangle_it1.0264.51035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.901→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 46 -
Rwork0.297 935 -
obs--97.51 %
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)
122.70186.54830.30679.85250.238613.16160.317-2.6872-1.07740.3869-0.8166-0.81320.86050.28830.49960.0373-0.166-0.07360.64250.44910.54515.197-31.0445.196
27.814412.2864-0.243319.88-3.179213.9170.08930.1322-0.5325-0.4633-0.3787-0.38311.35810.2530.2894-0.01430.04050.10120.37970.05730.219315.228-25.263-9.299
30.03740.68790.254818.5588-2.413510.27740.9202-0.1003-1.06230.4727-1.1082-2.40352.42970.87720.1880.4620.0212-0.12360.73310.22121.006317.713-36.949-0.737
418.62528.6156-1.543810.7710.85396.20530.5218-0.72290.99720.2752-0.36171.0637-0.4561-0.2235-0.1601-0.07790.02270.03670.33960.15910.213513.595-20.669-2.549
514.73428.5592-3.155621.8642.1711.62491.5151-2.9874-0.31552.1605-1.356-0.84510.56911.3607-0.15910.298-0.2175-0.0291.12720.40670.271819.311-24.3377.522
614.18321.767-21.83645.8063-2.254843.3939-1.11662.0707-1.6445-1.98640.41530.20092.7393-2.52640.70130.6716-0.12370.07360.6011-0.07130.52549.616-31.277-13.063
77.29521.4692-0.90974.6435-0.64175.3559-0.06390.240.0754-0.17270.2064-0.1019-0.22680.1156-0.14250.0482-0.0057-0.02140.2850.11440.102723.879-9.185-18.213
80.8596-2.6221-0.825214.8681-2.604814.01250.52320.0512-0.0403-0.19330.19860.120.58221.1202-0.7217-0.1096-0.04510.08630.27480.06660.144523.813-12.677-17.757
99.0493-4.2579-0.42877.717-4.620816.06340.20110.80690.315-0.61830.00570.1408-0.3265-0.4236-0.20670.0922-0.0746-0.04130.16420.08840.260120.954-8.7-21.831
103.139712.70392.382159.9406-9.763145.89880.4991-1.38251.7821.2179-0.682-2.3738-1.33950.52630.18290.2187-0.0383-0.11510.38950.05860.326329.841-3.223-8.067
113.7856-2.79537.02132.064-5.184513.02270.6688-0.29371.30230.506-0.2094-0.9149-2.0026-1.0483-0.45941.5574-0.120.10381.1411-0.17741.646225.0456.231-8.475
121.6887-0.107-0.82247.426-3.00813.93830.15120.0149-0.08180.49430.49511.1387-0.7186-0.4767-0.64630.21920.17250.0460.39380.0680.350611.1988.848-21.597
1327.8416-8.4261-5.552312.7577-9.170712.6423-0.32490.77412.1979-0.09321.83271.355-0.7427-2.2913-1.50780.60830.2950.16340.79080.33361.09654.33624.101-31.382
149.73555.08261.05023.2838-0.209814.60790.0074-1.50361.74491.3916-0.23321.6861-1.8702-0.72240.22581.21490.47490.45410.77170.06931.22174.22822.418-15.888
153.3954.79452.634212.6786-3.00439.6978-0.0221-0.47860.09521.41510.58290.5161-1.2649-0.4826-0.56080.60650.33820.30770.63880.01190.420610.12714.815-17.152
161.80980.97031.83578.6314-1.51472.6319-0.19120.2103-0.13140.33080.4297-0.1076-1.21460.095-0.23840.40260.05760.02390.2735-0.04860.203920.70518.58-31.262
179.3048-1.905-0.735110.2811-4.338217.20990.0162-0.27570.75811.24050.25620.1592-1.7513-0.2478-0.27240.70090.00610.03890.236-0.0190.329122.26130.798-33.317
1812.898212.6237-1.470434.6998-7.299912.4736-0.01750.2306-0.00350.44580.323-0.6447-1.19030.7272-0.30550.49430.0102-0.22510.4181-0.0380.497827.01415.615-24.514
194.36380.1635-3.28373.7311-2.76224.3408-0.23340.6725-0.5007-0.23070.73620.7824-0.1709-0.8946-0.50270.42890.0091-0.01880.3869-0.00350.37514.19815.919-35.59
209.2221-1.49848.396616.4733-3.53657.93580.16570.20020.2176-0.53790.66820.22260.1341-1.4437-0.8338-0.00290.18160.07330.57410.18250.5317.8482.027-23.412
2117.9635.273815.803315.009717.255325.72610.0585-0.6068-1.8036-2.43631.59540.1551-0.97362.3303-1.65390.64990.08910.26550.7830.27741.198427.02-28.287-7.949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A421 - 434
2X-RAY DIFFRACTION2A435 - 447
3X-RAY DIFFRACTION3A448 - 464
4X-RAY DIFFRACTION4A465 - 486
5X-RAY DIFFRACTION5A487 - 498
6X-RAY DIFFRACTION6A499 - 513
7X-RAY DIFFRACTION7A514 - 552
8X-RAY DIFFRACTION8A553 - 563
9X-RAY DIFFRACTION9A564 - 578
10X-RAY DIFFRACTION10A579 - 585
11X-RAY DIFFRACTION11A586 - 631
12X-RAY DIFFRACTION12A632 - 656
13X-RAY DIFFRACTION13A657 - 668
14X-RAY DIFFRACTION14A669 - 699
15X-RAY DIFFRACTION15A700 - 721
16X-RAY DIFFRACTION16A722 - 737
17X-RAY DIFFRACTION17A738 - 755
18X-RAY DIFFRACTION18A756 - 767
19X-RAY DIFFRACTION19A768 - 791
20X-RAY DIFFRACTION20A792 - 802
21X-RAY DIFFRACTION21B1134 - 1140

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