BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 15154

Title: HtrA1 bound to an optimized peptide: NMR assignment of PDZ domain and ligand resonances   PubMed: 17962403

Authors: Runyon, Steven; Zhang, Yingnan; Appleton, Brent; Sazinksy, Stephen; Wu, Ping; Pan, Borlan; Wiesmann, Christian; Skelton, Nicholas; Sidhu, Sachdev

Citation: Runyon, Steven; Zhang, Yingnan; Appleton, Brent; Sazinksy, Stephen; Wu, Ping; Pan, Borlan; Wiesmann, Christian; Skelton, Nicholas; Sidhu, Sachdev. "Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3"  Protein Sci. 16, 2454-2471 (2007).

Assembly members:
HtrA1-PDZ, polymer, 105 residues, 11587.366 Da.
synthetic_peptide_H1-C1, polymer, 7 residues, 962.093 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
HtrA1-PDZ: GSHMKKYIGIRMMSLTSSKA KELKDRHRDFPDVISGAYII EVIPDTPAEAGGLKENDVII SINGQSVVSANDVSDVIKRE STLNMVVRRGNEDIMITVIP EEIDP
synthetic_peptide_H1-C1: DSRIWWV

Data sets:
Data typeCount
1H chemical shifts782
13C chemical shifts432
15N chemical shifts105

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1HtrA1-PDZ1
2peptide2

Entities:

Entity 1, HtrA1-PDZ 105 residues - 11587.366 Da.

Residues 376-379 represent a non-native addition due to the construction

1   GLYSERHISMETLYSLYSTYRILEGLYILE
2   ARGMETMETSERLEUTHRSERSERLYSALA
3   LYSGLULEULYSASPARGHISARGASPPHE
4   PROASPVALILESERGLYALATYRILEILE
5   GLUVALILEPROASPTHRPROALAGLUALA
6   GLYGLYLEULYSGLUASNASPVALILEILE
7   SERILEASNGLYGLNSERVALVALSERALA
8   ASNASPVALSERASPVALILELYSARGGLU
9   SERTHRLEUASNMETVALVALARGARGGLY
10   ASNGLUASPILEMETILETHRVALILEPRO
11   GLUGLUILEASPPRO

Entity 2, peptide 7 residues - 962.093 Da.

synthetic, N-acylated peptide derived from phage-displayed peptide library

1   ASPSERARGILETRPTRPVAL

Samples:

sample_1: HtrA1-PDZ, [U-15N], 2 mM; synthetic peptide H1-C1 4 mM; sodium phosphate 25 mM; sodium azide 1 mM

sample_2: HtrA1-PDZ, [U-13C; U-15N], 2 mM; synthetic peptide H1-C1 4 mM; sodium phosphate 25 mM; sodium azide 1 mM

sample_3: HtrA1-PDZ, [U-13C; U-15N], 2 mM; synthetic peptide H1-C1 4 mM; sodium phosphate 25 mM; sodium azide 1 mM

sample_4: HtrA1-PDZ, [U-10% 13C; U-99% 15N], 2 mM; synthetic peptide H1-C1 4 mM; sodium phosphate 25 mM; sodium azide 1 mM

sample_5: HtrA1-PDZ, [U-13C; U-15N], 2 mM; synthetic peptide H1-C1 1.8 mM; sodium phosphate 25 mM; sodium azide 1 mM

sample_6: HtrA1-PDZ, [U-13C; U-15N], 2 mM; synthetic peptide H1-C1 1.8 mM; sodium phosphate 25 mM; sodium azide 1 mM

sample_conditions_1: ionic strength: 0.025 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
2D 1H-1H NOESY 13C,15N-filtered in F1sample_5isotropicsample_conditions_1
2D 1H-1H TOCSY,13C,15N-filtered in F1sample_5isotropicsample_conditions_1
3D 1H-13C NOESY, 13C-filtered in F1sample_6isotropicsample_conditions_1

Software:

NMRPipe v2005 for LINUX, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.11, Goddard - data analysis

MONTE v2.02, Hitchens, T.K., Lukin, J.A., Zhan, Y. and Rule, G.S. - chemical shift assignment

CYANA v2.0, Guntert, Mumenthaler and Wuthrich - automated noe assignment

TOPSPIN v1.3, Bruker Biospin - collection

TALOS, Cornilescu, Delaglio and Bax - dihedral angle restraints

CNX v2002, Accelrys Software Inc. - structure solution

NMR spectrometers:

  • Bruker DRX 600 MHz
  • Bruker DRX 800 MHz

Related Database Links:

SWS Q92743
PDB
DBJ BAA13322 BAF82778 BAG52446 BAG52557 BAJ20722
EMBL CAA69226 CAI05909
GB AAC95151 AAC97211 AAD41525 AAH11352 AAI56553
REF NP_001245105 NP_001269011 NP_002766 XP_002807519 XP_002821267
SP F1N152 Q92743
TPG DAA14692