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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 / homologyRibosomal protein S15 / Ribosomal protein S15, bacterial-type / S15/NS1, RNA-binding / Ribosomal protein S15 / Ribosomal protein S15 signature. / ribosomal small subunit assembly / mRNA polyadenylation / cytosolic small ribosomal subunit / regulation of translation / rRNA binding ...Ribosomal protein S15 / Ribosomal protein S15, bacterial-type / S15/NS1, RNA-binding / Ribosomal protein S15 / Ribosomal protein S15 signature. / ribosomal small subunit assembly / mRNA polyadenylation / cytosolic small ribosomal subunit / regulation of translation / rRNA binding / structural constituent of ribosome / translation / cytosol / 30S ribosomal protein S15
Function and homology information
Specimen sourceESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 10 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 5, 2007 / Release: Oct 2, 2007
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 2, 2007Structure modelrepositoryInitial release
1.1Nov 14, 2012Structure modelOther / Version format compliance
1.2Aug 2, 2017Structure modelData collectionem_imaging / em_software_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
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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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
Polyers69,7182
Non-polymers00
Water0
1


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: (synth.) ESCHERICHIA COLI (E. coli)
#2: Protein/peptide 30S RIBOSOMAL PROTEIN S15 / / REPRESSOR S15 / Coordinate model: Cα atoms only


Mass: 10290.816 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid name: 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 / 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
Details: 20 MM TRIS-HCL PH 7.5, 60 MM KCL, 1MM DTT, 7.5 MM MGCL2
pH: 7.5
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
MicroscopyMicroscope model: 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 / Calibrated magnification: 51484 / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2 mm
Specimen holderTemperature: 77 kelvins
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber 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
3D reconstructionMethod: MANUAL FITTING / Resolution: 10 Å / Number of particles: 31415 / Nominal pixel size: 3 / Actual pixel size: 3
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 buildingDetails: METHOD--MANUAL REFINEMENT PROTOCOL--X-RAY AND HOMOLOGY MODELS
Ref protocol: OTHER / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
12AW71
22AWB1
Least-squares processHighest resolution: 1 Å
Refine hist #LASTHighest resolution: 1 Å
Number of atoms included #LASTProtein: 86 / Nucleic acid: 82 / Ligand: 0 / Solvent: 0 / Total: 168

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