BMRB: 19549

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

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	74.0 % (657 of 888)	79.0 % (368 of 466)	63.7 % (223 of 350)	91.7 % (66 of 72)
Backbone	66.5 % (321 of 483)	69.5 % (130 of 187)	56.0 % (131 of 234)	96.8 % (60 of 62)
Sidechain	84.7 % (393 of 464)	85.3 % (238 of 279)	85.1 % (149 of 175)	60.0 % (6 of 10)
Aromatic	17.9 % (10 of 56)	21.4 % (6 of 28)	16.7 % (4 of 24)	0.0 % (0 of 4)
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. RsmZ(36-44)

UCAGGACAU

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	RsmZ(36-44)	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	RsmZ(36-44)	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	RsmZ(36-44)	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	RsmZ(36-44)	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	RsmZ(36-44)	[U-100% 13C; U-100% 15N]		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	RsmZ(36-44)	[U-100% 13C; U-100% 15N]		1 mM
31	potassium phosphate	natural abundance		0.05 mM
32	sodium chloride	natural abundance		0.03 mM
33	D2O	[U-100% 2H]		100 %

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Chem. Shift Complete2

Sequence coverage: 27.0 %, Completeness: 49.2 %, Completeness (bb): 48.8 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	49.2 % (873 of 1776)	50.9 % (474 of 932)	45.9 % (321 of 700)	54.2 % (78 of 144)
Backbone	48.8 % (471 of 966)	52.9 % (198 of 374)	43.4 % (203 of 468)	56.5 % (70 of 124)
Sidechain	50.5 % (469 of 928)	49.5 % (276 of 558)	52.9 % (185 of 350)	40.0 % (8 of 20)
Aromatic	39.3 % (44 of 112)	41.1 % (23 of 56)	41.7 % (20 of 48)	12.5 % (1 of 8)
Methyl	55.9 % (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

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	RsmZ(36-44)	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	RsmZ(36-44)	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	RsmZ(36-44)	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	RsmZ(36-44)	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	RsmZ(36-44)	[U-100% 13C; U-100% 15N]		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	RsmZ(36-44)	[U-100% 13C; U-100% 15N]		1 mM
31	potassium phosphate	natural abundance		0.05 mM
32	sodium chloride	natural abundance		0.03 mM
33	D2O	[U-100% 2H]		100 %

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LACS Plot; CA

Referencing offset: 0.07 ppm, Outliers: 1 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: 0.07 ppm, Outliers: 1 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: -0.02 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: 2MFH, 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

Experiments performed 12 experiments Detail