BMRB Entry 15351

Name: Solution structure of first SH3 domain of adaptor Nck
Published: 2008-02-29

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PDB ID: 2js2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15351
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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:

Solution structure of first SH3 domain of adaptor Nck

Deposition date:

2007-06-29

Original release date:

2008-02-29

Authors:

Hake, Michael; Choowongkomon, Kiattawee; Carlin, Cathleen; Sonnichsen, Frank

Citation:

Citation: Hake, Michael; Choowongkomon, Kiattawee; Kostenko, Olga; Carlin, Cathleen; Sonnichsen, Frank. "Specificity Determinants of a Novel Nck Interaction with the Juxtamembrane Domain of the Epidermal Growth Factor Receptor" Biochemistry 47, 3096-3108 (2008).
PubMed: 18269246

Assembly members:

Assembly members:
Nck1-1, polymer, 63 residues, 7461.453 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: pGEV2

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Nck1-1: GSMAEEVVVVAKFDYVAQQE QELDIKKNERLWLLDDSKSW WRVRNSMNKTGFVPSNYVER KNS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	281
15N chemical shifts	67
1H chemical shifts	441

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Nck1-1 SH3	1

Entities:

Entity 1, Nck1-1 SH3 63 residues - 7461.453 Da.

1

GLY

SER

MET

ALA

GLU

VAL

2

ALA

LYS

PHE

ASP

TYR

VAL

ALA

GLN

GLU

3

GLN

GLU

LEU

ASP

ILE

LYS

ASN

GLU

ARG

4

LEU

TRP

LEU

ASP

SER

LYS

SER

TRP

5

TRP

ARG

VAL

ARG

ASN

SER

MET

ASN

LYS

THR

6

GLY

PHE

VAL

PRO

SER

ASN

TYR

VAL

GLU

ARG

7

LYS

ASN

SER

Samples:

sample_1: Nck1-1, [U-99% 13C; U-99% 15N], 0.5 – 1.0 mM; sodium phosphate 20 mM; sodium chloride 100 mM; sodium azide 2 mM; EDTA 1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 100 mM; pH: 6.1; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMRView v5.2.1, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - water refinement

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 500 MHz
Bruker Avance 600 MHz

PDB	2JS2
DBJ	BAG35571 BAG73433 BAK63238
EMBL	CAA35599
GB	AAD13752 AAH02015 AAH06403 AAI16110 AAI67009
REF	NP_001069540 NP_001100321 NP_001131102 NP_001159671 NP_001233509
SP	P16333 Q99M51
TPG	DAA33097
AlphaFold	P16333 Q99M51