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- PDB-2xl1: Structural basis of translational stalling by human cytomegalovir... -

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Basic information

Entry
Database: PDB / ID: 2xl1
TitleStructural basis of translational stalling by human cytomegalovirus (hCMV) and fungal arginine attenuator peptide (AAP)
ComponentsARGININE ATTENUATOR PEPTIDE
KeywordsTRANSLATION / ANTIBIOTIC / RIBOSOME / CYTOMEGALOVIRUS
Function / homologyLeader peptide, Arg-2/CPA1 / arg-2/CPA1 leader peptide / translational attenuation / Arginine attenuator peptide
Function and homology information
Biological speciesNEUROSPORA CRASSA (fungus)
MethodSOLUTION NMR / CYANA, CNS
AuthorsMeyer, N.H. / Sattler, M.
CitationJournal: Mol Cell / Year: 2010
Title: Structural basis for translational stalling by human cytomegalovirus and fungal arginine attenuator peptide.
Authors: Shashi Bhushan / Helge Meyer / Agata L Starosta / Thomas Becker / Thorsten Mielke / Otto Berninghausen / Michael Sattler / Daniel N Wilson / Roland Beckmann /
Abstract: Specific regulatory nascent chains establish direct interactions with the ribosomal tunnel, leading to translational stalling. Despite a wealth of biochemical data, structural insight into the ...Specific regulatory nascent chains establish direct interactions with the ribosomal tunnel, leading to translational stalling. Despite a wealth of biochemical data, structural insight into the mechanism of translational stalling in eukaryotes is still lacking. Here we use cryo-electron microscopy to visualize eukaryotic ribosomes stalled during the translation of two diverse regulatory peptides: the fungal arginine attenuator peptide (AAP) and the human cytomegalovirus (hCMV) gp48 upstream open reading frame 2 (uORF2). The C terminus of the AAP appears to be compacted adjacent to the peptidyl transferase center (PTC). Both nascent chains interact with ribosomal proteins L4 and L17 at tunnel constriction in a distinct fashion. Significant changes at the PTC were observed: the eukaryotic-specific loop of ribosomal protein L10e establishes direct contact with the CCA end of the peptidyl-tRNA (P-tRNA), which may be critical for silencing of the PTC during translational stalling. Our findings provide direct structural insight into two distinct eukaryotic stalling processes.
History
DepositionJul 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARGININE ATTENUATOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)2,7821
Polymers2,7821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide ARGININE ATTENUATOR PEPTIDE / AAP / ARG-2 LEADER PEPTIDE


Mass: 2782.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) NEUROSPORA CRASSA (fungus) / References: UniProt: P22702

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 50% D2O, 50% TFE
Sample conditionsIonic strength: 100 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 278.0 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
SPARKYstructure solution
CYANAstructure solution
RefinementMethod: CYANA, CNS / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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