BMRB Entry 34689

Name: Two-state liquid NMR Structure of a PDZ2 Domain from hPTP1E, complexed with RA-GEF2 peptide
Published: 2022-09-02

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PDB ID: 7qcy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34689
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Two-state liquid NMR Structure of a PDZ2 Domain from hPTP1E, complexed with RA-GEF2 peptide

Deposition date:

2021-11-25

Original release date:

2022-09-02

Authors:

Ashkinadze, D.; Kadavath, H.; Chi, C.; Friedmann, M.; Strotz, D.; Kumari, P.; Minges, M.; Cadalbert, R.; Koenigl, S.; Guentert, P.; Voegeli, B.; Riek, R.

Citation:

Citation: Ashkinadze, Dzmitry; Kadavath, Harindranath; Pokharna, Aditya; Chi, Celestine; Friedmann, Michael; Strotz, Dean; Kumari, Pratibha; Minges, Martina; Cadalbert, Riccardo; Konigl, Stefan; Guentert, Peter; Vogeli, Beat; Riek, Roland. "Atomic resolution protein allostery from the multi-state structure of a PDZ domain" Nat. Commun. 13, 6232-6232 (2022).
PubMed: 36266302

Assembly members:

Assembly members:
entity_1, polymer, 96 residues, 10020.252 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 BL21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: PKPGDIFEVELAKNDNSLGI SVTGGVNTSVRHGGIYVKAV IPQGAAESDGRIHKGDRVLA VNGVSLEGATHKQAVETLRN TGQVVHLLLEKGQSPT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	252
15N chemical shifts	92
1H chemical shifts	587

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 96 residues - 10020.252 Da.

1

PRO

LYS

PRO

GLY

ASP

ILE

PHE

GLU

VAL

GLU

2

LEU

ALA

LYS

ASN

ASP

ASN

SER

LEU

GLY

ILE

3

SER

VAL

THR

GLY

VAL

ASN

THR

SER

VAL

4

ARG

HIS

GLY

ILE

TYR

VAL

LYS

ALA

VAL

5

ILE

PRO

GLN

GLY

ALA

GLU

SER

ASP

GLY

6

ARG

ILE

HIS

LYS

GLY

ASP

ARG

VAL

LEU

ALA

7

VAL

ASN

GLY

VAL

SER

LEU

GLU

GLY

ALA

THR

8

HIS

LYS

GLN

ALA

VAL

GLU

THR

LEU

ARG

ASN

9

THR

GLY

GLN

VAL

HIS

LEU

GLU

10

LYS

GLY

GLN

SER

PRO

THR

Samples:

sample_1: PDZ2 domain, [U-100% 13C; U-100% 15N], 2 mM; RA-GEF2 peptide 2 mM

sample_conditions_1: ionic strength: 150 mM; pH: 6.8 pD; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

XEASY, Bartels et al. - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - peak picking

NMR spectrometers:

Bruker AVANCE 700 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks