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HtrA1 bound to an optimized peptide: NMR assignment of PDZ domain and ligand resonances
Authors
Runyon, S.T., Zhang, Y., Appleton, B.A., Sazinksy, S.L., Wu, P., Pan, B., Wiesmann, C., Skelton, N.J., Sidhu, S.S.
Assembly
protein-peptide complex
Entity
1. HtrA1-PDZ (polymer, Thiol state: not present), 105 monomers, 11567.11 Da Detail

GSHMKKYIGI RMMSLTSSKA KELKDRHRDF PDVISGAYII EVIPDTPAEA GGLKENDVII SINGQSVVSA NDVSDVIKRE STLNMVVRRG NEDIMITVIP EEIDP


2. synthetic peptide H1-C1 (polymer, Thiol state: not present), 7 monomers, 961.0744 Da Detail

DSRIWWV


Total weight
12528.185 Da
Max. entity weight
11567.11 Da
Source organism
Homo sapiens
Exptl. method
solution NMR
Refine. method
torsion angle dynamics
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 96.4 %, Completeness: 89.4 %, Completeness (bb): 90.7 % Detail

Polymer type: polypeptide(L)

Total1H13C15N
All89.4 % (1158 of 1295)92.5 % (620 of 670)86.1 % (433 of 503)86.1 % (105 of 122)
Backbone90.7 % (594 of 655)94.1 % (206 of 219)88.8 % (292 of 329)89.7 % (96 of 107)
Sidechain88.5 % (659 of 745)91.8 % (414 of 451)84.6 % (236 of 279)60.0 % (9 of 15)
Aromatic36.2 % (21 of 58)62.1 % (18 of 29)11.1 % (3 of 27) 0.0 % (0 of 2)
Methyl95.7 % (132 of 138)97.1 % (67 of 69)94.2 % (65 of 69)

1. HtrA1-PDZ

GSHMKKYIGI RMMSLTSSKA KELKDRHRDF PDVISGAYII EVIPDTPAEA GGLKENDVII SINGQSVVSA NDVSDVIKRE STLNMVVRRG NEDIMITVIP EEIDP

2. synthetic peptide H1-C1

DSRIWWV

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 25mM sodium phosphate pH 6.0 + 1mM sodium azide - slight excess of peptide


#NameIsotope labelingTypeConcentration
1HtrA1-PDZ[U-15N]2 mM
2synthetic peptide H1-C1natural abundance4 mM
3sodium phosphatenatural abundance25 mM
4sodium azidenatural abundance1 mM
Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 25mM sodium phosphate pH 6.0 + 1mM sodium azide - excess peptide


#NameIsotope labelingTypeConcentration
5HtrA1-PDZ[U-13C; U-15N]2 mM
6synthetic peptide H1-C1natural abundance4 mM
7sodium phosphatenatural abundance25 mM
8sodium azidenatural abundance1 mM
Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 25mM sodium phosphate pH 6.0 + 1mM sodium azide - excess of peptide


#NameIsotope labelingTypeConcentration
9HtrA1-PDZ[U-13C; U-15N]2 mM
10synthetic peptide H1-C1natural abundance4 mM
11sodium phosphatenatural abundance25 mM
12sodium azidenatural abundance1 mM
Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 25mM sodium phosphate pH 6.0 + 1mM sodium azide -slight excess of peptide; partial carbon label for stereo specific methyl assignment


#NameIsotope labelingTypeConcentration
13HtrA1-PDZ[U-10% 13C; U-99% 15N]2 mM
14synthetic peptide H1-C1natural abundance4 mM
15sodium phosphatenatural abundance25 mM
16sodium azidenatural abundance1 mM
Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 25mM sodium phosphate pH 6.0 + 1mM sodium azide - slight excess of PDZ


#NameIsotope labelingTypeConcentration
17HtrA1-PDZ[U-13C; U-15N]2 mM
18synthetic peptide H1-C1natural abundance1.8 mM
19sodium phosphatenatural abundance25 mM
20sodium azidenatural abundance1 mM
Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 25mM sodium phosphate pH 6.0 + 1mM sodium azide - slight excess of PDZ


#NameIsotope labelingTypeConcentration
21HtrA1-PDZ[U-13C; U-15N]2 mM
22synthetic peptide H1-C1natural abundance1.8 mM
23sodium phosphatenatural abundance25 mM
24sodium azidenatural abundance1 mM

Protein Blocks Logo
Calculated from 20 models in PDB: 2JOA, Strand ID: A, B Detail


Release date
2008-02-10
Citation 1
Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3
Runyon, S.T., Zhang, Y., Appleton, B.A., Sazinksy, S.L., Wu, P., Pan, B., Wiesmann, C., Skelton, N.J., Sidhu, S.S.
Protein Sci. (2007), 16, 2454-2471, PubMed 17962403 , DOI 10.1110/ps.073049407 ,
Citation 2
HtrA1 bound to an optimized peptide: NMR assignment of PDZ domain and ligand resonances
Runyon, S.T., Pan, B., Skelton, N.J.
J. Biomol. NMR (2007), PubMed , DOI:
Entries sharing articles Swiss-Prot: 1 entries Detail
  Swiss-Prot: P83110 released on 2001-09-26
    Title HTRA3_HUMAN Entity Serine protease HTRA3
Related entities 1. HtrA1-PDZ, : 1 : 53 entities Detail
Experiments performed 13 experiments Detail
Keywords HtrA, PDZ domain, peptide-binding module, protein-protein interaction, serine-protease, beta-sandwich, cyclically-permuted, PDZ