BMRB Entry 19534

Name: Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex
Published: 2014-05-20

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PDB ID: 2mf0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19534
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:

Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex

Deposition date:

2013-10-02

Original release date:

2014-05-20

Authors:

Duss, Olivier; Michel, Erich; Yulikov, Maxim; Schubert, Mario; Jeschke, Gunnar; Allain, Frederic

Citation:

Citation: Duss, Olivier; Michel, Erich; Yulikov, Maxim; Schubert, Mario; Jeschke, Gunnar; Allain, Frederic H-T. "Structural basis of the non-coding RNA RsmZ acting as a protein sponge." Nature 509, 588-592 (2014).
PubMed: 24828038

Assembly members:

Assembly members:
RsmE, polymer, 59 residues, 6405.423 Da.
RNA_(72-MER), polymer, 72 residues, 23372.182 Da.

Natural source:

Natural source: Common Name: Pseudomonas fluorescens 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 AVHREEIYQRIQAGLTAPD
RNA_(72-MER): UGUCGACGGAUAGACACAGC CAUCAAGGACGAUGGUCAGG ACAUCGCAGGAAGCGAUUCA UCAGGACGAUGA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	125
15N chemical shifts	21
1H chemical shifts	146

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	RsmE, 2	1
3	RsmE, 3	1
4	RsmE, 4	1
5	RsmE, 5	1
6	RsmE, 6	1
7	RNA (72-MER)	2

Entities:

Entity 1, RsmE, 1 59 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

Entity 2, RNA (72-MER) 72 residues - 23372.182 Da.

1

U

G

U

C

G

A

C

G

A

2

U

A

G

A

C

A

C

A

G

C

3

C

A

U

C

A

G

A

C

4

G

A

U

G

U

C

A

G

5

A

C

A

U

C

G

C

A

G

6

A

G

C

G

A

U

C

A

7

U

C

A

G

A

C

G

A

U

8

G

A

Samples:

sample_1: RNA (72-MER), [U-13C; U-15N], segmentally labeled, 0.2 mM; RsmE, [U-100% 15N; U-80% 2H], 1.2 mM; sodium chloride 0.03 mM; potassium phosphate 0.05 mM

sample_2: RNA (72-MER), [U-13C; U-15N], segmentally labeled, 0.2 mM; RsmE, [U-100% 15N; U-80% 2H], 1.2 mM; sodium chloride 0.03 mM; potassium phosphate 0.05 mM

sample_3: RNA (72-MER), [U-13C; U-15N], segmentally labeled, 0.2 mM; RsmE, [U-100% 15N; U-80% 2H], 1.2 mM; sodium chloride 0.03 mM; potassium phosphate 0.05 mM

sample_4: RNA (72-MER), [U-13C; U-15N], segmentally labeled, 0.2 mM; RsmE, [U-100% 15N; U-80% 2H], 1.2 mM; sodium chloride 0.03 mM; potassium phosphate 0.05 mM

sample_5: RNA (72-MER), [U-13C; U-15N], segmentally labeled, 0.2 mM; RsmE, [U-100% 15N; U-80% 2H], 1.2 mM; sodium chloride 0.03 mM; potassium phosphate 0.05 mM

sample_6: RNA (72-MER) 0.2 mM; RsmE, [U-100% 15N; U-80% 2H], 1.2 mM; sodium chloride 0.03 mM; potassium phosphate 0.05 mM

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
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-13C TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C TROSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C TROSY	sample_3	isotropic	sample_conditions_1
2D 1H-13C TROSY	sample_4	isotropic	sample_conditions_1
2D 1H-13C TROSY	sample_5	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_6	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

TOPSPIN, Bruker Biospin - processing

SPARKY, Goddard - data analysis

NMR spectrometers:

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

BMRB	15257 19544 19546 19547 19548 19549
PDB	2JPP 2MF0 2MF1 2MFC 2MFE 2MFF 2MFG 2MFH
DBJ	BAO61455 BAQ73744 BAQ80031
EMBL	CAY50674 CDF93721 CEL28723
GB	AAT27429 AAY91370 ABA73655 ABW16953 AEA70068
REF	WP_003179932 WP_003192511 WP_007905913 WP_007920550 WP_007938114