BMRB: 19547

Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(SL3)/RsmE(dimer) 2:1 complex

Authors

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

Assembly

RsmZ(SL3)/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. SL3(RsmZ) (polymer, Thiol state: not present), 21 monomers, 6869.111 × 2 Da Detail

GGGAUCGCAG GAAGCGAUCC C

Total weight

28032.488 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: 59.9 %, Completeness (bb): 50.4 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	59.9 % (645 of 1076)	64.0 % (365 of 570)	50.5 % (216 of 428)	82.1 % (64 of 78)
Backbone	50.4 % (310 of 615)	49.4 % (128 of 259)	41.8 % (123 of 294)	95.2 % (59 of 62)
Sidechain	75.6 % (393 of 520)	76.2 % (237 of 311)	78.2 % (151 of 193)	31.3 % (5 of 16)
Aromatic	9.6 % (10 of 104)	11.5 % (6 of 52)	9.5 % (4 of 42)	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. SL3(RsmZ)

GGGAUCGCAG GAAGCGAUCC 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	SL3(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	SL3(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	SL3(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	SL3(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	SL3(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	SL3(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	SL3(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	SL3(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: 27.9 %, Completeness: 45.6 %, Completeness (bb): 43.9 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	45.6 % (982 of 2152)	48.2 % (549 of 1140)	41.6 % (356 of 856)	49.4 % (77 of 156)
Backbone	43.9 % (540 of 1230)	48.6 % (252 of 518)	38.4 % (226 of 588)	50.0 % (62 of 124)
Sidechain	48.2 % (501 of 1040)	47.7 % (297 of 622)	49.0 % (189 of 386)	46.9 % (15 of 32)
Aromatic	47.1 % (98 of 208)	48.1 % (50 of 104)	45.2 % (38 of 84)	50.0 % (10 of 20)
Methyl	52.1 % (98 of 188)	52.1 % (49 of 94)	52.1 % (49 of 94)

1. RsmE

MLILTRKVGE SINIGDDITI TILGVSGQQV RIGINAPKDV AVHREEIYQR IQAGLTAPDK RETPH

2. SL3(RsmZ)

GGGAUCGCAG GAAGCGAUCC 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	SL3(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	SL3(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	SL3(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	SL3(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	SL3(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	SL3(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	SL3(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	SL3(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: 0.16 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: 0.16 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: -0.01 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: 2MFF, 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. SL3(RsmZ), : 1 entities Detail

Experiments performed 21 experiments Detail