BMRB: 19548

Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(SL4)/RsmE(dimer) 2:1 complex

Authors

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

Assembly

RsmZ(SL4)/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. SL4(RsmZ) (polymer, Thiol state: not present), 21 monomers, 6830.071 × 2 Da Detail

GGGUCAUCAG GACGAUGACC C

Total weight

27954.41 Da

Max. entity weight

7147.134 Da

Source organism

Pseudomonas fluorescens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 75.6 %, Completeness: 60.8 %, Completeness (bb): 51.2 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	60.8 % (655 of 1078)	64.6 % (369 of 571)	51.5 % (221 of 429)	83.3 % (65 of 78)
Backbone	51.2 % (315 of 615)	49.8 % (129 of 259)	43.2 % (127 of 294)	95.2 % (59 of 62)
Sidechain	76.2 % (398 of 522)	76.9 % (240 of 312)	78.4 % (152 of 194)	37.5 % (6 of 16)
Aromatic	9.4 % (10 of 106)	11.3 % (6 of 53)	9.3 % (4 of 43)	0.0 % (0 of 10)
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. SL4(RsmZ)

GGGUCAUCAG GACGAUGACC C

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	SL4(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	SL4(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	SL4(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	SL4(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	SL4(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	SL4(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	SL4(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	SL4(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: 37.2 %, Completeness: 48.8 %, Completeness (bb): 47.6 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	48.8 % (1053 of 2156)	50.7 % (579 of 1142)	45.5 % (390 of 858)	53.8 % (84 of 156)
Backbone	47.6 % (586 of 1230)	51.4 % (266 of 518)	42.9 % (252 of 588)	54.8 % (68 of 124)
Sidechain	50.9 % (531 of 1044)	50.2 % (313 of 624)	52.1 % (202 of 388)	50.0 % (16 of 32)
Aromatic	47.2 % (100 of 212)	48.1 % (51 of 106)	45.3 % (39 of 86)	50.0 % (10 of 20)
Methyl	55.3 % (104 of 188)	55.3 % (52 of 94)	55.3 % (52 of 94)

1. RsmE

MLILTRKVGE SINIGDDITI TILGVSGQQV RIGINAPKDV AVHREEIYQR IQAGLTAPDK RETPH

2. SL4(RsmZ)

GGGUCAUCAG GACGAUGACC C

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	SL4(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	SL4(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	SL4(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	SL4(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	SL4(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	SL4(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	SL4(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	SL4(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: 0.13 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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LACS Plot; CB

Referencing offset: 0.13 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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LACS Plot; HA

Referencing offset: -0.03 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: 2MFG, 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. SL4(RsmZ), : 1 entities Detail

Experiments performed 21 experiments Detail