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Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex
Authors
Duss, O., Diarra Dit Konte, N., Michel, E., Schubert, M., Allain, F.H. T.
Assembly
RsmZ(36-44)/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. RsmZ(36-44) (polymer, Thiol state: not present), 9 monomers, 2918.739 × 2 Da Detail

UCAGGACAU


Total weight
20131.746 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: 86.5 %, Completeness: 74.0 %, Completeness (bb): 66.5 % Detail

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C15N
All74.0 % (657 of 888)79.0 % (368 of 466)63.7 % (223 of 350)91.7 % (66 of 72)
Backbone66.5 % (321 of 483)69.5 % (130 of 187)56.0 % (131 of 234)96.8 % (60 of 62)
Sidechain84.7 % (393 of 464)85.3 % (238 of 279)85.1 % (149 of 175)60.0 % (6 of 10)
Aromatic17.9 % (10 of 56)21.4 % (6 of 28)16.7 % (4 of 24) 0.0 % (0 of 4)
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. RsmZ(36-44)

UCAGGACAU

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
2RsmZ(36-44)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
8RsmZ(36-44)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
13RsmZ(36-44)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
19RsmZ(36-44)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
24RsmZ(36-44)[U-100% 13C; U-100% 15N]1 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
30RsmZ(36-44)[U-100% 13C; U-100% 15N]1 mM
31potassium phosphatenatural abundance0.05 mM
32sodium chloridenatural abundance0.03 mM
33D2O[U-100% 2H]100 %

Chem. Shift Complete2
Sequence coverage: 27.0 %, Completeness: 49.2 %, Completeness (bb): 48.8 % Detail

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C15N
All49.2 % (873 of 1776)50.9 % (474 of 932)45.9 % (321 of 700)54.2 % (78 of 144)
Backbone48.8 % (471 of 966)52.9 % (198 of 374)43.4 % (203 of 468)56.5 % (70 of 124)
Sidechain50.5 % (469 of 928)49.5 % (276 of 558)52.9 % (185 of 350)40.0 % (8 of 20)
Aromatic39.3 % (44 of 112)41.1 % (23 of 56)41.7 % (20 of 48)12.5 % (1 of 8)
Methyl55.9 % (105 of 188)55.3 % (52 of 94)56.4 % (53 of 94)

1. RsmE

MLILTRKVGE SINIGDDITI TILGVSGQQV RIGINAPKDV AVHREEIYQR IQAGLTAPDK RETPH

2. RsmZ(36-44)

UCAGGACAU

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
2RsmZ(36-44)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
8RsmZ(36-44)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
13RsmZ(36-44)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
19RsmZ(36-44)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
24RsmZ(36-44)[U-100% 13C; U-100% 15N]1 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
30RsmZ(36-44)[U-100% 13C; U-100% 15N]1 mM
31potassium phosphatenatural abundance0.05 mM
32sodium chloridenatural abundance0.03 mM
33D2O[U-100% 2H]100 %

LACS Plot; CA
Referencing offset: 0.07 ppm, Outliers: 1 Detail
LACS Plot; CB
Referencing offset: 0.07 ppm, Outliers: 1 Detail
LACS Plot; HA
Referencing offset: -0.02 ppm, Outliers: 2 Detail
Protein Blocks Logo
Calculated from 20 models in PDB: 2MFH, 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
Experiments performed 12 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