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- PDB-2koh: NMR structure of mouse Par3-PDZ3 in complex with VE-Cadherin C-te... -

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Basic information

Entry
Database: PDB / ID: 2koh
TitleNMR structure of mouse Par3-PDZ3 in complex with VE-Cadherin C-terminus
Components
  • Cadherin-5
  • Partitioning defective 3 homolog
KeywordsPROTEIN BINDING / Par3 / PDZ domain / VE Cadherin / Alternative splicing / Cell cycle / Cell division / Cell junction / Coiled coil / Cytoplasm / Cytoskeleton / Membrane / Phosphoprotein / Tight junction / Calcium / Cell adhesion / Cell membrane / Cleavage on pair of basic residues / Glycoprotein / Transmembrane
Function / homology
Function and homology information


Tight junction interactions / regulation of actin filament-based process / internode region of axon / regulation of cellular localization / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / PAR polarity complex / positive regulation of establishment of endothelial barrier / apical constriction / blood vessel maturation / VEGFR2 mediated vascular permeability ...Tight junction interactions / regulation of actin filament-based process / internode region of axon / regulation of cellular localization / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / PAR polarity complex / positive regulation of establishment of endothelial barrier / apical constriction / blood vessel maturation / VEGFR2 mediated vascular permeability / establishment of centrosome localization / Adherens junctions interactions / blood vessel endothelial cell migration / lateral loop / positive regulation of myelination / establishment of epithelial cell polarity / cell-cell adhesion mediated by cadherin / protein localization to bicellular tight junction / regulation of vascular permeability / BMP receptor binding / cell-cell adhesion via plasma-membrane adhesion molecules / Schmidt-Lanterman incisure / bicellular tight junction assembly / fibrinogen binding / myelination in peripheral nervous system / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / vascular endothelial growth factor receptor 2 binding / positive regulation of BMP signaling pathway / phosphatidylinositol-3-phosphate binding / establishment or maintenance of epithelial cell apical/basal polarity / vasculature development / catenin complex / protein targeting to membrane / regulation of establishment of cell polarity / cell-cell junction assembly / adherens junction organization / wound healing, spreading of cells / centrosome localization / negative regulation of microtubule polymerization / apical junction complex / establishment or maintenance of cell polarity / establishment of cell polarity / negative regulation of peptidyl-threonine phosphorylation / homophilic cell adhesion via plasma membrane adhesion molecules / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / bicellular tight junction / endomembrane system / negative regulation of endothelial cell apoptotic process / axonal growth cone / positive regulation of protein dephosphorylation / phosphatidylinositol-4,5-bisphosphate binding / protein tyrosine kinase binding / phosphatidylinositol binding / transforming growth factor beta receptor signaling pathway / cell periphery / positive regulation of protein-containing complex assembly / adherens junction / regulation of protein phosphorylation / cell morphogenesis / protein localization / cell-cell adhesion / microtubule cytoskeleton organization / spindle / beta-catenin binding / intracellular calcium ion homeostasis / negative regulation of inflammatory response / positive regulation of angiogenesis / cell-cell junction / cell junction / cell cortex / protein phosphatase binding / nuclear membrane / transmembrane transporter binding / membrane => GO:0016020 / cell adhesion / positive regulation of cell migration / cadherin binding / cell cycle / apical plasma membrane / cell division / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / neuronal cell body / calcium ion binding / positive regulation of gene expression / cell surface / protein-containing complex / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
VE-cadherin / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...VE-cadherin / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Cadherin-5 / Partitioning defective 3 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Model detailslowest energy, model 1
AuthorsVolkman, B.F. / Tyler, R.C. / Peterson, F.C.
CitationJournal: Biochemistry / Year: 2010
Title: Distal interactions within the par3-VE-cadherin complex.
Authors: Tyler, R.C. / Peterson, F.C. / Volkman, B.F.
History
DepositionSep 22, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Partitioning defective 3 homolog
B: Cadherin-5


Theoretical massNumber of molelcules
Total (without water)13,7262
Polymers13,7262
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Partitioning defective 3 homolog / PARD-3 / PAR-3 / Atypical PKC isotype-specific-interacting protein / ASIP / Ephrin-interacting protein / PHIP


Mass: 11905.420 Da / Num. of mol.: 1 / Fragment: UNP residues 581-689, PDZ 3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Par3, Pard3 / Production host: Escherichia coli (E. coli) / Strain (production host): SG130099[pREP4] / References: UniProt: Q99NH2
#2: Protein/peptide Cadherin-5 / / Vascular endothelial cadherin / VE-cadherin


Mass: 1821.054 Da / Num. of mol.: 1 / Fragment: UNP residues 769-784
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh5, VE-Cadherin / Production host: Escherichia coli (E. coli) / Strain (production host): SG130099[pREP4] / References: UniProt: P55284

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)
1423D 15N-separated NOESY
1523D 13C-separated NOESY
1623D 13C-separated NOESY (AROMATIC)
1723D 13C-F1-filtered 13C-F3-separated NOESY
1813D 13C-F1-filtered 13C-F3-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] MmPar3 PDZ3-1, 2 mM MmVE-Cadherin-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4, 10 % D2O-5, 0.02 % sodium azide-6, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] MmVE-Cadherin-7, 1 mM MmPar3 PDZ3-8, 20 mM sodium phosphate-9, 50 mM sodium chloride-10, 10 % D2O-11, 0.02 % sodium chloride-12, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMmPar3 PDZ3-1[U-100% 13C; U-100% 15N]1
2 mMMmVE-Cadherin-21
20 mMsodium phosphate-31
50 mMsodium chloride-41
10 %D2O-51
0.02 %sodium azide-61
1 mMMmVE-Cadherin-7[U-100% 13C; U-100% 15N]2
1 mMMmPar3 PDZ3-82
20 mMsodium phosphate-92
50 mMsodium chloride-102
10 %D2O-112
0.02 %sodium chloride-122
Sample conditionsIonic strength: 53 / pH: 6.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
TopSpin2.1Brukercollection
NMRPipe2007Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 1868 NOE CONSTRAINTS ( 434 INTRA, 383 SEQUENTIAL, 254 MEDIUM, AND 797 LONG RANGE) AND 114 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 1868 / NOE intraresidue total count: 434 / NOE long range total count: 797 / NOE medium range total count: 254 / NOE sequential total count: 383
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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