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- PDB-2ejy: Solution structure of the p55 PDZ T85C domain complexed with the ... -

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Basic information

Entry
Database: PDB / ID: 2ejy
TitleSolution structure of the p55 PDZ T85C domain complexed with the glycophorin C F127C peptide
Components
  • 55 kDa erythrocyte membrane protein
  • Glycophorin C
KeywordsMEMBRANE PROTEIN / GPC / MAGUK / p55 / PDZ
Function / homology
Function and homology information


regulation of neutrophil chemotaxis / guanylate kinase activity / stereocilium / Sensory processing of sound by outer hair cells of the cochlea / cortical cytoskeleton / leukocyte migration / plasma membrane => GO:0005886 / centriolar satellite / Cell surface interactions at the vascular wall / cell-cell junction ...regulation of neutrophil chemotaxis / guanylate kinase activity / stereocilium / Sensory processing of sound by outer hair cells of the cochlea / cortical cytoskeleton / leukocyte migration / plasma membrane => GO:0005886 / centriolar satellite / Cell surface interactions at the vascular wall / cell-cell junction / signaling receptor binding / signal transduction / membrane / plasma membrane
Similarity search - Function
Glycophorin-C / MPP1, SH3 domain / Glycophorin / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit ...Glycophorin-C / MPP1, SH3 domain / Glycophorin / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / 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
Glycophorin-C / 55 kDa erythrocyte membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKusunoki, H. / Kohno, T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Structural insight into the interaction between the p55 PDZ domain and glycophorin C
Authors: Kusunoki, H. / Kohno, T.
History
DepositionMar 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / 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_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: 55 kDa erythrocyte membrane protein
B: Glycophorin C


Theoretical massNumber of molelcules
Total (without water)12,2962
Polymers12,2962
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 55 kDa erythrocyte membrane protein / p55 / Membrane protein / palmitoylated 1


Mass: 10950.690 Da / Num. of mol.: 1 / Fragment: PDZ domain, Residues 69-153 / Mutation: T85C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q00013
#2: Protein/peptide Glycophorin C / PAS-2' / Glycoprotein beta / GLPC / Glycoconnectin / Sialoglycoprotein D / Glycophorin D / GPD / CD236 antigen


Mass: 1345.438 Da / Num. of mol.: 1 / Fragment: C-terminal region, Residues 117-128 / Mutation: F127C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUBK19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04921

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1332D F2 13C filtered NOESY
1432D F1F2 13C filtered NOESY
1543D 15N-separated NOESY
1653D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM p55 PDZ domain-GPC peptide complex (PDZ U-15N, peptide NA); 22.5mM sodium phosphate, 45mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
21.2mM p55 PDZ domain-GPC peptide complex (PDZ U-13C, 15N, peptide NA); 22.5mM sodium phosphate, 45mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
31.2mM p55 PDZ domain-GPC peptide complex (PDZ U-13C, 15N, peptide NA); 22.5mM sodium phosphate, 45mM NaCl, 100% D2O100% D2O
40.6mM p55 PDZ domain-GPC peptide complex (peptide U-15N, PDZ NA); 22.5mM sodium phosphate, 45mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
50.9mM p55 PDZ domain-GPC peptide complex (peptide U-13C, 15N, PDZ NA); 22.5mM sodium phosphate, 45mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 45 mM / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCE IIBrukerAVANCE II7002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1491 restraints, 1291 are NOE-derived distance constraints, 130 dihedral angle restraints, 70 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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