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- PDB-2jpp: Structural basis of RsmA/CsrA RNA recognition: Structure of RsmE ... -

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Basic information

Entry
Database: PDB / ID: 2jpp
TitleStructural basis of RsmA/CsrA RNA recognition: Structure of RsmE bound to the Shine-Dalgarno sequence of hcnA mRNA
Components
  • RNA (5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*CP*GP*GP*AP*UP*GP*AP*AP*GP*CP*CP*C)-3')
  • Translational repressor
KeywordsTRANSLATION/RNA / RNA recognition / PROTEIN/RNA / CsrA / RsmA / Shine-Dalgarno / 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 detailsStructure of RsmE bound to the Shine-Dalgarno sequence of hcnA mRNA
AuthorsSchubert, M. / Lapouge, K. / Duss, O. / Oberstrass, F.C. / Jelesarov, I. / Haas, D. / Allain, F.H.-T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA
Authors: Schubert, M. / Lapouge, K. / Duss, O. / Oberstrass, F.C. / Jelesarov, I. / Haas, D. / Allain, F.H.-T.
History
DepositionMay 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 9, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 2.1Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: RNA (5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*CP*GP*GP*AP*UP*GP*AP*AP*GP*CP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*CP*GP*GP*AP*UP*GP*AP*AP*GP*CP*CP*C)-3')
A: Translational repressor
B: Translational repressor


Theoretical massNumber of molelcules
Total (without water)28,5724
Polymers28,5724
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)10 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*CP*GP*GP*AP*UP*GP*AP*AP*GP*CP*CP*C)-3')


Mass: 6437.895 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Translational repressor


Mass: 7847.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: rsmE / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+RIL / References: UniProt: Q5MXB2, UniProt: P0DPC3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of RsmE bound to the Shine-Dalgarno sequence of hcnA mRNA
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1333D CBCA(CO)NH
1433D HNCA
1533D HN(CA)CB
1633D HNCO
1712D 1H-1H TOCSY
1833D H(CCO)NH
1912D 1H-1H NOESY
11022D 1H-13C HSQC
11133D 1H-13C NOESY
11233D HN(CO)CA
11372D 1H-13C HSQC
11473D 1H-13C NOESY
11562D 1H-13C HSQC
11663D 1H-13C NOESY
11782D 1H-15N HSQC
11852D 1H-15N HSQC
11922D 1Ff2Ff NOESY
12072D 1Ff2Ff NOESY
12162D 1Ff2Ff NOESY
12223D 1Fe3Ff NOESY
12373D 1Fe3Ff NOESY
12463D 1Fe3Ff NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] RsmE, 1 mM RNA, 93% H2O/7% D2O93% H2O/7% D2O
21 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA, 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA, 93% H2O/7% D2O93% H2O/7% D2O
41 mM [U-100% 15N] RsmE, 1 mM RNA, 100% D2O100% D2O
51 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Gua/Ura RNA, 93% H2O/7% D2O93% H2O/7% D2O
61 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Gua/Ura RNA, 100% D2O100% D2O
71 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Cyt/Ade RNA, 100% D2O100% D2O
81 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Cyt/Ade RNA, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRsmE[U-100% 15N]1
1 mMRNA1
1 mMRsmE[U-100% 13C; U-100% 15N]2
1 mMRNA2
1 mMRsmE[U-100% 13C; U-100% 15N]3
1 mMRNA3
1 mMRsmE[U-100% 15N]4
1 mMRNA4
1 mMRsmE[U-100% 15N]5
1 mMRNA[U-13C; U-15N]-Gua/Ura5
1 mMRsmE[U-100% 15N]6
1 mMRNA[U-13C; U-15N]-Gua/Ura6
1 mMRsmE[U-100% 15N]7
1 mMRNA[U-13C; U-15N]-Cyt/Ade7
1 mMRsmE[U-100% 15N]8
1 mMRNA[U-13C; U-15N]-Cyt/Ade8
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 DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX7503
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
Amber7Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollrefinement
DYANA3.02Guntert, Braun and Wuthrichgeometry optimization
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CCP4CCP4 Executuve Committeerename chains
CCP4CCP4 Executuve Committeesuperpose ensemble
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: in implicit water
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

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