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BMRB: 15349

2JS0

Solution structure of second SH3 domain of adaptor Nck

Authors

Hake, M.J., Choowongkomon, K., Carlin, C.R., Sonnichsen, F.D.

Assembly

Nck1-2 SH3

Entity

1. Nck1-2 SH3 (polymer, Thiol state: all free), 61 monomers, 6984.746 Da Detail

GSLNMPAYVK FNYMAEREDE LSLIKGTKVI VMEKCSDGWW RGSYNGQVGW FPSNYVTEEG D

Formula weight

6984.746 Da

Source organism

Exptl. method

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 92.6 %, Completeness (bb): 93.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.6 % (663 of 716)	93.3 % (347 of 372)	93.1 % (258 of 277)	86.6 % (58 of 67)
Backbone	93.6 % (339 of 362)	93.7 % (119 of 127)	93.8 % (165 of 176)	93.2 % (55 of 59)
Sidechain	92.2 % (376 of 408)	93.1 % (228 of 245)	93.5 % (145 of 155)	37.5 % (3 of 8)
Aromatic	81.8 % (72 of 88)	81.8 % (36 of 44)	85.4 % (35 of 41)	33.3 % (1 of 3)
Methyl	95.8 % (46 of 48)	95.8 % (23 of 24)	95.8 % (23 of 24)

1. Nck1-2

GSLNMPAYVK FNYMAEREDE LSLIKGTKVI VMEKCSDGWW RGSYNGQVGW FPSNYVTEEG D

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.1 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	Nck1-2	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		2 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		4 mM

LACS Plot; CA

Referencing offset: -0.34 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.34 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.54 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JS0, Strand ID: A Detail

Release date

2008-02-28

Citation

Specificity determinants of a novel Nck interaction with the juxtamembrane domain of the epidermal growth factor receptor
Hake, M.J., Choowongkomon, K., Kostenko, O., Carlin, C.R., Sonnichsen, F.D.
Biochemistry (2008), 47, 3096-3108, PubMed 18269246 , DOI 10.1021/bi701549a , Abstract

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

  BMRB: 15351 released on 2008-02-28
    Title Solution structure of first SH3 domain of adaptor Nck
  Swiss-Prot: P16333 released on 1990-08-01
    Title NCK1_HUMAN Entity Cytoplasmic protein NCK1

Related entities 1. Nck1-2 SH3, : 1 : 3 : 256 entities Detail

Interaction partners 1. Nck1-2 SH3, : 124 interactors Detail

More details for 124 interactors identified by 36 citations

Experiments performed 10 experiments Detail

1 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.1 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	Nck1-2	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		2 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		4 mM

2 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.1 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	Nck1-2	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		2 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		4 mM

3 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.1 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	Nck1-2	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		2 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		4 mM

4 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.1 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	Nck1-2	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		2 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		4 mM

5 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.1 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	Nck1-2	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		2 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		4 mM

6 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.1 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	Nck1-2	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		2 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		4 mM

7 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.1 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	Nck1-2	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		2 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		4 mM

8 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.1 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	Nck1-2	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		2 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		4 mM

9 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.1 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	Nck1-2	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		2 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		4 mM

10 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.1 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	Nck1-2	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	sodium azide	natural abundance		2 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		4 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15349_2js0.nef
Input source #2: Coordindates	2js0.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60-
GSLNMPAYVKFNYMAEREDELSLIKGTKVIVMEKCSDGWWRGSYNGQVGWFPSNYVTEEGD
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSLNMPAYVKFNYMAEREDELSLIKGTKVIVMEKCSDGWWRGSYNGQVGWFPSNYVTEEGD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	61	0	0	100.0

Content subtype: combined_15349_2js0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	669		98.4 (chain: A, length: 61)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	897 (1)	noe	95.1 (chain: A, length: 61)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 348
  - ¹³C chemical shifts: 263
  - ¹⁵N chemical shifts: 58
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 95.1%
- Total number of restraints: 897
- Weight of restraints: 1.0 (897)
- Potential type of restraints: upper-bound-parabolic (897)
- Range of distance target values: 2.09, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords adaptor, SH3 domain, signaling