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- PDB-3tsz: crystal structure of PDZ3-SH3-GUK core module from human ZO-1 in ... -

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Basic information

Entry
Database: PDB / ID: 3tsz
Titlecrystal structure of PDZ3-SH3-GUK core module from human ZO-1 in complex with 12mer peptide from human JAM-A cytoplasmic tail
Components
  • Junctional adhesion molecule A
  • Tight junction protein ZO-1
KeywordsCELL ADHESION / PDZ3-SH3-GUK / scaffolding / JAM / tight junction
Function / homology
Function and homology information


positive regulation of blood-brain barrier permeability / positive regulation of establishment of endothelial barrier / adherens junction maintenance / memory T cell extravasation / positive regulation of cell-cell adhesion mediated by cadherin / RUNX1 regulates expression of components of tight junctions / ameloblast differentiation / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of endothelial intestinal barrier ...positive regulation of blood-brain barrier permeability / positive regulation of establishment of endothelial barrier / adherens junction maintenance / memory T cell extravasation / positive regulation of cell-cell adhesion mediated by cadherin / RUNX1 regulates expression of components of tight junctions / ameloblast differentiation / Tight junction interactions / 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 membrane permeability / Regulation of gap junction activity / protein localization to bicellular tight junction / protein localization to adherens junction / gap junction / actomyosin structure organization / cell-cell junction organization / Apoptotic cleavage of cell adhesion proteins / positive regulation of platelet aggregation / tight junction / Signaling by Hippo / cell-cell junction assembly / regulation of bicellular tight junction assembly / intestinal absorption / podosome / negative regulation of stress fiber assembly / apical junction complex / leukocyte cell-cell adhesion / positive regulation of Rho protein signal transduction / maintenance of blood-brain barrier / positive regulation of sprouting angiogenesis / regulation of cytoskeleton organization / bicellular tight junction / Integrin cell surface interactions / cell adhesion molecule binding / regulation of cytokine production / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / protein localization to plasma membrane / cell projection / Cell surface interactions at the vascular wall / PDZ domain binding / regulation of actin cytoskeleton organization / adherens junction / cell-cell adhesion / cellular response to mechanical stimulus / cell-cell junction / integrin binding / cell junction / apical part of cell / virus receptor activity / regulation of cell shape / actin cytoskeleton organization / basolateral plasma membrane / calmodulin binding / positive regulation of cell migration / cadherin binding / inflammatory response / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein homodimerization activity / protein-containing complex / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Junctional adhesion molecule A / 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 ...Junctional adhesion molecule A / 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 / SH3 Domains / Immunoglobulin domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / PDZ domain / Immunoglobulin V-Type / PDZ superfamily / Immunoglobulin V-set domain / SH3 type barrels. / Immunoglobulin V-set domain / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Immunoglobulin subtype / Immunoglobulin / P-loop containing nucleotide triphosphate hydrolases / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tight junction protein ZO-1 / Junctional adhesion molecule A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsNomme, J. / Lavie, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Src Homology 3 Domain Is Required for Junctional Adhesion Molecule Binding to the Third PDZ Domain of the Scaffolding Protein ZO-1.
Authors: Nomme, J. / Fanning, A.S. / Caffrey, M. / Lye, M.F. / Anderson, J.M. / Lavie, A.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Junctional adhesion molecule A


Theoretical massNumber of molelcules
Total (without water)46,0332
Polymers46,0332
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.500, 49.700, 91.800
Angle α, β, γ (deg.)90.00, 101.10, 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: 44660.914 Da / Num. of mol.: 1 / Fragment: PDZ3-SH3-GUK (UNP Residues 417-803)
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(C41) / References: UniProt: Q07157
#2: Protein/peptide Junctional adhesion molecule A / JAM-A / Junctional adhesion molecule 1 / JAM-1 / Platelet F11 receptor / Platelet adhesion molecule 1 / PAM-1


Mass: 1372.499 Da / Num. of mol.: 1 / Fragment: JAM-A_P12 (UNP Residues 288-299) / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y624
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 9% PEG 3350, 0.1 M Sodium Malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→90.1 Å / Num. all: 15077 / Num. obs: 15077 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.08
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.63 / Num. unique all: 849 / % possible all: 74.6

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LH5

3lh5


Resolution: 2.502→90.08 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.877 / SU B: 32.833 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.724 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30889 1520 10.1 %RANDOM
Rwork0.23966 ---
all0.24675 13557 --
obs0.24675 13557 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0.76 Å2
2---0.22 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.502→90.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 0 0 40 2849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222860
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9593859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2655347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21724.014142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5915517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8481524
X-RAY DIFFRACTIONr_chiral_restr0.0710.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212167
X-RAY DIFFRACTIONr_mcbond_it0.331.51743
X-RAY DIFFRACTIONr_mcangle_it0.6222809
X-RAY DIFFRACTIONr_scbond_it0.78431117
X-RAY DIFFRACTIONr_scangle_it1.3934.51050
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 83 -
Rwork0.365 764 -
obs--74.76 %
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)
13.44751.75452.13254.04562.01035.6861-0.05280.0577-0.0039-0.60130.04520.7021-0.2694-0.50770.00770.31740.0241-0.07710.07610.03110.2586-45.7739-10.2445-41.8357
25.0644-1.97243.70691.1764-1.67693.8986-0.087-0.2980.087-0.00470.01450.1299-0.2157-0.04790.07250.2689-0.0380.06090.1166-0.03390.1291-32.8063-5.7743-21.4875
32.6969-0.10831.68442.741-0.12823.9103-0.0826-0.3142-0.05730.15050.0305-0.38160.01550.41550.05210.15840.0380.08950.35380.05140.2202-13.6261-12.4343-6.1623
422.86650.00219.25490.3180.18913.866-0.7696-1.91590.36790.01150.11460.5744-0.3013-0.81230.65510.66310.05960.06540.2166-0.11141.0495-50.1051-1.8902-34.4802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A421 - 529
2X-RAY DIFFRACTION2A530 - 653
3X-RAY DIFFRACTION3A654 - 802
4X-RAY DIFFRACTION4B418 - 427

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