BMRB Entry 15154

Name: HtrA1 bound to an optimized peptide: NMR assignment of PDZ domain and ligand resonances
Published: 2008-02-11

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PDB ID: 2joa
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15154
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2007-03-01

Original release date:

2008-02-11

Authors:

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

Citation:

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).
PubMed: 17962403

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15b

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	782
13C chemical shifts	432
15N chemical shifts	105

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HtrA1-PDZ	1
2	peptide	2

Entities:

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

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

1

GLY

SER

HIS

MET

LYS

TYR

ILE

GLY

ILE

2

ARG

MET

SER

LEU

THR

SER

LYS

ALA

3

LYS

GLU

LEU

LYS

ASP

ARG

HIS

ARG

ASP

PHE

4

PRO

ASP

VAL

ILE

SER

GLY

ALA

TYR

ILE

5

GLU

VAL

ILE

PRO

ASP

THR

PRO

ALA

GLU

ALA

6

GLY

LEU

LYS

GLU

ASN

ASP

VAL

ILE

7

SER

ILE

ASN

GLY

GLN

SER

VAL

SER

ALA

8

ASN

ASP

VAL

SER

ASP

VAL

ILE

LYS

ARG

GLU

9

SER

THR

LEU

ASN

MET

VAL

ARG

GLY

10

ASN

GLU

ASP

ILE

MET

ILE

THR

VAL

ILE

PRO

11

GLU

ILE

ASP

PRO

Entity 2, peptide 7 residues - 962.093 Da.

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

1

ASP

SER

ARG

ILE

TRP

VAL

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY 13C,15N-filtered in F1	sample_5	isotropic	sample_conditions_1
2D 1H-1H TOCSY,13C,15N-filtered in F1	sample_5	isotropic	sample_conditions_1
3D 1H-13C NOESY, 13C-filtered in F1	sample_6	isotropic	sample_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

SWS	Q92743
PDB	2JOA 2YTW 3NUM 3NZI
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
AlphaFold	F1N152 Q92743