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- PDB-2mfe: Csr/Rsm protein-RNA recognition - A molecular affinity ruler: Rsm... -

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Basic information

Entry
Database: PDB / ID: 2mfe
TitleCsr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(SL2)/RsmE(dimer) 2:1 complex
Components
  • Carbon storage regulator homolog
  • SL2(RsmZ) RNA
KeywordsTRANSLATION/RNA / CsrA / RsmA / RsmE / RsmZ / CsrB / translation repressor protein / translation activation / protein sequestration / bacterial protein / non-coding RNA / sRNA / Pseudomonas aeruginosa / RNA-Binding Proteins / messenger RNA / modulation of binding affinity / molecular mimicry / TRANSLATION-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 fluorescens (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsDuss, O. / Diarra Dit Konte, N. / Michel, E. / Schubert, M. / Allain, F.H.-T.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.
Authors: Duss, O. / Michel, E. / Diarra Dit Konte, N. / Schubert, M. / Allain, F.H.
History
DepositionOct 11, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3May 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: SL2(RsmZ) RNA
C: Carbon storage regulator homolog
D: SL2(RsmZ) RNA


Theoretical massNumber of molelcules
Total (without water)29,9214
Polymers29,9214
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-42 kcal/mol
Surface area11790 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 999structures 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: rsmE, csrA / Production host: Escherichia coli (E. coli) / References: UniProt: Q5MXB2, UniProt: P0DPC3*PLUS
#2: RNA chain SL2(RsmZ) RNA


Mass: 7112.307 Da / Num. of mol.: 2 / 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
1213D 1H-15N NOESY
1312D 1H-1H NOESY
1422D 1H-1H NOESY
1542D 1H-13C HSQC
1633D 1H-13C NOESY aliphatic
1743D 1Fe3Ff NOESY
1843D (H)CCH-TOCSY
1933D HNCA
11033D HN(CA)CB
11122D 1H-1H TOCSY
11252D 1H-15N HSQC
11372D 1H-15N HSQC
11462D 1H-13C HSQC
11582D 1H-13C HSQC
11663D 1H-13C NOESY
11783D 1H-13C NOESY
11863D 1Fe3Ff NOESY
11983D 1Fe3Ff NOESY
12063D (H)CCH-TOCSY
12183D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] RsmE, 1 mM SL2(RsmZ), 0.05 mM potassium phosphate, 0.03 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 15N] RsmE, 1 mM SL2(RsmZ), 0.05 mM potassium phosphate, 0.03 mM sodium chloride, 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM SL2(RsmZ), 0.05 mM potassium phosphate, 0.03 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
41 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM SL2(RsmZ), 0.05 mM potassium phosphate, 0.03 mM sodium chloride, 100% D2O100% D2O
51 mM [U-100% 15N] RsmE, 1 mM [U-100% 13C; U-100% 15N]-Ade/Ura RNA SL2(RsmZ), 0.05 mM potassium phosphate, 0.03 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
61 mM [U-100% 15N] RsmE, 1 mM [U-100% 13C; U-100% 15N]-Ade/Ura RNA SL2(RsmZ), 0.05 mM potassium phosphate, 0.03 mM sodium chloride, 100% D2O100% D2O
71 mM [U-100% 15N] RsmE, 1 mM [U-100% 13C; U-100% 15N]-Cyt/Gua RNA SL2(RsmZ), 0.05 mM potassium phosphate, 0.03 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
81 mM [U-100% 15N] RsmE, 1 mM [U-100% 13C; U-100% 15N]-Cyt/Gua RNA SL2(RsmZ), 0.05 mM potassium phosphate, 0.03 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRsmE-1[U-100% 15N]1
1 mMSL2(RsmZ)-21
0.05 mMpotassium phosphate-31
0.03 mMsodium chloride-41
1 mMRsmE-5[U-100% 15N]2
1 mMSL2(RsmZ)-62
0.05 mMpotassium phosphate-72
0.03 mMsodium chloride-82
1 mMRsmE-9[U-100% 13C; U-100% 15N]3
1 mMSL2(RsmZ)-103
0.05 mMpotassium phosphate-113
0.03 mMsodium chloride-123
1 mMRsmE-13[U-100% 13C; U-100% 15N]4
1 mMSL2(RsmZ)-144
0.05 mMpotassium phosphate-154
0.03 mMsodium chloride-164
1 mMRsmE-17[U-100% 15N]5
1 mMSL2(RsmZ)-18[U-100% 13C; U-100% 15N]-Ade/Ura RNA5
0.05 mMpotassium phosphate-195
0.03 mMsodium chloride-205
1 mMRsmE-21[U-100% 15N]6
1 mMSL2(RsmZ)-22[U-100% 13C; U-100% 15N]-Ade/Ura RNA6
0.05 mMpotassium phosphate-236
0.03 mMsodium chloride-246
1 mMRsmE-25[U-100% 15N]7
1 mMSL2(RsmZ)-26[U-100% 13C; U-100% 15N]-Cyt/Gua RNA7
0.05 mMpotassium phosphate-277
0.03 mMsodium chloride-287
1 mMRsmE-29[U-100% 15N]8
1 mMSL2(RsmZ)-30[U-100% 13C; U-100% 15N]-Cyt/Gua RNA8
0.05 mMpotassium phosphate-318
0.03 mMsodium chloride-328
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
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA sugar pucker constraints total count: 12 / NOE constraints total: 2700
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 999 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 13.7 ° / Maximum upper distance constraint violation: 0.42 Å

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