BMRB Entry 17149

Name: Folding Intermediate of the Fyn SH3 A39V/N53P/V55L from NMR Relaxation Dispersion Experiments
Published: 2012-08-01

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PDB ID: 2l2p
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17149
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2010-08-25

Original release date:

2012-08-01

Authors:

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

Citation:

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" .

Assembly members:

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

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assignments_fynsh3a39vn53pv55l
- assignments_fynsh3a39vn53pv55l_intermediate

Data type	Count
13C chemical shifts	314
15N chemical shifts	122
1H chemical shifts	505

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	native	1
2	intermediate	1
3	unfolded	1

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

GLY

ALA

MET

VAL

GLN

ILE

SER

THR

LEU

PHE

2

GLU

ALA

LEU

TYR

ASP

TYR

GLU

ALA

ARG

THR

3

GLU

ASP

LEU

SER

PHE

HIS

LYS

GLY

GLU

4

LYS

PHE

GLN

ILE

LEU

ASN

SER

GLU

GLY

5

ASP

TRP

GLU

VAL

ARG

SER

LEU

THR

6

GLY

GLU

THR

GLY

TYR

ILE

PRO

SER

PRO

TYR

7

LEU

ALA

PRO

VAL

ASP

ARG

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'-13C glucose; U-15N], 1.0 mM; EDTA 0.2 mM; sodium azide 0.05%; potassium phosphate 50 mM; D2O 100%

sample_1-13C15N_H2O: Fyn SH3 A39V/N53P/V55L, [1'-13C glucose; U-15N], 1.0 mM; EDTA 0.2 mM; sodium azide 0.05%; potassium phosphate 50 mM; H2O 90%; D2O 10%

sample_1-13C15N_D2O: Fyn SH3 A39V/N53P/V55L, [1'-13C glucose; U-15N], 1.2 mM; EDTA 0.2 mM; sodium azide 0.05%; potassium phosphate 50 mM; D2O 10%

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

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_15N2H_H2O	isotropic	sample_conditions_1
3D 1H-15N NOESY-HSQC	sample_15N_H2O	isotropic	sample_conditions_1
3D HNCO	sample_13C15N50%2H_H2O	isotropic	sample_conditions_1
3D HNCA	sample_13C15N50%2H_H2O	isotropic	sample_conditions_1
3D C(CO)NH	sample_13C15N50%2H_H2O	isotropic	sample_conditions_1
2D 1H-13C CTHSQC	sample_13C15N50%2H_D2O	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1-13C15N_H2O	isotropic	sample_conditions_1
15N SQ CPMG	sample_15N2H_H2O	isotropic	sample_conditions_1
15N SQ CPMG	sample_15N2H_H2O	isotropic	sample_conditions_1
15N TROSY/AntiTROSY CPMG	sample_15N2H_H2O	isotropic	sample_conditions_1
15N TROSY/AntiTROSY CPMG	sample_15N2H_H2O	isotropic	sample_conditions_1
15N SQ CPMG	sample_15N2H_H2O_Pf1	anisotropic	sample_conditions_1
15N SQ CPMG	sample_15N2H_H2O_Pf1	anisotropic	sample_conditions_1
15N TROSY/AntiTROSY CPMG	sample_15N2H_H2O_Pf1	anisotropic	sample_conditions_1
15N TROSY/AntiTROSY CPMG	sample_15N2H_H2O_Pf1	anisotropic	sample_conditions_1
15N SQ CPMG	sample_15N2H_H2O_PEG	anisotropic	sample_conditions_1
15N SQ CPMG	sample_15N2H_H2O_PEG	anisotropic	sample_conditions_1
15N TROSY/AntiTROSY CPMG	sample_15N2H_H2O_PEG	anisotropic	sample_conditions_1
15N TROSY/AntiTROSY CPMG	sample_15N2H_H2O_PEG	anisotropic	sample_conditions_1
1HN SQ CPMG	sample_15N2H_H2O	isotropic	sample_conditions_1
1HN SQ CPMG	sample_15N2H_H2O	isotropic	sample_conditions_1
15N SQ CPMG	sample_13C15N50%2H_H2O	isotropic	sample_conditions_1
13CO SQ CPMG	sample_13C15N50%2H_H2O	isotropic	sample_conditions_1
13CO SQ CPMG	sample_13C15N50%2H_H2O	isotropic	sample_conditions_1
15N SQ CPMG	sample_13C15N2H_H2O	isotropic	sample_conditions_1
13CO SQ CPMG	sample_13C15N2H_H2O	isotropic	sample_conditions_1
13CO SQ CPMG	sample_13C15N2H_H2O	isotropic	sample_conditions_1
15N SQ CPMG	sample_13C15N2H_H2O_Pf1	anisotropic	sample_conditions_1
13CO SQ CPMG	sample_13C15N2H_H2O_Pf1	anisotropic	sample_conditions_1
13CO SQ CPMG	sample_13C15N2H_H2O_Pf1	anisotropic	sample_conditions_1
13CA SQ CPMG	sample_2-13C15N_D2O	isotropic	sample_conditions_1
13CA SQ CPMG	sample_2-13C15N_D2O	isotropic	sample_conditions_1
13CA SQ CPMG	sample_1-13C15N_D2O	isotropic	sample_conditions_1
13CA SQ CPMG	sample_1-13C15N_D2O	isotropic	sample_conditions_1
1HA SQ CPMG	sample_13C15N50%2H_D2O	isotropic	sample_conditions_1
1HA SQ CPMG	sample_13C15N50%2H_D2O	isotropic	sample_conditions_1
13CH3 SQ CPMG	sample_1-13C15N_H2O	isotropic	sample_conditions_1
13CH3 SQ CPMG	sample_1-13C15N_H2O	isotropic	sample_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