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- PDB-1n7t: ERBIN PDZ domain bound to a phage-derived peptide -

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Basic information

Entry
Database: PDB / ID: 1n7t
TitleERBIN PDZ domain bound to a phage-derived peptide
Components
  • 99-mer peptide of densin-180-like protein
  • phage-derived peptide
KeywordsSIGNALING PROTEIN / pdz domain / c-terminal peptide complex / high affnity ligand
Function / homology
Function and homology information


basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / neurotransmitter receptor transport postsynaptic membrane to endosome / embryo development / neurotransmitter receptor transport, endosome to postsynaptic membrane / intermediate filament cytoskeleton organization / negative regulation of monocyte chemotactic protein-1 production / establishment or maintenance of epithelial cell apical/basal polarity ...basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / neurotransmitter receptor transport postsynaptic membrane to endosome / embryo development / neurotransmitter receptor transport, endosome to postsynaptic membrane / intermediate filament cytoskeleton organization / negative regulation of monocyte chemotactic protein-1 production / establishment or maintenance of epithelial cell apical/basal polarity / RHOB GTPase cycle / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / negative regulation of NF-kappaB transcription factor activity / RHOC GTPase cycle / receptor clustering / response to muramyl dipeptide / RHOG GTPase cycle / basement membrane / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / protein targeting / Signaling by ERBB2 / RAC1 GTPase cycle / Constitutive Signaling by Overexpressed ERBB2 / basal plasma membrane / integrin-mediated signaling pathway / adherens junction / Signaling by ERBB2 TMD/JMD mutants / Signaling by ERBB2 ECD mutants / neuromuscular junction / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / structural constituent of cytoskeleton / Downregulation of ERBB2 signaling / cell-cell adhesion / cell junction / cellular response to tumor necrosis factor / basolateral plasma membrane / postsynaptic membrane / nuclear membrane / response to lipopolysaccharide / postsynaptic density / cell adhesion / nuclear speck / signaling receptor binding / glutamatergic synapse / signal transduction / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat ...Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsSkelton, N.J. / Koehler, M.F.T. / Zobel, K. / Wong, W.L. / Yeh, S. / Pisabarro, M.T. / Yin, J.P. / Lasky, L.A. / Sidhu, S.S.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain.
Authors: Skelton, N.J. / Koehler, M.F.T. / Zobel, K. / Wong, W.L. / Yeh, S. / Pisabarro, M.T. / Yin, J.P. / Lasky, L.A. / Sidhu, S.S.
History
DepositionNov 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The phage-derived peptide, chain B, is de novo design. No sequence database reference is ...SEQUENCE The phage-derived peptide, chain B, is de novo design. No sequence database reference is available for the peptide.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 99-mer peptide of densin-180-like protein
B: phage-derived peptide


Theoretical massNumber of molelcules
Total (without water)12,0752
Polymers12,0752
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 / 100least violation of experimental restraints
RepresentativeModel #2closest to the average

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Components

#1: Protein 99-mer peptide of densin-180-like protein


Mass: 11196.597 Da / Num. of mol.: 1 / Fragment: Erbin pdz domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: erbin / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q96RT1
#2: Protein/peptide phage-derived peptide


Mass: 877.939 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. IT WAS selected from A phage display library.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1313D HNHB
1413D 15N-separated low mixing time TOCSY
1512D-15N-filtered NOESY
3633D 13C-separated NOESY
3733D-13 filtered, 13C-edited NOESY
3832D-13C-filtered NOESY
NMR detailsText: The resonance assignments were determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM Erbin PDZ (15N) + 2.2 mM peptide; 25 mM sodium phosphate pH 6.5; 50 mM sodium chloride90% H2O, 10% D20
22 mM Erbin PDZ (15N,13C) + 2.2 mM peptide; 25 mM sodium phosphate pH 6.5; 50 mM sodium chloride90% H2O, 10% D20
32 mM Erbin PDZ (15N,13C) + 2.2 mM peptide; 25 mM sodium phosphate pH 6.5; 50 mM sodium chloride100% D2O
42 mM Erbin PDZ (15N) + 2.2 mM peptide; 25 mM sodium phosphate pH 6.5; 50 mM sodium chloride; 15 mg/ml Pf1 phage90% H2O, 10% D20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1250 mM 6.5 1 atm298 K
2250 mM 6.5 1 atm298 K
3250 mM 6.5 1 atm298 K
4250 mM 6.5 1 atm298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1brukercollection
Felix98Accelrysdata analysis
CNS2000.1Accelrysrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The complex was determined using a total of 1717 NOE distance restraints (148 intra residue, 339 sequential, 328 medium range, 699 long-range and 203 intermolecular), 36 hydrogen bond ...Details: The complex was determined using a total of 1717 NOE distance restraints (148 intra residue, 339 sequential, 328 medium range, 699 long-range and 203 intermolecular), 36 hydrogen bond restraints, 156 dihedral angle restraints (86 phi, 44 psi and 26 chi-1) and 82 15N residual dipolar coupling restraints. The best 20 conformers (of 100) had no distance violations greater than 0.12A and no dihedral angle violations greater than 3.0 degrees. RMSD from experimental distance restraints was 0.0055+/-0.0007. The mean backbone rmsd from the mean structure was 0.40+/- 0.05 A for N, Ca and C atoms of residues 10-100. 74% (25%) of residues were in the most favoured (allowed) region of phi/psi space; no residues were in the disallowed region.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: least violation of experimental restraints
Conformers calculated total number: 100 / Conformers submitted total number: 20

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