BMRB Entry 19544

Name: Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(SL1)/RsmE(dimer) 2:1 complex
Published: 2014-02-24

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PDB ID: 2mfc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19544
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(SL1)/RsmE(dimer) 2:1 complex

Deposition date:

2013-10-10

Original release date:

2014-02-24

Authors:

Duss, Olivier; Diarra Dit Konte, Nana; Michel, Erich; Schubert, Mario; Allain, Frederic

Citation:

Citation: Duss, Olivier; Michel, Erich; Diarra Dit Konte, Nana; Schubert, Mario; Allain, Frederic H-T. "Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition." Nucleic Acids Res. ., .-. (2014).
PubMed: 24561806

Assembly members:

Assembly members:
RsmE, polymer, 65 residues, 6405.423 Da.
SL1(RsmZ), polymer, 22 residues, 7112.354 Da.

Natural source:

Natural source: Common Name: g-proteobacteria Taxonomy ID: 294 Superkingdom: Bacteria Kingdom: not available Genus/species: Pseudomonas fluorescens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RsmE: MLILTRKVGESINIGDDITI TILGVSGQQVRIGINAPKDV AVHREEIYQRIQAGLTAPDK RETPH
SL1(RsmZ): GGGUGUCGACGGAUAGACAC CC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	360
15N chemical shifts	78
1H chemical shifts	648

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RsmE_1	1
2	SL1(RsmZ)_1	2
3	RsmE_2	1
4	SL1(RsmZ)_2	2

Entities:

Entity 1, RsmE_1 65 residues - 6405.423 Da.

1

MET

LEU

ILE

LEU

THR

ARG

LYS

VAL

GLY

GLU

2

SER

ILE

ASN

ILE

GLY

ASP

ILE

THR

ILE

3

THR

ILE

LEU

GLY

VAL

SER

GLY

GLN

VAL

4

ARG

ILE

GLY

ILE

ASN

ALA

PRO

LYS

ASP

VAL

5

ALA

VAL

HIS

ARG

GLU

ILE

TYR

GLN

ARG

6

ILE

GLN

ALA

GLY

LEU

THR

ALA

PRO

ASP

LYS

7

ARG

GLU

THR

PRO

HIS

Entity 2, SL1(RsmZ)_1 22 residues - 7112.354 Da.

1

G

U

G

U

C

G

A

C

2

G

A

U

A

G

A

C

A

C

3

C

Samples:

sample_1: RsmE, [U-100% 15N], 1 mM; SL1(RsmZ) 1 mM; potassium phosphate 0.05 mM; sodium chloride 0.03 mM; H2O 95%; D2O, [U-100% 2H], 5%

sample_2: RsmE, [U-100% 15N], 1 mM; SL1(RsmZ) 1 mM; potassium phosphate 0.05 mM; sodium chloride 0.03 mM; D2O, [U-100% 2H], 100%

sample_3: RsmE, [U-100% 13C; U-100% 15N], 1 mM; SL1(RsmZ) 1 mM; potassium phosphate 0.05 mM; sodium chloride 0.03 mM; H2O 95%; D2O, [U-100% 2H], 5%

sample_4: RsmE, [U-100% 13C; U-100% 15N], 1 mM; SL1(RsmZ) 1 mM; potassium phosphate 0.05 mM; sodium chloride 0.03 mM; D2O, [U-100% 2H], 100%

sample_5: RsmE, [U-100% 15N], 1 mM; SL1(RsmZ), [U-100% 13C; U-100% 15N]-Ade/Ura RNA, 1 mM; potassium phosphate 0.05 mM; sodium chloride 0.03 mM; H2O 95%; D2O, [U-100% 2H], 5%

sample_6: RsmE, [U-100% 15N], 1 mM; SL1(RsmZ), [U-100% 13C; U-100% 15N]-Ade/Ura RNA, 1 mM; potassium phosphate 0.05 mM; sodium chloride 0.03 mM; D2O, [U-100% 2H], 100%

sample_7: RsmE, [U-100% 15N], 1 mM; SL1(RsmZ), [U-100% 13C; U-100% 15N]-Cyt/Gua RNA, 1 mM; potassium phosphate 0.05 mM; sodium chloride 0.03 mM; H2O 95%; D2O, [U-100% 2H], 5%

sample_8: RsmE, [U-100% 15N], 1 mM; SL1(RsmZ), [U-100% 13C; U-100% 15N]-Cyt/Gua RNA, 1 mM; potassium phosphate 0.05 mM; sodium chloride 0.03 mM; D2O, [U-100% 2H], 100%

sample_conditions_1: ionic strength: 0.18 M; pH: 7.2; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1
3D 1Fe3Ff NOESY	sample_4	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_1
3D HNCA	sample_3	isotropic	sample_conditions_1
3D HNCACB	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_7	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_6	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_8	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_6	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_8	isotropic	sample_conditions_1
3D 1Fe3Ff NOESY	sample_6	isotropic	sample_conditions_1
3D 1Fe3Ff NOESY	sample_8	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_6	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_8	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - processing

SPARKY, Goddard - chemical shift assignment, data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 600 MHz
Bruker Avance 700 MHz
Bruker Avance 900 MHz

BMRB	15257 19534 19546 19547 19548 19549
PDB	2JPP 2MF0 2MF1 2MFC 2MFE 2MFF 2MFG 2MFH
DBJ	BAO61455 BAQ73744 BAQ80031
GB	AAT27429 AAY91370 AEL31265 AGL83913 AIC19187
REF	WP_007920550 WP_017337657 WP_045057924 WP_057444113