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- PDB-2kxs: ZO1 ZU5 domain in complex with GRINL1A peptide -

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Basic information

Entry
Database: PDB / ID: 2kxs
TitleZO1 ZU5 domain in complex with GRINL1A peptide
ComponentsTight junction protein ZO-1,Myocardial zonula adherens protein
KeywordsPROTEIN BINDING / beta-barrel
Function / homology
Function and homology information


maintenance of ER location / RNA polymerase II, holoenzyme / 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 ...maintenance of ER location / RNA polymerase II, holoenzyme / 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 / Regulation of gap junction activity / protein localization to bicellular tight junction / protein localization to adherens junction / gap junction / cell-cell junction organization / actomyosin structure organization / Apoptotic cleavage of cell adhesion proteins / podosome / anchoring junction / I band / Signaling by Hippo / tight junction / regulation of bicellular tight junction assembly / cell-cell junction assembly / negative regulation of stress fiber assembly / regulation of cytoskeleton organization / apical junction complex / maintenance of blood-brain barrier / cortical actin cytoskeleton / positive regulation of sprouting angiogenesis / bicellular tight junction / cell adhesion molecule binding / cell projection / adherens junction / cytoplasmic side of plasma membrane / cell-cell adhesion / Z disc / apical part of cell / cell junction / nuclear envelope / actin cytoskeleton organization / basolateral plasma membrane / calmodulin binding / intracellular signal transduction / positive regulation of cell migration / cadherin binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein-containing complex / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Chondroitinase Ac; Chain A, domain 3 - #30 / Tight junction protein ZO-1 / ZO-1, SH3 domain / Tight junction protein ZO / Chondroitinase Ac; Chain A, domain 3 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Guanylate kinase-like domain profile. ...Chondroitinase Ac; Chain A, domain 3 - #30 / Tight junction protein ZO-1 / ZO-1, SH3 domain / Tight junction protein ZO / Chondroitinase Ac; Chain A, domain 3 / 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 / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Myocardial zonula adherens protein / Tight junction protein ZO-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsWen, W. / Zhang, M.
CitationJournal: Embo J. / Year: 2011
Title: Cdc42-dependent formation of the ZO-1/MRCKb complex at the leading edge controls cell migration
Authors: Huo, L. / Wen, W. / Wang, R. / Kam, C. / Xia, J. / Feng, W. / Zhang, M.
History
DepositionMay 12, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 10, 2024Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tight junction protein ZO-1,Myocardial zonula adherens protein


Theoretical massNumber of molelcules
Total (without water)15,5411
Polymers15,5411
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 #1closest to the average

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Components

#1: Protein Tight junction protein ZO-1,Myocardial zonula adherens protein / / Tight junction protein 1 / Zona occludens protein 1 / Zonula occludens protein 1 / GRINL1A upstream ...Tight junction protein 1 / Zona occludens protein 1 / Zonula occludens protein 1 / GRINL1A upstream protein / Gup


Mass: 15540.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chimera of residues 1631 to 1748 of Tight junction protein ZO-1 and residues 70-79 of Myocardium-enriched Zo-associated protein from human.
Source: (gene. exp.) Homo sapiens (human) / Gene: TJP1, ZO1, MYZAP, MYOZAP / Production host: Escherichia coli (E. coli) / References: UniProt: Q07157, UniProt: P0CAP1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1333D HN(CA)CB
1433D CBCA(CO)NH
1542D 1H-1H NOESY
1613D 1H-15N NOESY
1723D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] protein-1, 1 mM DTT-2, 50 mM TRIS-3, 1 mM EDTA-4, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] protein-5, 50 mM [U-100% 2H] TRIS-6, 1 mM [U-100% 2H] DTT-7, 1 mM EDTA-8, 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] protein-9, 1 mM DTT-10, 50 mM TRIS-11, 1 mM EDTA-12, 90% H2O/10% D2O90% H2O/10% D2O
41 mM protein-13, 1 mM [U-100% 2H] DTT-14, 50 mM [U-100% 2H] TRIS-15, 1 mM EDTA-16, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-1[U-100% 15N]1
1 mMDTT-21
50 mMTRIS-31
1 mMEDTA-41
1 mMprotein-5[U-100% 13C; U-100% 15N]2
50 mMTRIS-6[U-100% 2H]2
1 mMDTT-7[U-100% 2H]2
1 mMEDTA-82
1 mMprotein-9[U-100% 13C; U-100% 15N]3
1 mMDTT-103
50 mMTRIS-113
1 mMEDTA-123
1 mMprotein-134
1 mMDTT-14[U-100% 2H]4
50 mMTRIS-15[U-100% 2H]4
1 mMEDTA-164
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
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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