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Yorodumi- PDB-1qzc: Coordinates of S12, SH44, LH69 and SRL separately fitted into the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qzc | ||||||
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Title | Coordinates of S12, SH44, LH69 and SRL separately fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome | ||||||
Components |
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Keywords | RNA Binding Protein/RNA / ribosomal protein / rRNA / RNA Binding Protein-RNA COMPLEX | ||||||
Function / homology | Function and homology information endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Thermus thermophilus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å | ||||||
Authors | Valle, M. / Zavialov, A. / Li, W. / Stagg, S.M. / Sengupta, J. / Nielsen, R.C. / Nissen, P. / Harvey, S.C. / Ehrenberg, M. / Frank, J. | ||||||
Citation | Journal: Nat Struct Biol / Year: 2003 Title: Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Authors: Mikel Valle / Andrey Zavialov / Wen Li / Scott M Stagg / Jayati Sengupta / Rikke C Nielsen / Poul Nissen / Stephen C Harvey / Måns Ehrenberg / Joachim Frank / Abstract: Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a cryo-electron microscopy (cryo-EM) study, ...Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a cryo-electron microscopy (cryo-EM) study, at a resolution of approximately 9 A, showing that during the incorporation of the aa-tRNA into the 70S ribosome of Escherichia coli, the flexibility of aa-tRNA allows the initial codon recognition and its accommodation into the ribosomal A site. In addition, a conformational change observed in the GTPase-associated center (GAC) of the ribosomal 50S subunit may provide the mechanism by which the ribosome promotes a relative movement of the aa-tRNA with respect to EF-Tu. This relative rearrangement seems to facilitate codon recognition by the incoming aa-tRNA, and to provide the codon-anticodon recognition-dependent signal for the GTPase activity of EF-Tu. From these new findings we propose a mechanism that can explain the sequence of events during the decoding of mRNA on the ribosome. | ||||||
History |
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Remark 999 | SEQUENCE THE PROTEIN STRUCTURE CONTAINS CA ATOMS and THE RNA STRUCTURES CONTAIN P ATOMS ONLY |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1qzc.cif.gz | 20 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qzc.ent.gz | 8.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qzc_validation.pdf.gz | 778.1 KB | Display | wwPDB validaton report |
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Full document | 1qzc_full_validation.pdf.gz | 777.7 KB | Display | |
Data in XML | 1qzc_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 1qzc_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/1qzc ftp://data.pdbj.org/pub/pdb/validation_reports/qz/1qzc | HTTPS FTP |
-Related structure data
Related structure data | 1056MC 1055C 1395C 1qzaC 1qzbC 1qzdC 1r2wC 1r2xC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: RNA chain | Mass: 14245.544 Da / Num. of mol.: 1 / Fragment: helix 44 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 |
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#2: RNA chain | Mass: 6688.036 Da / Num. of mol.: 1 / Fragment: helix 69 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 |
#3: RNA chain | Mass: 8775.319 Da / Num. of mol.: 1 / Fragment: Sarcin/ricin loop (SRL) / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 |
#4: Protein | Mass: 14506.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN3 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Buffer solution | Name: Polymix buffer / pH: 7.5 / Details: Polymix buffer | |||||||||||||||||||||||||
Specimen | Conc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: Quantifoil holley carbon film grids | |||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: electron microscopy / Details: electron microscopy |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49696 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm |
Specimen holder | Temperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software | Name: SPIDER / Category: 3D reconstruction | |||||||||||||||||||||
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CTF correction | Details: CTF correction of 3D maps by Wiener filteration | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Method: 3D projection matching; conjugate gradient with regularization Resolution: 9 Å / Num. of particles: 52181 / Actual pixel size: 2.82 Å / Magnification calibration: TMV / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: METHOD--Manual fitting in O | |||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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