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- PDB-2vaz: Model of the S15-mRNA complex fitted into the cryo-EM map of the ... -

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Basic information

Entry
Database: PDB / ID: 2vaz
TitleModel of the S15-mRNA complex fitted into the cryo-EM map of the 70S entrapment complex.
Components
  • 30S RIBOSOMAL PROTEIN S15
  • RPSO MRNA OPERATOR
KeywordsTRANSLATION / PLATFORM-BINDING CENTER / GENE EXPRESSION REGULATION / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / PROTEIN SYNTHESIS / TRANSLATION INITIATION / RIBOSOME / RIBOSWITCH / RNA-BINDING / RRNA-BINDING / RNA PSEUDOKNOT / MRNA STRUCTURE / REPRESSOR PROTEIN
Function / homology
Function and homology information


mRNA base-pairing translational repressor activity / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / translation / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S15, bacterial-type / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / S15/NS1, RNA-binding
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å
Model type detailsP ATOMS ONLY, CHAIN A ; CA ATOMS ONLY, CHAIN F
AuthorsMarzi, S. / Myasnikov, A.G. / Serganov, A. / Ehresmann, C. / Romby, P. / Yusupov, M. / Klaholz, B.P.
CitationJournal: Cell / Year: 2007
Title: Structured mRNAs regulate translation initiation by binding to the platform of the ribosome.
Authors: Stefano Marzi / Alexander G Myasnikov / Alexander Serganov / Chantal Ehresmann / Pascale Romby / Marat Yusupov / Bruno P Klaholz /
Abstract: Gene expression can be regulated at the level of initiation of protein biosynthesis via structural elements present at the 5' untranslated region of mRNAs. These folded mRNA segments may bind to the ...Gene expression can be regulated at the level of initiation of protein biosynthesis via structural elements present at the 5' untranslated region of mRNAs. These folded mRNA segments may bind to the ribosome, thus blocking translation until the mRNA unfolds. Here, we report a series of cryo-electron microscopy snapshots of ribosomal complexes directly visualizing either the mRNA structure blocked by repressor protein S15 or the unfolded, active mRNA. In the stalled state, the folded mRNA prevents the start codon from reaching the peptidyl-tRNA (P) site inside the ribosome. Upon repressor release, the mRNA unfolds and moves into the mRNA channel allowing translation initiation. A comparative structure and sequence analysis suggests the existence of a universal stand-by site on the ribosome (the 30S platform) dedicated for binding regulatory 5' mRNA elements. Different types of mRNA structures may be accommodated during translation preinitiation and regulate gene expression by transiently stalling the ribosome.
History
DepositionSep 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Other / Version format compliance
Revision 1.2Aug 2, 2017Group: Data collection / Category: em_imaging / em_software
Item: _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min ..._em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-1391
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-1391
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RPSO MRNA OPERATOR
F: 30S RIBOSOMAL PROTEIN S15


Theoretical massNumber of molelcules
Total (without water)69,7182
Polymers69,7182
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

#1: RNA chain RPSO MRNA OPERATOR / Coordinate model: P atoms only


Mass: 59427.113 Da / Num. of mol.: 1 / Fragment: HAIRPIN LOOP DOMAIN I AND PSEUDOKNOT / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#2: Protein 30S RIBOSOMAL PROTEIN S15 / / REPRESSOR S15 / Coordinate model: Cα atoms only


Mass: 10290.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET11C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ADZ4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 70S PRE-INITIATION COMPLEX ENTRAPPED BY S15- RPSOMRNA / Type: RIBOSOME
Buffer solutionName: 20 MM TRIS-HCL PH 7.5, 60 MM KCL, 1MM DTT, 7.5 MM MGCL2
pH: 7.5
Details: 20 MM TRIS-HCL PH 7.5, 60 MM KCL, 1MM DTT, 7.5 MM MGCL2
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: BLOT FOR 2 SECONDS BEFORE PLUNGING IN LIQUID ETHANE USING A HOME-MADE CRYO- PLUNGER

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 5, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 51484 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2 mm
Specimen holderTemperature: 77 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 67
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1Omodel fitting
2PyMOLmodel fitting
3IMAGIC53D reconstruction
CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MANUAL FITTING / Resolution: 10 Å / Num. of particles: 31415 / Nominal pixel size: 3 Å / Actual pixel size: 3 Å
Details: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE RECORDS ...Details: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE RECORDS ARE MEANINGLESS. THE MRNA HAS BEEN MODELED USING MANIP (MASSIRE AND WESTHOF).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: METHOD--MANUAL REFINEMENT PROTOCOL--X-RAY AND HOMOLOGY MODELS
Atomic model building
IDPDB-ID 3D fitting-ID
12AW7

2aw7
PDB Unreleased entry

1
22AWB

2awb
PDB Unreleased entry

1
RefinementHighest resolution: 10 Å
Refinement stepCycle: LAST / Highest resolution: 10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms86 82 0 0 168

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