BMRB: 19546

Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(SL2)/RsmE(dimer) 2:1 complex

Authors

Duss, O., Diarra Dit Konte, N., Michel, E., Schubert, M., Allain, F.H. T.

Assembly

RsmZ(SL2)/RsmE(dimer) 2:1 complex

Entity

1. RsmE (polymer, Thiol state: not present), 65 monomers, 7147.134 × 2 Da Detail

MLILTRKVGE SINIGDDITI TILGVSGQQV RIGINAPKDV AVHREEIYQR IQAGLTAPDK RETPH

2. SL2(RsmZ) (polymer, Thiol state: not present), 22 monomers, 7175.277 × 2 Da Detail

GGGCCAUCAA GGACGAUGGU CC

Total weight

28644.82 Da

Max. entity weight

7175.277 Da

Source organism

Pseudomonas fluorescens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 74.7 %, Completeness: 60.0 %, Completeness (bb): 51.8 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	60.0 % (656 of 1093)	62.9 % (364 of 579)	52.0 % (226 of 435)	83.5 % (66 of 79)
Backbone	51.8 % (324 of 626)	48.7 % (129 of 265)	45.2 % (135 of 299)	96.8 % (60 of 62)
Sidechain	74.0 % (389 of 526)	74.8 % (235 of 314)	75.9 % (148 of 195)	35.3 % (6 of 17)
Aromatic	9.1 % (10 of 110)	10.9 % (6 of 55)	9.1 % (4 of 44)	0.0 % (0 of 11)
Methyl	100.0 % (94 of 94)	100.0 % (47 of 47)	100.0 % (47 of 47)

1. RsmE

MLILTRKVGE SINIGDDITI TILGVSGQQV RIGINAPKDV AVHREEIYQR IQAGLTAPDK RETPH

2. SL2(RsmZ)

GGGCCAUCAA GGACGAUGGU CC

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	RsmE	[U-100% 15N]		1 mM
2	SL2(RsmZ)	natural abundance		1 mM
3	potassium phosphate	natural abundance		0.05 mM
4	sodium chloride	natural abundance		0.03 mM
5	H2O	natural abundance		95 %
6	D2O	[U-100% 2H]		5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
7	RsmE	[U-100% 15N]		1 mM
8	SL2(RsmZ)	natural abundance		1 mM
9	potassium phosphate	natural abundance		0.05 mM
10	sodium chloride	natural abundance		0.03 mM
11	D2O	[U-100% 2H]		100 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
12	RsmE	[U-100% 13C; U-100% 15N]		1 mM
13	SL2(RsmZ)	natural abundance		1 mM
14	potassium phosphate	natural abundance		0.05 mM
15	sodium chloride	natural abundance		0.03 mM
16	H2O	natural abundance		95 %
17	D2O	[U-100% 2H]		5 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
18	RsmE	[U-100% 13C; U-100% 15N]		1 mM
19	SL2(RsmZ)	natural abundance		1 mM
20	potassium phosphate	natural abundance		0.05 mM
21	sodium chloride	natural abundance		0.03 mM
22	D2O	[U-100% 2H]		100 %

Sample #5

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
23	RsmE	[U-100% 15N]		1 mM
24	SL2(RsmZ)	[U-100% 13C; U-100% 15N]-Ade/Ura RNA		1 mM
25	potassium phosphate	natural abundance		0.05 mM
26	sodium chloride	natural abundance		0.03 mM
27	H2O	natural abundance		95 %
28	D2O	[U-100% 2H]		5 %

Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
29	RsmE	[U-100% 15N]		1 mM
30	SL2(RsmZ)	[U-100% 13C; U-100% 15N]-Ade/Ura RNA		1 mM
31	potassium phosphate	natural abundance		0.05 mM
32	sodium chloride	natural abundance		0.03 mM
33	D2O	[U-100% 2H]		100 %

Sample #7

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
34	RsmE	[U-100% 15N]		1 mM
35	SL2(RsmZ)	[U-100% 13C; U-100% 15N]-Cyt/Gua RNA		1 mM
36	potassium phosphate	natural abundance		0.05 mM
37	sodium chloride	natural abundance		0.03 mM
38	H2O	natural abundance		95 %
39	D2O	[U-100% 2H]		5 %

Sample #8

Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
40	RsmE	[U-100% 15N]		1 mM
41	SL2(RsmZ)	[U-100% 13C; U-100% 15N]-Cyt/Gua RNA		1 mM
42	potassium phosphate	natural abundance		0.05 mM
43	sodium chloride	natural abundance		0.03 mM
44	D2O	[U-100% 2H]		100 %

