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- PDB-2mf1: Structural basis of the non-coding RNA RsmZ acting as protein spo... -

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Basic information

Entry
Database: PDB / ID: 2mf1
TitleStructural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer R of RsmZ(1-72)/RsmE(dimer) 1to3 complex
Components
  • Carbon storage regulator homolog
  • RNA_(72-MER)
KeywordsRNA BINDING PROTEIN/RNA / Protein/RNA / non-coding RNA / translation repressor protein / Pseudomonas aeruginosa / messenger RNA / protein sequestration / two conformations / RNAse E cleave sites / homo-dimeric proteins / cooperativity / multiple protein binding sites / translation activation / ribosome binding site / large solution structure / electron paramagnetic resonance / protein sponge / RNP assembly / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of carbohydrate metabolic process / mRNA catabolic process / positive regulation of translational initiation / negative regulation of translational initiation / mRNA 5'-UTR binding / cytosol
Similarity search - Function
Translational regulator CsrA / Carbon storage regulator superfamily / Global regulator protein family
Similarity search - Domain/homology
RNA / RNA (> 10) / Translational regulator CsrA1 / Translational regulator CsrA
Similarity search - Component
Biological speciesPseudomonas protegens Pf-5 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsDuss, O. / Michel, E. / Yulikov, M. / Schubert, M. / Jeschke, G. / Allain, F.H.-T.
CitationJournal: Nature / Year: 2014
Title: Structural basis of the non-coding RNA RsmZ acting as a protein sponge.
Authors: Duss, O. / Michel, E. / Yulikov, M. / Schubert, M. / Jeschke, G. / Allain, F.H.
History
DepositionOct 2, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon storage regulator homolog
B: Carbon storage regulator homolog
C: Carbon storage regulator homolog
D: Carbon storage regulator homolog
E: Carbon storage regulator homolog
F: Carbon storage regulator homolog
G: RNA_(72-MER)


Theoretical massNumber of molelcules
Total (without water)70,4607
Polymers70,4607
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
Carbon storage regulator homolog


Mass: 7847.951 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens Pf-5 (bacteria) / Strain: CHA0 / Gene: rsmE, csrA, PFL_2095 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4KEY0, UniProt: P0DPC3*PLUS
#2: RNA chain RNA_(72-MER)


Mass: 23372.031 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1442D 1H-15N HSQC
1552D 1H-15N HSQC
1612D 1H-13C TROSY
1722D 1H-13C TROSY
1832D 1H-13C TROSY
1942D 1H-13C TROSY
11052D 1H-13C TROSY
11162D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-13C; U-15N], segmentally labeled RNA (1-16 LABELED), 1.2 mM [U-100% 15N; U-80% 2H] RsmE, 0.03 mM sodium chloride, 0.05 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
20.2 mM [U-13C; U-15N], segmentally labeled RNA (17-40 LABELED), 1.2 mM [U-100% 15N; U-80% 2H] RsmE, 0.03 mM sodium chloride, 0.05 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
30.2 mM [U-13C; U-15N], segmentally labeled RNA (41-58 LABELED), 1.2 mM [U-100% 15N; U-80% 2H] RsmE, 0.03 mM sodium chloride, 0.05 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
40.2 mM [U-13C; U-15N], segmentally labeled RNA (59-72 LABELED), 1.2 mM [U-100% 15N; U-80% 2H] RsmE, 0.03 mM sodium chloride, 0.05 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
50.2 mM [U-13C; U-15N], segmentally labeled RNA (36-44 LABELED), 1.2 mM [U-100% 15N; U-80% 2H] RsmE, 0.03 mM sodium chloride, 0.05 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
60.2 mM RNA (72-MER), 1.2 mM [U-100% 15N; U-80% 2H] RsmE, 0.03 mM sodium chloride, 0.05 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMRNA (72-MER)-1[U-13C; U-15N], segmentally labeled1
1.2 mMRsmE-2[U-100% 15N; U-80% 2H]1
0.03 mMsodium chloride-31
0.05 mMpotassium phosphate-41
0.2 mMRNA (72-MER)-5[U-13C; U-15N], segmentally labeled2
1.2 mMRsmE-6[U-100% 15N; U-80% 2H]2
0.03 mMsodium chloride-72
0.05 mMpotassium phosphate-82
0.2 mMRNA (72-MER)-9[U-13C; U-15N], segmentally labeled3
1.2 mMRsmE-10[U-100% 15N; U-80% 2H]3
0.03 mMsodium chloride-113
0.05 mMpotassium phosphate-123
0.2 mMRNA (72-MER)-13[U-13C; U-15N], segmentally labeled4
1.2 mMRsmE-14[U-100% 15N; U-80% 2H]4
0.03 mMsodium chloride-154
0.05 mMpotassium phosphate-164
0.2 mMRNA (72-MER)-17[U-13C; U-15N], segmentally labeled5
1.2 mMRsmE-18[U-100% 15N; U-80% 2H]5
0.03 mMsodium chloride-195
0.05 mMpotassium phosphate-205
0.2 mMRNA (72-MER)-216
1.2 mMRsmE-22[U-100% 15N; U-80% 2H]6
0.03 mMsodium chloride-236
0.05 mMpotassium phosphate-246
Sample conditionsIonic strength: 0.18 / pH: 7.2 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollmanrefinement
TopSpinBruker Biospinprocessing
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA sugar pucker constraints total count: 29 / NOE constraints total: 7441 / Protein phi angle constraints total count: 288 / Protein psi angle constraints total count: 292
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 2500 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 1.22 ° / Maximum upper distance constraint violation: 0.3 Å

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