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- PDB-2rrm: Interplay between phosphatidyl-inositol-phosphates and claudins u... -

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Basic information

Entry
Database: PDB / ID: 2rrm
TitleInterplay between phosphatidyl-inositol-phosphates and claudins upon binding to the 1st PDZ domain of zonula occludens 1
ComponentsTight junction protein ZO-1
KeywordsCELL ADHESION / PDZ Domain / protein protein interaction / tight junction protein 1 / intercellular adhesion
Function / homology
Function and homology information


: / Regulation of gap junction activity / Signaling by Hippo / positive regulation of blood-brain barrier permeability / adherens junction maintenance / Apoptotic cleavage of cell adhesion proteins / positive regulation of cell-cell adhesion mediated by cadherin / response to magnetism / : / establishment of endothelial intestinal barrier ...: / Regulation of gap junction activity / Signaling by Hippo / positive regulation of blood-brain barrier permeability / adherens junction maintenance / Apoptotic cleavage of cell adhesion proteins / positive regulation of cell-cell adhesion mediated by cadherin / response to magnetism / : / establishment of endothelial intestinal barrier / protein localization to cell-cell junction / regulation of cell junction assembly / response to xenobiotic stimulus => GO:0009410 / protein localization to bicellular tight junction / protein localization to adherens junction / apicolateral plasma membrane / gap junction / intercellular canaliculus / cell-cell junction organization / blastocyst formation / connexin binding / actomyosin structure organization / negative regulation of vascular permeability / I band / tight junction / regulation of bicellular tight junction assembly / negative regulation of stress fiber assembly / apical junction complex / positive regulation of sprouting angiogenesis / regulation of cytoskeleton organization / intercalated disc / bicellular tight junction / cellular response to glucose stimulus / sensory perception of sound / adherens junction / cell-cell junction / apical part of cell / cell junction / basolateral plasma membrane / response to ethanol / response to lipopolysaccharide / calmodulin binding / positive regulation of cell migration / apical plasma membrane / protein domain specific binding / cell surface / protein-containing complex / membrane / nucleus / 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. / 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
Tight junction protein ZO-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHiroaki, H. / Satomura, K. / Goda, N. / Umetsu, Y. / Taniguchi, R. / Ikegami, T. / Furuse, M.
CitationJournal: Biomol.Nmr Assign. / Year: 2011
Title: 1H, 13C, and 15N resonance assignment of the first PDZ domain of mouse ZO-1
Authors: Umetsu, Y. / Goda, N. / Taniguchi, R. / Satomura, K. / Ikegami, T. / Furuse, M. / Hiroaki, H.
History
DepositionJan 6, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tight junction protein ZO-1


Theoretical massNumber of molelcules
Total (without water)10,8171
Polymers10,8171
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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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: 10817.159 Da / Num. of mol.: 1 / Fragment: the first PDZ domain, UNP residues 18-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P39447

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCA
1613D HN(CO)CA
1713D HNCO
1813D HN(CA)CO
1913D C(CO)NH
11013D H(CCO)NH
11113D (H)CCH-TOCSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.7mM [U-13C; U-15N] ZO-1(PDZ1)-1; 20mM MES-2; 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMZO-1(PDZ1)-1[U-13C; U-15N]1
20 mMMES-21
Sample conditionspH: 5.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.11Goddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxpredicts angles from chemical shift homology
MOLMOL2K.2Koradi, Billeter and Wuthrichdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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