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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

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C15N
All60.0 % (656 of 1093)62.9 % (364 of 579)52.0 % (226 of 435)83.5 % (66 of 79)
Backbone51.8 % (324 of 626)48.7 % (129 of 265)45.2 % (135 of 299)96.8 % (60 of 62)
Sidechain74.0 % (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)
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. SL2(RsmZ)

GGGCCAUCAA GGACGAUGGU CC

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
2SL2(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
8SL2(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
13SL2(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
19SL2(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
24SL2(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
30SL2(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
35SL2(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
41SL2(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: 37.9 %, Completeness: 48.9 %, Completeness (bb): 47.5 % Detail

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C15N
All48.9 % (1069 of 2186)50.1 % (580 of 1158)46.2 % (402 of 870)55.1 % (87 of 158)
Backbone47.5 % (595 of 1252)50.0 % (265 of 530)43.5 % (260 of 598)56.5 % (70 of 124)
Sidechain51.2 % (539 of 1052)50.2 % (315 of 628)53.1 % (207 of 390)50.0 % (17 of 34)
Aromatic46.4 % (102 of 220)47.3 % (52 of 110)44.3 % (39 of 88)50.0 % (11 of 22)
Methyl59.6 % (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

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
2SL2(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
8SL2(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
13SL2(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
19SL2(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
24SL2(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
30SL2(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
35SL2(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
41SL2(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: 0.15 ppm, Outliers: 1 Detail
LACS Plot; CB
Referencing offset: 0.15 ppm, Outliers: 1 Detail
LACS Plot; HA
Referencing offset: -0.02 ppm, Outliers: 2 Detail
Protein Blocks Logo
Calculated from 20 models in PDB: 2MFE, 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. SL2(RsmZ), : 1 : 2 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