BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17149

Title: Folding Intermediate of the Fyn SH3 A39V/N53P/V55L from NMR Relaxation Dispersion Experiments

Authors: Neudecker, Philipp; Robustelli, Paul; Cavalli, Andrea; Vendruscolo, Michele; Kay, Lewis

Citation: Neudecker, Philipp; Robustelli, Paul; Cavalli, Andrea; Walsh, Patrick; Lundstrom, Patrik; Zarrine-Afsar, Arash; Vendruscolo, Michele; Kay, Lewis. "High-Resolution Structure of an Amyloidogenic Low-Populated Folding Intermediate from NMR Relaxation Dispersion Experiments"  Not known ., .-..

Assembly members:
Fyn_SH3_A39V-N53P-V55L, polymer, 66 residues, 7532.2 Da.

Natural source:   Common Name: Chicken   Taxonomy ID: 9031   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Gallus gallus

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

Entity Sequences (FASTA):
Fyn_SH3_A39V-N53P-V55L: GAMVQISTLFEALYDYEART EDDLSFHKGEKFQILNSSEG DWWEVRSLTTGETGYIPSPY LAPVDR

Data typeCount
13C chemical shifts314
15N chemical shifts122
1H chemical shifts505

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1native1
2intermediate1
3unfolded1

Entities:

Entity 1, native 66 residues - 7532.2 Da.

The sequence has a short N-terminal cloning artifact up to and including Ser1 (GAMVQIS). Residues 2..84 are a mutant of the Fyn SH3 domain. Arg60 is a cloning artifact.

1   GLYALAMETVALGLNILESERTHRLEUPHE
2   GLUALALEUTYRASPTYRGLUALAARGTHR
3   GLUASPASPLEUSERPHEHISLYSGLYGLU
4   LYSPHEGLNILELEUASNSERSERGLUGLY
5   ASPTRPTRPGLUVALARGSERLEUTHRTHR
6   GLYGLUTHRGLYTYRILEPROSERPROTYR
7   LEUALAPROVALASPARG

Samples:

sample_15N_H2O: Fyn SH3 A39V/N53P/V55L, [U-15N], 0.7 mM; EDTA 0.2 mM; sodium azide 0.05%; potassium phosphate 50 mM; H2O 90%; D2O 10%

sample_15N2H_H2O: Fyn SH3 A39V/N53P/V55L, [U-15N; U-2H], 1.0 mM; EDTA 0.2 mM; sodium azide 0.05%; potassium phosphate 50 mM; H2O 90%; D2O 10%

sample_15N2H_H2O_Pf1: Fyn SH3 A39V/N53P/V55L, [U-15N; U-2H], 0.8 mM; EDTA 0.2 mM; sodium azide 0.05%; potassium phosphate 50 mM; Pf1 phage 24 mg/ml; H2O 90%; D2O 10%

sample_15N2H_H2O_PEG: Fyn SH3 A39V/N53P/V55L, [U-15N; U-2H], 0.5 mM; EDTA 0.2 mM; sodium azide 0.05%; potassium phosphate 50 mM; PEG/hexanol uncertain v/v; H2O 90%; D2O 10%

sample_13C15N2H_H2O: Fyn SH3 A39V/N53P/V55L, [U-13C; U-15N; U-2H], 1.2 mM; EDTA 0.2 mM; sodium azide 0.05%; potassium phosphate 50 mM; H2O 90%; D2O 10%

sample_13C15N2H_H2O_Pf1: Fyn SH3 A39V/N53P/V55L, [U-13C; U-15N; U-2H], 0.8 mM; EDTA 0.2 mM; sodium azide 0.05%; potassium phosphate 50 mM; Pf1 phage 36 mg/ml; H2O 90%; D2O 10%

sample_13C15N50%2H_H2O: Fyn SH3 A39V/N53P/V55L, [U-13C; U-15N; U-50% 2H], 1.0 mM; EDTA 0.2 mM; sodium azide 0.05%; potassium phosphate 50 mM; H2O 90%; D2O 10%

sample_13C15N50%2H_D2O: Fyn SH3 A39V/N53P/V55L, [U-13C; U-15N; U-50% 2H], 1.0 mM; EDTA 0.2 mM; sodium azide 0.05%; potassium phosphate 50 mM; D2O 100%

sample_2-13C15N_D2O: Fyn SH3 A39V/N53P/V55L, [2, $Fyn_SH3_A39V-N53P-V55L 1.0; 17149, 9, 0.2; 17149, 9, 0.05; 17149, 9, 50; 17149, 9, 100; 17149, 9,

sample_1-13C15N_H2O: Fyn SH3 A39V/N53P/V55L, [1, $Fyn_SH3_A39V-N53P-V55L 1.0; 17149, 10, 0.2; 17149, 10, 0.05; 17149, 10, 50; 17149, 10, 90; 17149, 10, 10; 17149, 10,

