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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

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C15N
All60.8 % (655 of 1078)64.6 % (369 of 571)51.5 % (221 of 429)83.3 % (65 of 78)
Backbone51.2 % (315 of 615)49.8 % (129 of 259)43.2 % (127 of 294)95.2 % (59 of 62)
Sidechain76.2 % (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)
Methyl100.0 % (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

Sample #1

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


#NameIsotope labelingTypeConcentration
1RsmE[U-100% 15N]1 mM
2SL4(RsmZ)natural abundance1 mM
3potassium phosphatenatural abundance0.05 mM
4sodium chloridenatural abundance0.03 mM
5H2Onatural abundance95 %
6D2O[U-100% 2H]5 %
Sample #2

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


#NameIsotope labelingTypeConcentration
7RsmE[U-100% 15N]1 mM
8SL4(RsmZ)natural abundance1 mM
9potassium phosphatenatural abundance0.05 mM
10sodium chloridenatural abundance0.03 mM
11D2O[U-100% 2H]100 %
Sample #3

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


#NameIsotope labelingTypeConcentration
12RsmE[U-100% 13C; U-100% 15N]1 mM
13SL4(RsmZ)natural abundance1 mM
14potassium phosphatenatural abundance0.05 mM
15sodium chloridenatural abundance0.03 mM
16H2Onatural abundance95 %
17D2O[U-100% 2H]5 %
Sample #4

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


#NameIsotope labelingTypeConcentration
18RsmE[U-100% 13C; U-100% 15N]1 mM
19SL4(RsmZ)natural abundance1 mM
20potassium phosphatenatural abundance0.05 mM
21sodium chloridenatural abundance0.03 mM
22D2O[U-100% 2H]100 %
Sample #5

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


#NameIsotope labelingTypeConcentration
23RsmE[U-100% 15N]1 mM
24SL4(RsmZ)[U-100% 13C; U-100% 15N]-Ade/Ura RNA1 mM
25potassium phosphatenatural abundance0.05 mM
26sodium chloridenatural abundance0.03 mM
27H2Onatural abundance95 %
28D2O[U-100% 2H]5 %
Sample #6

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


#NameIsotope labelingTypeConcentration
29RsmE[U-100% 15N]1 mM
30SL4(RsmZ)[U-100% 13C; U-100% 15N]-Ade/Ura RNA1 mM
31potassium phosphatenatural abundance0.05 mM
32sodium chloridenatural abundance0.03 mM
33D2O[U-100% 2H]100 %
Sample #7

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


#NameIsotope labelingTypeConcentration
34RsmE[U-100% 15N]1 mM
35SL4(RsmZ)[U-100% 13C; U-100% 15N]-Cyt/Gua RNA1 mM
36potassium phosphatenatural abundance0.05 mM
37sodium chloridenatural abundance0.03 mM
38H2Onatural abundance95 %
39D2O[U-100% 2H]5 %
Sample #8

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


#NameIsotope labelingTypeConcentration
40RsmE[U-100% 15N]1 mM
41SL4(RsmZ)[U-100% 13C; U-100% 15N]-Cyt/Gua RNA1 mM
42potassium phosphatenatural abundance0.05 mM
43sodium chloridenatural abundance0.03 mM
44D2O[U-100% 2H]100 %

Chem. Shift Complete2
Sequence coverage: 37.2 %, Completeness: 48.8 %, Completeness (bb): 47.6 % Detail

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C15N
All48.8 % (1053 of 2156)50.7 % (579 of 1142)45.5 % (390 of 858)53.8 % (84 of 156)
Backbone47.6 % (586 of 1230)51.4 % (266 of 518)42.9 % (252 of 588)54.8 % (68 of 124)
Sidechain50.9 % (531 of 1044)50.2 % (313 of 624)52.1 % (202 of 388)50.0 % (16 of 32)
Aromatic47.2 % (100 of 212)48.1 % (51 of 106)45.3 % (39 of 86)50.0 % (10 of 20)
Methyl55.3 % (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

