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- PDB-2jwe: Solution structure of the second PDZ domain from human zonula occ... -

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Basic information

Entry
Database: PDB / ID: 2jwe
TitleSolution structure of the second PDZ domain from human zonula occludens-1: A dimeric form with 3D domain swapping
ComponentsTight junction protein ZO-1
KeywordsCELL ADHESION / ZO-1 / dimer / domain swapping / TJP1 / Cell junction / Membrane / Phosphorylation / SH3 domain / Tight junction
Function / homology
Function and homology information


positive regulation of blood-brain barrier permeability / adherens junction maintenance / positive regulation of cell-cell adhesion mediated by cadherin / RUNX1 regulates expression of components of tight junctions / 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 / protein localization to adherens junction / Regulation of gap junction activity ...positive regulation of blood-brain barrier permeability / adherens junction maintenance / positive regulation of cell-cell adhesion mediated by cadherin / RUNX1 regulates expression of components of tight junctions / 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 / protein localization to adherens junction / Regulation of gap junction activity / protein localization to bicellular tight junction / gap junction / cell-cell junction organization / Apoptotic cleavage of cell adhesion proteins / tight junction / actomyosin structure organization / podosome / Signaling by Hippo / regulation of bicellular tight junction assembly / cell-cell junction assembly / negative regulation of stress fiber assembly / apical junction complex / maintenance of blood-brain barrier / positive regulation of sprouting angiogenesis / regulation of cytoskeleton organization / bicellular tight junction / cell adhesion molecule binding / cell projection / adherens junction / cell-cell adhesion / apical part of cell / cell junction / actin cytoskeleton organization / basolateral plasma membrane / calmodulin binding / positive regulation of cell migration / cadherin binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein-containing complex / plasma membrane / cytoplasm / cytosol
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsJi, P. / Wu, J.W. / Zhang, J.H. / Yang, Y.S. / Wu, J.H. / Shi, Y.Y.
CitationJournal: Proteins / Year: 2011
Title: Solution structure of the second PDZ domain of Zonula Occludens 1
Authors: Ji, P. / Yang, G. / Zhang, J.H. / Wu, J.W. / Chen, Z. / Gong, Q. / Wu, J.H. / Shi, Y.Y.
History
DepositionOct 10, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Remark 700SHEET Determination method: Author determined

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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


Theoretical massNumber of molelcules
Total (without water)20,0632
Polymers20,0632
Non-polymers00
Water00
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 / Zonula occludens protein 1 / Zona occludens protein 1 / Tight junction protein 1


Mass: 10031.432 Da / Num. of mol.: 2 / Fragment: the second PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TJP1, ZO1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q07157

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HN(CA)CO
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D C(CO)NH
1923D 1H-15N NOESY
11023D (H)CCH-TOCSY
11123D (H)CCH-COSY
11223D 1H-13C NOESY
11332D 1H-13C HSQC
11432D 1H-1H 13C-Filtered NOESY
11522D 1H-13C HSQC
11642D 1H-1H TOCSY
11742D 1H-1H NOESY
11812D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1mM [U-99% 13C; U-99% 15N] ZO-1, 90% H2O/10% D2O90% H2O/10% D2O
20.8-1mM [U-99% 13C; U-99% 15N] ZO-1, 100% D2O100% D2O
30.4-0.5mM [U-99% 13C; U-99% 15N] ZO-1, 100% D2O100% D2O
40.5-0.8mM ZO-1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMZO-1[U-99% 13C; U-99% 15N]1
0.8 mMZO-1[U-99% 13C; U-99% 15N]2
0.4 mMZO-1-1[U-99% 13C; U-99% 15N]3
0.5 mMZO-1-2natural abundance3
0.5 mMZO-1natural abundance4
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
XwinNMR3.5Bruker Biospincollection
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.112Goddardchemical shift assignment
Sparky3.112Goddarddata analysis
Sparky3.112Goddardpeak picking
TALOS2003.027.13.05Cornilescu, Delaglio and Baxpredicts angles from chemical shift homology
MOLMOL2K.2Koradi, Billeter and Wuthrichdata analysis
ProcheckNMR3.5.4Laskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2626 / NOE intraresidue total count: 560 / NOE long range total count: 868 / NOE medium range total count: 466 / NOE sequential total count: 732 / Hydrogen bond constraints total count: 100 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 78 / Protein psi angle constraints total count: 76
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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