sample_1-13C15N_D2O: Fyn SH3 A39V/N53P/V55L, [1, $Fyn_SH3_A39V-N53P-V55L 1.2; 17149, 11, 0.2; 17149, 11, 0.05; 17149, 11, 50; 17149, 11, 10; 17149, 11,

sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 293.15 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_15N2H_H2Oisotropicsample_conditions_1
3D 1H-15N NOESY-HSQCsample_15N_H2Oisotropicsample_conditions_1
3D HNCOsample_13C15N50%2H_H2Oisotropicsample_conditions_1
3D HNCAsample_13C15N50%2H_H2Oisotropicsample_conditions_1
3D C(CO)NHsample_13C15N50%2H_H2Oisotropicsample_conditions_1
2D 1H-13C CTHSQCsample_13C15N50%2H_D2Oisotropicsample_conditions_1
2D 1H-13C HSQCsample_1-13C15N_H2Oisotropicsample_conditions_1
15N SQ CPMGsample_15N2H_H2Oisotropicsample_conditions_1
15N SQ CPMGsample_15N2H_H2Oisotropicsample_conditions_1
15N TROSY/AntiTROSY CPMGsample_15N2H_H2Oisotropicsample_conditions_1
15N TROSY/AntiTROSY CPMGsample_15N2H_H2Oisotropicsample_conditions_1
15N SQ CPMGsample_15N2H_H2O_Pf1anisotropicsample_conditions_1
15N SQ CPMGsample_15N2H_H2O_Pf1anisotropicsample_conditions_1
15N TROSY/AntiTROSY CPMGsample_15N2H_H2O_Pf1anisotropicsample_conditions_1
15N TROSY/AntiTROSY CPMGsample_15N2H_H2O_Pf1anisotropicsample_conditions_1
15N SQ CPMGsample_15N2H_H2O_PEGanisotropicsample_conditions_1
15N SQ CPMGsample_15N2H_H2O_PEGanisotropicsample_conditions_1
15N TROSY/AntiTROSY CPMGsample_15N2H_H2O_PEGanisotropicsample_conditions_1
15N TROSY/AntiTROSY CPMGsample_15N2H_H2O_PEGanisotropicsample_conditions_1
1HN SQ CPMGsample_15N2H_H2Oisotropicsample_conditions_1
1HN SQ CPMGsample_15N2H_H2Oisotropicsample_conditions_1
15N SQ CPMGsample_13C15N50%2H_H2Oisotropicsample_conditions_1
13CO SQ CPMGsample_13C15N50%2H_H2Oisotropicsample_conditions_1
13CO SQ CPMGsample_13C15N50%2H_H2Oisotropicsample_conditions_1
15N SQ CPMGsample_13C15N2H_H2Oisotropicsample_conditions_1
13CO SQ CPMGsample_13C15N2H_H2Oisotropicsample_conditions_1
13CO SQ CPMGsample_13C15N2H_H2Oisotropicsample_conditions_1
15N SQ CPMGsample_13C15N2H_H2O_Pf1anisotropicsample_conditions_1
13CO SQ CPMGsample_13C15N2H_H2O_Pf1anisotropicsample_conditions_1
13CO SQ CPMGsample_13C15N2H_H2O_Pf1anisotropicsample_conditions_1
13CA SQ CPMGsample_2-13C15N_D2Oisotropicsample_conditions_1
13CA SQ CPMGsample_2-13C15N_D2Oisotropicsample_conditions_1
13CA SQ CPMGsample_1-13C15N_D2Oisotropicsample_conditions_1
13CA SQ CPMGsample_1-13C15N_D2Oisotropicsample_conditions_1
1HA SQ CPMGsample_13C15N50%2H_D2Oisotropicsample_conditions_1
1HA SQ CPMGsample_13C15N50%2H_D2Oisotropicsample_conditions_1
13CH3 SQ CPMGsample_1-13C15N_H2Oisotropicsample_conditions_1
13CH3 SQ CPMGsample_1-13C15N_H2Oisotropicsample_conditions_1

Software:

NMRPipe v3.0 Rev 2007.068.09.07, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRViewJ v8.0.rc4, Johnson, One Moon Scientific - spectra analysis

MUNIN v1.0, Orekhov, Ibraghimov, Billeter - peak picking

CATIA v0.52p, Hansen - CPMG analysis

almost v1.0.4, Cavalli - structure solution

CamShift v1.2, Kohlhoff, Robustelli, Cavalli, Salvatella, Vendruscolo - chemical shift restraints

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz
  • Varian INOVA 500 MHz
  • Varian INOVA 500 MHz

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