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Yorodumi- PDB-1mj1: FITTING THE TERNARY COMPLEX OF EF-Tu/tRNA/GTP AND RIBOSOMAL PROTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mj1 | ||||||
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Title | FITTING THE TERNARY COMPLEX OF EF-Tu/tRNA/GTP AND RIBOSOMAL PROTEINS INTO A 13 A CRYO-EM MAP OF THE COLI 70S RIBOSOME | ||||||
Components |
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Keywords | RIBOSOME / 70S RIBOSOME / LOW RESOLUTION MODEL TERNARY COMPLEX / EF-Tu | ||||||
Function / homology | Function and homology information endo-alpha-N-acetylgalactosaminidase activity / misfolded RNA binding / Group I intron splicing / RNA folding / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / positive regulation of RNA splicing / maintenance of translational fidelity / small ribosomal subunit / large ribosomal subunit rRNA binding ...endo-alpha-N-acetylgalactosaminidase activity / misfolded RNA binding / Group I intron splicing / RNA folding / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / positive regulation of RNA splicing / maintenance of translational fidelity / small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / GTP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13 Å | ||||||
Authors | Stark, H. / Rodnina, M.V. / Wieden, H.-J. / Zemlin, F. / Wintermeyer, W. / Vanheel, M. | ||||||
Citation | Journal: Nat Struct Biol / Year: 2002 Title: Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex. Authors: Holger Stark / Marina V Rodnina / Hans-Joachim Wieden / Friedrich Zemlin / Wolfgang Wintermeyer / Marin van Heel / Abstract: The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional ...The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional reconstruction determined by cryo-electron microscopy of the kirromycin-stalled codon-recognition complex. The structure of the ternary complex is distorted by binding of the tRNA anticodon arm in the decoding center. The aa-tRNA interacts with 16S rRNA, helix 69 of 23S rRNA and proteins S12 and L11, while the sarcin-ricin loop of 23S rRNA contacts domain 1 of EF-Tu near the nucleotide-binding pocket. These results provide a detailed snapshot view of an important functional state of the ribosome and suggest mechanisms of decoding and GTPase activation. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1mj1.cif.gz | 163.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mj1.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 1mj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mj1_validation.pdf.gz | 779.1 KB | Display | wwPDB validaton report |
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Full document | 1mj1_full_validation.pdf.gz | 835.5 KB | Display | |
Data in XML | 1mj1_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 1mj1_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/1mj1 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/1mj1 | HTTPS FTP |
-Related structure data
Related structure data | 1004MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 4 molecules DCQR
#1: RNA chain | Mass: 24890.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRIES 1GIX, 1TRA / Source: (natural) Escherichia coli (E. coli) #2: RNA chain | | Mass: 13369.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1GIY / Source: (natural) Escherichia coli (E. coli) #3: RNA chain | | Mass: 8688.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1GIY / Source: (natural) Escherichia coli (E. coli) |
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-Protein , 4 types, 4 molecules AOPL
#4: Protein | Mass: 46064.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1B23 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q01698*PLUS |
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#5: Protein | Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1GIX / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3, UniProt: Q5SHN3*PLUS |
#6: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1GIX / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P80377*PLUS |
#7: Protein | Mass: 15111.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TAKEN FROM PDB ENTRY 1GIY / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P29395*PLUS |
-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 | Name: EF-Tu/tRNA/GTP E. COLI 70S RIBOSOME / Type: RIBOSOME |
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Buffer solution | Name: Tris-HCl / pH: 7.5 / Details: Tris-HCl |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
Crystal grow | *PLUS Method: cryo-electron microscopy / Details: cryo-electron microscopy |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG/SOPHIE / Date: Mar 10, 2000 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 58500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 1.35 mm |
Specimen holder | Temperature: 4.2 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
Software |
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EM software |
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CTF correction | Details: phase flip | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Method: "exact filter" backprojection / Resolution: 13 Å / Num. of particles: 24000 / Actual pixel size: 2.25 Å / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Target criteria: best visual fit using the program Amira (ribosomal proteins), best fit using the program Situs (EF-Tu) Details: REFINEMENT PROTOCOL--rigid body DETAILS--FOR S12, S13, SRL, HELIX69 ANS L11 ONLY BACKBONE COORDINATES ARE DEPOSITED | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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