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BMRB: 15351

2JS2

Solution structure of first SH3 domain of adaptor Nck

Authors

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

Assembly

Nck1-1 SH3

Entity

1. Nck1-1 SH3 (polymer, Thiol state: not present), 63 monomers, 7450.293 Da Detail

GSMAEEVVVV AKFDYVAQQE QELDIKKNER LWLLDDSKSW WRVRNSMNKT GFVPSNYVER KNS

Formula weight

7450.293 Da

Source organism

Exptl. method

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 91.3 %, Completeness (bb): 94.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.3 % (704 of 771)	88.9 % (360 of 405)	94.5 % (277 of 293)	91.8 % (67 of 73)
Backbone	94.4 % (355 of 376)	92.1 % (117 of 127)	95.2 % (178 of 187)	96.8 % (60 of 62)
Sidechain	89.7 % (409 of 456)	87.4 % (243 of 278)	95.2 % (159 of 167)	63.6 % (7 of 11)
Aromatic	97.2 % (70 of 72)	100.0 % (36 of 36)	93.9 % (31 of 33)	100.0 % (3 of 3)
Methyl	100.0 % (60 of 60)	100.0 % (30 of 30)	100.0 % (30 of 30)

1. Nck1-1

GSMAEEVVVV AKFDYVAQQE QELDIKKNER LWLLDDSKSW WRVRNSMNKT GFVPSNYVER KNS

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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

LACS Plot; CA

Referencing offset: -0.43 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.43 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.55 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JS2, 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., 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: 15349 released on 2008-02-28
    Title Solution structure of second SH3 domain of adaptor Nck
  Swiss-Prot: P16333 released on 1990-08-01
    Title NCK1_HUMAN Entity Cytoplasmic protein NCK1

Related entities 1. Nck1-1 SH3, : 1 : 13 : 252 entities Detail

Interaction partners 1. Nck1-1 SH3, : 21 interactors Detail

More details for 21 interactors identified by 6 citations

Experiments performed 11 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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

5 2D 1H-13C HSQC

Instrument

Bruker Avance - 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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

11 3D HNHB

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	Nck1-1	[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	H2O			90 %
7	D2O			10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15351_2js2.nef
Input source #2: Coordindates	2js2.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---
GSMAEEVVVVAKFDYVAQQEQELDIKKNERLWLLDDSKSWWRVRNSMNKTGFVPSNYVERKNS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSMAEEVVVVAKFDYVAQQEQELDIKKNERLWLLDDSKSWWRVRNSMNKTGFVPSNYVERKNS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	63	0	0	100.0

Content subtype: combined_15351_2js2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	729		98.4 (chain: A, length: 63)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1087 (1)	noe	93.7 (chain: A, length: 63)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	89 (89)	.	85.7 (chain: A, length: 63)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 381
  - ¹³C chemical shifts: 281
  - ¹⁵N chemical shifts: 67
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 93.7%
- Total number of restraints: 1086
- Weight of restraints: 1.0 (1086)
- Potential type of restraints: upper-bound-parabolic (1086)
- Range of distance target values: 2.16, 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 85.7%
- Total number of restraints: 89
- Total number of restraints per polymer type: 89
- Weight of restraints: 1.0 (89)
- Potential type of restraints: square-well-parabolic (89)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords adaptor, SH3 domain, signaling