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BMRB: 16010

8R5V

How do Proteins Form Amyloid? Insight from the NMR Spectroscopic Characterization of 13C, 15N-labeled Ribonuclease A in 40% Acetic Acid

Authors

Lopez-Alonso, J.P., Bruix, M., Font, J., Ribo, M., Vilanova, M., Morbio, M., Jimenez, M.A., Rico, M., Santoro, J., Gonzalez, C., Laurents, D.V.

Assembly

bovine pancreas ribonuclease A

Entity

1. bovine pancreas ribonuclease A (polymer, Thiol state: all disulfide bound), 124 monomers, 13690.17 Da Detail

KETAAAKFER QHMDSSTSAA SSSNYCNQMM KSRNLTKDRC KPVNTFVHES LADVQAVCSQ KNVACKNGQT NCYQSYSTMS ITDCRETGSS KYPNCAYKTT QANKHIIVAC EGNPYVPVHF DASV

Formula weight

13690.17 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS26:SG	1:CYS84:SG
2	disulfide	sing	1:CYS40:SG	1:CYS95:SG
3	disulfide	sing	1:CYS58:SG	1:CYS110:SG
4	disulfide	sing	1:CYS65:SG	1:CYS72:SG

Source organism

Bos taurus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 56.5 %, Completeness (bb): 95.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	56.5 % (777 of 1376)	40.6 % (290 of 714)	70.3 % (369 of 525)	86.1 % (118 of 137)
Backbone	95.2 % (701 of 736)	93.9 % (232 of 247)	95.7 % (353 of 369)	96.7 % (116 of 120)
Sidechain	25.2 % (192 of 761)	12.4 % (58 of 467)	47.7 % (132 of 277)	11.8 % (2 of 17)
Aromatic	5.3 % (5 of 94)	10.6 % (5 of 47)	0.0 % (0 of 47)
Methyl	24.0 % (24 of 100)	12.0 % (6 of 50)	36.0 % (18 of 50)

1. ribonuclease A

KETAAAKFER QHMDSSTSAA SSSNYCNQMM KSRNLTKDRC KPVNTFVHES LADVQAVCSQ KNVACKNGQT NCYQSYSTMS ITDCRETGSS KYPNCAYKTT QANKHIIVAC EGNPYVPVHF DASV

Show sample condition

Sample

Solvent system 40% acetic acid / 60% water, Pressure 1 atm, Temperature 298 (±0.1) K, pH 2.0 (±0.1), Details 40% acetic acid

#	Name	Isotope labeling	Concentration
1	ribonuclease A	[U-98% 13C; U-98% 15N]	1.75 mM
2	H2O	natural abundance	60 %
3	acetic acid	natural abundance	40 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.14 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.14 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.33 ppm, Outliers: 1 Detail

Release date

2010-10-17

Citation

NMR spectroscopy reveals that RNase A is chiefly denatured in 40% acetic acid: implications for oligomer formation by 3D domain swapping
Lopez-Alonso, J., Bruix, M., Font, J., Ribo, M., Vilanova, M., Jimenez, M., Santoro, J., Gonzalez, C., Laurents, D.V.
J. Am. Chem. Soc. (2010), 132, 1621-1630, PubMed 20085318 , DOI 10.1021/ja9081638 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 16011 released on 2010-10-17
    Title NMR Spectroscopic Characterization of 13C, 15N-labeled Ribonuclease A in urea 8M
  BMRB: 16503 released on 2010-01-25
    Title Ribonuclease A in 40% acetic acid and 8M urea pH 2

Related entities 1. bovine pancreas ribonuclease A, : 1 : 101 : 139 entities Detail

Interaction partners 1. bovine pancreas ribonuclease A, : 8 interactors Detail

More details for 8 interactors identified by 6 citations

Experiments performed 12 experiments Detail

1 2D 1H-1H NOESY