BMRB: 17149

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

Authors

Neudecker, P., Robustelli, P., Cavalli, A., Vendruscolo, M., Kay, L.E.

Assembly

Fyn SH3 A39V-N53P-V55L

Entity

1. Fyn SH3 A39V-N53P-V55L (polymer, Thiol state: not present), 66 monomers, 7532.191 × 3 Da Detail

GAMVQISTLF EALYDYEART EDDLSFHKGE KFQILNSSEG DWWEVRSLTT GETGYIPSPY LAPVDR

Total weight

22596.572 Da

Max. entity weight

7532.191 Da

Source organism

Gallus gallus

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 77.2 %, Completeness (bb): 85.4 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	77.2 % (590 of 764)	87.8 % (345 of 393)	58.7 % (178 of 303)	98.5 % (67 of 68)
Backbone	85.4 % (333 of 390)	97.0 % (130 of 134)	73.1 % (141 of 193)	98.4 % (62 of 63)
Sidechain	62.1 % (270 of 435)	83.0 % (215 of 259)	29.2 % (50 of 171)	100.0 % (5 of 5)
Aromatic	31.1 % (28 of 90)	53.3 % (24 of 45)	4.7 % (2 of 43)	100.0 % (2 of 2)
Methyl	100.0 % (66 of 66)	100.0 % (33 of 33)	100.0 % (33 of 33)

1. Fyn SH3 A39V-N53P-V55L

GAMVQISTLF EALYDYEART EDDLSFHKGE KFQILNSSEG DWWEVRSLTT GETGYIPSPY LAPVDR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Fyn SH3 A39V/N53P/V55L	[U-15N]		0.7 mM
2	EDTA	natural abundance		0.2 mM
3	sodium azide	natural abundance		0.05 %
4	potassium phosphate	natural abundance		50 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	Fyn SH3 A39V/N53P/V55L	[U-15N; U-2H]		1.0 mM
8	EDTA	natural abundance		0.2 mM
9	sodium azide	natural abundance		0.05 %
10	potassium phosphate	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
13	Fyn SH3 A39V/N53P/V55L	[U-15N; U-2H]		0.8 mM
14	EDTA	natural abundance		0.2 mM
15	sodium azide	natural abundance		0.05 %
16	potassium phosphate	natural abundance		50 mM
17	Pf1 phage	natural abundance		24 mg/mL
18	H2O	natural abundance		90 %
19	D2O	natural abundance		10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
20	Fyn SH3 A39V/N53P/V55L	[U-15N; U-2H]		0.5 mM
21	EDTA	natural abundance		0.2 mM
22	sodium azide	natural abundance		0.05 %
23	potassium phosphate	natural abundance		50 mM
24	PEG/hexanol	natural abundance		uncertain v/v
25	H2O	natural abundance		90 %
26	D2O	natural abundance		10 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
27	Fyn SH3 A39V/N53P/V55L	[U-13C; U-15N; U-2H]		1.2 mM
28	EDTA	natural abundance		0.2 mM
29	sodium azide	natural abundance		0.05 %
30	potassium phosphate	natural abundance		50 mM
31	H2O	natural abundance		90 %
32	D2O	natural abundance		10 %

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
33	Fyn SH3 A39V/N53P/V55L	[U-13C; U-15N; U-2H]		0.8 mM
34	EDTA	natural abundance		0.2 mM
35	sodium azide	natural abundance		0.05 %
36	potassium phosphate	natural abundance		50 mM
37	Pf1 phage	natural abundance		36 mg/mL
38	H2O	natural abundance		90 %
39	D2O	natural abundance		10 %

Sample #7

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
40	Fyn SH3 A39V/N53P/V55L	[U-13C; U-15N; U-50% 2H]		1.0 mM
41	EDTA	natural abundance		0.2 mM
42	sodium azide	natural abundance		0.05 %
43	potassium phosphate	natural abundance		50 mM
44	H2O	natural abundance		90 %
45	D2O	natural abundance		10 %

Sample #8

Solvent system 100% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
46	Fyn SH3 A39V/N53P/V55L	[U-13C; U-15N; U-50% 2H]		1.0 mM
47	EDTA	natural abundance		0.2 mM
48	sodium azide	natural abundance		0.05 %
49	potassium phosphate	natural abundance		50 mM
50	D2O	natural abundance		100 %

Sample #9

Solvent system 100% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
51	Fyn SH3 A39V/N53P/V55L	[2'-13C glucose; U-15N]		1.0 mM
52	EDTA	natural abundance		0.2 mM
53	sodium azide	natural abundance		0.05 %
54	potassium phosphate	natural abundance		50 mM
55	D2O	natural abundance		100 %

Sample #10

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
56	Fyn SH3 A39V/N53P/V55L	[1'-13C glucose; U-15N]		1.0 mM
57	EDTA	natural abundance		0.2 mM
58	sodium azide	natural abundance		0.05 %
59	potassium phosphate	natural abundance		50 mM
60	H2O	natural abundance		90 %
61	D2O	natural abundance		10 %

Sample #11

Solvent system 100% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
62	Fyn SH3 A39V/N53P/V55L	[1'-13C glucose; U-15N]		1.2 mM
63	EDTA	natural abundance		0.2 mM
64	sodium azide	natural abundance		0.05 %
65	potassium phosphate	natural abundance		50 mM
66	D2O	natural abundance		10 %