Sample #1

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


#NameIsotope labelingTypeConcentration
1RsmE[U-100% 15N]1 mM
2SL4(RsmZ)natural abundance1 mM
3potassium phosphatenatural abundance0.05 mM
4sodium chloridenatural abundance0.03 mM
5H2Onatural abundance95 %
6D2O[U-100% 2H]5 %
Sample #2

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


#NameIsotope labelingTypeConcentration
7RsmE[U-100% 15N]1 mM
8SL4(RsmZ)natural abundance1 mM
9potassium phosphatenatural abundance0.05 mM
10sodium chloridenatural abundance0.03 mM
11D2O[U-100% 2H]100 %
Sample #3

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


#NameIsotope labelingTypeConcentration
12RsmE[U-100% 13C; U-100% 15N]1 mM
13SL4(RsmZ)natural abundance1 mM
14potassium phosphatenatural abundance0.05 mM
15sodium chloridenatural abundance0.03 mM
16H2Onatural abundance95 %
17D2O[U-100% 2H]5 %
Sample #4

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


#NameIsotope labelingTypeConcentration
18RsmE[U-100% 13C; U-100% 15N]1 mM
19SL4(RsmZ)natural abundance1 mM
20potassium phosphatenatural abundance0.05 mM
21sodium chloridenatural abundance0.03 mM
22D2O[U-100% 2H]100 %
Sample #5

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


#NameIsotope labelingTypeConcentration
23RsmE[U-100% 15N]1 mM
24SL4(RsmZ)[U-100% 13C; U-100% 15N]-Ade/Ura RNA1 mM
25potassium phosphatenatural abundance0.05 mM
26sodium chloridenatural abundance0.03 mM
27H2Onatural abundance95 %
28D2O[U-100% 2H]5 %
Sample #6

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


#NameIsotope labelingTypeConcentration
29RsmE[U-100% 15N]1 mM
30SL4(RsmZ)[U-100% 13C; U-100% 15N]-Ade/Ura RNA1 mM
31potassium phosphatenatural abundance0.05 mM
32sodium chloridenatural abundance0.03 mM
33D2O[U-100% 2H]100 %
Sample #7

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


#NameIsotope labelingTypeConcentration
34RsmE[U-100% 15N]1 mM
35SL4(RsmZ)[U-100% 13C; U-100% 15N]-Cyt/Gua RNA1 mM
36potassium phosphatenatural abundance0.05 mM
37sodium chloridenatural abundance0.03 mM
38H2Onatural abundance95 %
39D2O[U-100% 2H]5 %
Sample #8

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


#NameIsotope labelingTypeConcentration
40RsmE[U-100% 15N]1 mM
41SL4(RsmZ)[U-100% 13C; U-100% 15N]-Cyt/Gua RNA1 mM
42potassium phosphatenatural abundance0.05 mM
43sodium chloridenatural abundance0.03 mM
44D2O[U-100% 2H]100 %

LACS Plot; CA
Referencing offset: 0.13 ppm, Outliers: 2 Detail
LACS Plot; CB
Referencing offset: 0.13 ppm, Outliers: 2 Detail
LACS Plot; HA
Referencing offset: -0.03 ppm, Outliers: 2 Detail
Protein Blocks Logo
Calculated from 20 models in PDB: 2MFG, Strand ID: A, C Detail


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 ,
Related entities 1. RsmE, : 1 : 7 : 103 entities Detail
Related entities 2. SL4(RsmZ), : 1 entities Detail
Experiments performed 21 experiments Detail
nullKeywords bacterial protein, CsrA, CsrB, homo-dimeric protein, messenger RNA, modulation of binding affinity, molecular mimicry, NMR, non-coding RNA, protein sequestration, Pseudomonas aeruginosa, RNA-Binding Proteins, RsmA, RsmE, RsmZ, sRNA, translation activation, translation repressor protein