2L2P

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


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC1.0 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide-7, 50 mM potassium phosphate-890% H2O/10% D2O507.01 atm293.15
23D 1H-15N NOESY-HSQC0.7 mM [U-15N] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
33D HNCO1.0 mM [U-13C; U-15N; U-50% 2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
43D HNCA1.0 mM [U-13C; U-15N; U-50% 2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
53D C(CO)NH1.0 mM [U-13C; U-15N; U-50% 2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
62D 1H-13C CTHSQC1.0 mM [U-13C; U-15N; U-50% 2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate100% D2O507.01 atm293.15
72D 1H-13C HSQC1.0 mM [1'-13C glucose; U-15N] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
815N SQ CPMG1.0 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide-7, 50 mM potassium phosphate-890% H2O/10% D2O507.01 atm293.15
915N SQ CPMG1.0 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide-7, 50 mM potassium phosphate-890% H2O/10% D2O507.01 atm293.15
1015N TROSY/AntiTROSY CPMG1.0 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide-7, 50 mM potassium phosphate-890% H2O/10% D2O507.01 atm293.15
1115N TROSY/AntiTROSY CPMG1.0 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide-7, 50 mM potassium phosphate-890% H2O/10% D2O507.01 atm293.15
1215N SQ CPMG0.8 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA-10, 0.05 % sodium azide, 50 mM potassium phosphate, 24 mg/ml Pf1 phage90% H2O/10% D2O507.01 atm293.15
1315N SQ CPMG0.8 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA-10, 0.05 % sodium azide, 50 mM potassium phosphate, 24 mg/ml Pf1 phage90% H2O/10% D2O507.01 atm293.15
1415N TROSY/AntiTROSY CPMG0.8 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA-10, 0.05 % sodium azide, 50 mM potassium phosphate, 24 mg/ml Pf1 phage90% H2O/10% D2O507.01 atm293.15
1515N TROSY/AntiTROSY CPMG0.8 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA-10, 0.05 % sodium azide, 50 mM potassium phosphate, 24 mg/ml Pf1 phage90% H2O/10% D2O507.01 atm293.15
1615N SQ CPMG0.5 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate, uncertain v/v PEG/hexanol90% H2O/10% D2O507.01 atm293.15
1715N SQ CPMG0.5 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate, uncertain v/v PEG/hexanol90% H2O/10% D2O507.01 atm293.15
1815N TROSY/AntiTROSY CPMG0.5 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate, uncertain v/v PEG/hexanol90% H2O/10% D2O507.01 atm293.15
1915N TROSY/AntiTROSY CPMG0.5 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate, uncertain v/v PEG/hexanol90% H2O/10% D2O507.01 atm293.15
201HN SQ CPMG1.0 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide-7, 50 mM potassium phosphate-890% H2O/10% D2O507.01 atm293.15
211HN SQ CPMG1.0 mM [U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide-7, 50 mM potassium phosphate-890% H2O/10% D2O507.01 atm293.15
2215N SQ CPMG1.0 mM [U-13C; U-15N; U-50% 2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
2313CO SQ CPMG1.0 mM [U-13C; U-15N; U-50% 2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
2413CO SQ CPMG1.0 mM [U-13C; U-15N; U-50% 2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
2515N SQ CPMG1.2 mM [U-13C; U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
2613CO SQ CPMG1.2 mM [U-13C; U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
2713CO SQ CPMG1.2 mM [U-13C; U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
2815N SQ CPMG0.8 mM [U-13C; U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate, 36 mg/ml Pf1 phage90% H2O/10% D2O507.01 atm293.15
2913CO SQ CPMG0.8 mM [U-13C; U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate, 36 mg/ml Pf1 phage90% H2O/10% D2O507.01 atm293.15
3013CO SQ CPMG0.8 mM [U-13C; U-15N; U-2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate, 36 mg/ml Pf1 phage90% H2O/10% D2O507.01 atm293.15
3113CA SQ CPMG1.0 mM [2'-13C glucose; U-15N] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate100% D2O507.01 atm293.15
3213CA SQ CPMG1.0 mM [2'-13C glucose; U-15N] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate100% D2O507.01 atm293.15
3313CA SQ CPMG1.2 mM [1'-13C glucose; U-15N] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate100% D2O507.01 atm293.15
3413CA SQ CPMG1.2 mM [1'-13C glucose; U-15N] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate100% D2O507.01 atm293.15
351HA SQ CPMG1.0 mM [U-13C; U-15N; U-50% 2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate100% D2O507.01 atm293.15
361HA SQ CPMG1.0 mM [U-13C; U-15N; U-50% 2H] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate100% D2O507.01 atm293.15
3713CH3 SQ CPMG1.0 mM [1'-13C glucose; U-15N] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
3813CH3 SQ CPMG1.0 mM [1'-13C glucose; U-15N] Fyn SH3 A39V/N53P/V55L, 0.2 mM EDTA, 0.05 % sodium azide, 50 mM potassium phosphate90% H2O/10% D2O507.01 atm293.15
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianINOVA800
2VarianINOVA600
3VarianINOVA500
4VarianINOVA500
NMR Refinement
MethodDetailsSoftware
molecular dynamicsReplica exchange molecular dynamics simulation of residues 1 to 56 with CamShift chemical shift restraints, DNH RDCs and 13CO RCSAs. Residues 57 to 60 were excluded because they exhibit random coil chemical shifts and are unstructured in the folding intermediate.NMRPipe
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number6666
Conformers Submitted Total Number10
Representative Model1 (lowest energy)
Additional NMR Experimental Information
DetailsThe CPMG experiments were supplemented with sign determination experiments as appropriate.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1processingNMRPipe3.0 Rev 2007.068.09.07Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2spectra analysisNMRViewJ8.0.rc4Johnson, One Moon Scientific
3peak pickingMUNIN1.0Orekhov, Ibraghimov, Billeter
4cpmg analysisCATIA0.52pHansen
5structure solutionALMOST1.0.4Cavalli
6chemical shift restraintsCamShift1.2Kohlhoff, Robustelli, Cavalli, Salvatella, Vendruscolo
7refinementALMOST1.0.4Cavalli