Hide sample codition

Chem. Shift Complete2

Sequence coverage: 37.9 %, Completeness: 48.9 %, Completeness (bb): 47.5 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	48.9 % (1069 of 2186)	50.1 % (580 of 1158)	46.2 % (402 of 870)	55.1 % (87 of 158)
Backbone	47.5 % (595 of 1252)	50.0 % (265 of 530)	43.5 % (260 of 598)	56.5 % (70 of 124)
Sidechain	51.2 % (539 of 1052)	50.2 % (315 of 628)	53.1 % (207 of 390)	50.0 % (17 of 34)
Aromatic	46.4 % (102 of 220)	47.3 % (52 of 110)	44.3 % (39 of 88)	50.0 % (11 of 22)
Methyl	59.6 % (112 of 188)	59.6 % (56 of 94)	59.6 % (56 of 94)

1. RsmE

MLILTRKVGE SINIGDDITI TILGVSGQQV RIGINAPKDV AVHREEIYQR IQAGLTAPDK RETPH

2. SL2(RsmZ)

GGGCCAUCAA GGACGAUGGU CC

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	RsmE	[U-100% 15N]		1 mM
2	SL2(RsmZ)	natural abundance		1 mM
3	potassium phosphate	natural abundance		0.05 mM
4	sodium chloride	natural abundance		0.03 mM
5	H2O	natural abundance		95 %
6	D2O	[U-100% 2H]		5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
7	RsmE	[U-100% 15N]		1 mM
8	SL2(RsmZ)	natural abundance		1 mM
9	potassium phosphate	natural abundance		0.05 mM
10	sodium chloride	natural abundance		0.03 mM
11	D2O	[U-100% 2H]		100 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
12	RsmE	[U-100% 13C; U-100% 15N]		1 mM
13	SL2(RsmZ)	natural abundance		1 mM
14	potassium phosphate	natural abundance		0.05 mM
15	sodium chloride	natural abundance		0.03 mM
16	H2O	natural abundance		95 %
17	D2O	[U-100% 2H]		5 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
18	RsmE	[U-100% 13C; U-100% 15N]		1 mM
19	SL2(RsmZ)	natural abundance		1 mM
20	potassium phosphate	natural abundance		0.05 mM
21	sodium chloride	natural abundance		0.03 mM
22	D2O	[U-100% 2H]		100 %

Sample #5

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
23	RsmE	[U-100% 15N]		1 mM
24	SL2(RsmZ)	[U-100% 13C; U-100% 15N]-Ade/Ura RNA		1 mM
25	potassium phosphate	natural abundance		0.05 mM
26	sodium chloride	natural abundance		0.03 mM
27	H2O	natural abundance		95 %
28	D2O	[U-100% 2H]		5 %

Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
29	RsmE	[U-100% 15N]		1 mM
30	SL2(RsmZ)	[U-100% 13C; U-100% 15N]-Ade/Ura RNA		1 mM
31	potassium phosphate	natural abundance		0.05 mM
32	sodium chloride	natural abundance		0.03 mM
33	D2O	[U-100% 2H]		100 %

Sample #7

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
34	RsmE	[U-100% 15N]		1 mM
35	SL2(RsmZ)	[U-100% 13C; U-100% 15N]-Cyt/Gua RNA		1 mM
36	potassium phosphate	natural abundance		0.05 mM
37	sodium chloride	natural abundance		0.03 mM
38	H2O	natural abundance		95 %
39	D2O	[U-100% 2H]		5 %

Sample #8

Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
40	RsmE	[U-100% 15N]		1 mM
41	SL2(RsmZ)	[U-100% 13C; U-100% 15N]-Cyt/Gua RNA		1 mM
42	potassium phosphate	natural abundance		0.05 mM
43	sodium chloride	natural abundance		0.03 mM
44	D2O	[U-100% 2H]		100 %

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LACS Plot; CA

Referencing offset: 0.15 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

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LACS Plot; CB

Referencing offset: 0.15 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

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LACS Plot; HA

Referencing offset: -0.02 ppm, Outliers: 2 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

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Protein Blocks Logo

Calculated from 20 models in PDB: 2MFE, Strand ID: A, C Detail

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Release date

2014-02-23

Citation

Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition
Duss, O., Michel, E., Diarra Dit Konte, N., Schubert, M., Allain, F.
Nucleic Acids Res. (2014), 42, 5332-5346, PubMed 24561806 , DOI 10.1093/nar/gku141 , Abstract

Related entities 1. RsmE, : 1 : 7 : 103 entities Detail

Related entities 2. SL2(RsmZ), : 1 : 2 entities Detail

Experiments performed 21 experiments Detail