Hide sample codition

Chem. Shift Complete2

Sequence coverage: 90.9 %, Completeness: 59.0 %, Completeness (bb): 77.1 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	59.0 % (901 of 1528)	57.9 % (455 of 786)	53.6 % (325 of 606)	89.0 % (121 of 136)
Backbone	77.1 % (601 of 780)	84.0 % (225 of 268)	67.9 % (262 of 386)	90.5 % (114 of 126)
Sidechain	37.1 % (323 of 870)	44.4 % (230 of 518)	25.1 % (86 of 342)	70.0 % (7 of 10)
Aromatic	17.8 % (32 of 180)	28.9 % (26 of 90)	2.3 % (2 of 86)	100.0 % (4 of 4)
Methyl	74.2 % (98 of 132)	56.1 % (37 of 66)	92.4 % (61 of 66)

1. Fyn SH3 A39V-N53P-V55L

GAMVQISTLF EALYDYEART EDDLSFHKGE KFQILNSSEG DWWEVRSLTT GETGYIPSPY LAPVDR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Fyn SH3 A39V/N53P/V55L	[U-15N]		0.7 mM
2	EDTA	natural abundance		0.2 mM
3	sodium azide	natural abundance		0.05 %
4	potassium phosphate	natural abundance		50 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	Fyn SH3 A39V/N53P/V55L	[U-15N; U-2H]		1.0 mM
8	EDTA	natural abundance		0.2 mM
9	sodium azide	natural abundance		0.05 %
10	potassium phosphate	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
13	Fyn SH3 A39V/N53P/V55L	[U-15N; U-2H]		0.8 mM
14	EDTA	natural abundance		0.2 mM
15	sodium azide	natural abundance		0.05 %
16	potassium phosphate	natural abundance		50 mM
17	Pf1 phage	natural abundance		24 mg/mL
18	H2O	natural abundance		90 %
19	D2O	natural abundance		10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
20	Fyn SH3 A39V/N53P/V55L	[U-15N; U-2H]		0.5 mM
21	EDTA	natural abundance		0.2 mM
22	sodium azide	natural abundance		0.05 %
23	potassium phosphate	natural abundance		50 mM
24	PEG/hexanol	natural abundance		uncertain v/v
25	H2O	natural abundance		90 %
26	D2O	natural abundance		10 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
27	Fyn SH3 A39V/N53P/V55L	[U-13C; U-15N; U-2H]		1.2 mM
28	EDTA	natural abundance		0.2 mM
29	sodium azide	natural abundance		0.05 %
30	potassium phosphate	natural abundance		50 mM
31	H2O	natural abundance		90 %
32	D2O	natural abundance		10 %

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
33	Fyn SH3 A39V/N53P/V55L	[U-13C; U-15N; U-2H]		0.8 mM
34	EDTA	natural abundance		0.2 mM
35	sodium azide	natural abundance		0.05 %
36	potassium phosphate	natural abundance		50 mM
37	Pf1 phage	natural abundance		36 mg/mL
38	H2O	natural abundance		90 %
39	D2O	natural abundance		10 %

Sample #7

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
40	Fyn SH3 A39V/N53P/V55L	[U-13C; U-15N; U-50% 2H]		1.0 mM
41	EDTA	natural abundance		0.2 mM
42	sodium azide	natural abundance		0.05 %
43	potassium phosphate	natural abundance		50 mM
44	H2O	natural abundance		90 %
45	D2O	natural abundance		10 %

Sample #8

Solvent system 100% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
46	Fyn SH3 A39V/N53P/V55L	[U-13C; U-15N; U-50% 2H]		1.0 mM
47	EDTA	natural abundance		0.2 mM
48	sodium azide	natural abundance		0.05 %
49	potassium phosphate	natural abundance		50 mM
50	D2O	natural abundance		100 %

Sample #9

Solvent system 100% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
51	Fyn SH3 A39V/N53P/V55L	[2'-13C glucose; U-15N]		1.0 mM
52	EDTA	natural abundance		0.2 mM
53	sodium azide	natural abundance		0.05 %
54	potassium phosphate	natural abundance		50 mM
55	D2O	natural abundance		100 %

Sample #10

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
56	Fyn SH3 A39V/N53P/V55L	[1'-13C glucose; U-15N]		1.0 mM
57	EDTA	natural abundance		0.2 mM
58	sodium azide	natural abundance		0.05 %
59	potassium phosphate	natural abundance		50 mM
60	H2O	natural abundance		90 %
61	D2O	natural abundance		10 %

Sample #11

Solvent system 100% D2O, Pressure 1 atm, Temperature 293.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
62	Fyn SH3 A39V/N53P/V55L	[1'-13C glucose; U-15N]		1.2 mM
63	EDTA	natural abundance		0.2 mM
64	sodium azide	natural abundance		0.05 %
65	potassium phosphate	natural abundance		50 mM
66	D2O	natural abundance		10 %

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Protein Blocks Logo

Calculated from 10 models in PDB: 2L2P, Strand ID: A Detail

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Release date

2012-07-31

Citation

High-Resolution Structure of an Amyloidogenic Low-Populated Folding Intermediate from NMR Relaxation Dispersion Experiments
Neudecker, P., Robustelli, P., Cavalli, A., Walsh, P., Lundstrom, P., Zarrine-Afsar, A., Vendruscolo, M., Kay, L.E.
Not known

Related entities 1. Fyn SH3 A39V-N53P-V55L, : 1 : 1 : 1 : 288 entities Detail

Interaction partners 1. Fyn SH3 A39V-N53P-V55L, : 1 interactors Detail

Experiments performed 38 experiments Detail