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Yorodumi- PDB-4kzz: Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kzz | ||||||
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Title | Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1A | ||||||
Components |
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Keywords | RIBOSOME / translation initiation | ||||||
Function / homology | Function and homology information multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / ribosomal subunit / laminin receptor activity / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits ...multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / ribosomal subunit / laminin receptor activity / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / laminin binding / translational initiation / ribosome assembly / translation initiation factor activity / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / ribosomal small subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit / tRNA binding / cell differentiation / structural constituent of ribosome / translation / synapse / nucleolus / RNA binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) Synthetic (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.0305 Å | ||||||
Authors | Lomakin, I.B. / Steitz, T.A. | ||||||
Citation | Journal: Nature / Year: 2013 Title: The initiation of mammalian protein synthesis and mRNA scanning mechanism. Authors: Lomakin, I.B. / Steitz, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kzz.cif.gz | 4.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4kzz.ent.gz | 3.3 MB | Display | PDB format |
PDBx/mmJSON format | 4kzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/4kzz ftp://data.pdbj.org/pub/pdb/validation_reports/kz/4kzz | HTTPS FTP |
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-Related structure data
Related structure data | 4kzxC 4kzyC 3j3a 3j3d S: Starting model for refinement 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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Unit cell |
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-Components
+40S Ribosomal Protein ... , 33 types, 33 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
-RNA chain , 3 types, 3 molecules ijk
#34: RNA chain | Mass: 600900.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 283837872 |
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#35: RNA chain | Mass: 24231.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 174924 |
#36: RNA chain | Mass: 7635.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: mRNA / Source: (synth.) Synthetic (others) |
-Protein , 1 types, 1 molecules n
#37: Protein | Mass: 16488.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal His6/TEV / Source: (gene. exp.) Homo sapiens (human) / Strain: K12 / Gene: EIF1AX / Plasmid: pET28a-heIF1Atev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*DE3 / References: UniProt: P47813 |
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-Details
Sequence details | The reference for chain A is XP_002712810.1 at NCBI. For chain X, the first residue should be the ...The reference for chain A is XP_002712810.1 at NCBI. For chain X, the first residue should be the initiating M. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.87 Å3/Da / Density % sol: 74.75 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 8.5 Details: 0.1M Ammonium acetate, 0.05M Tris-HCl pH 8.5, 2.5% PEG-20K, 4-6% MPD, 5.0mM Mg acetate, 2.0mM TCEP, vapor diffusion, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 7.03→80 Å / Num. all: 39353 / Num. obs: 38696 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 551.17 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3J3A AND 3J3D Resolution: 7.0305→77.529 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6057 / SU ML: 1.62 / σ(F): 1.34 / Phase error: 43.5 / Stereochemistry target values: ML Details: AUTHORS PERFORMED RIGID BODY REFINEMENT USING THE HUMAN PROTEINS WITH SIDECHAINS FROM PDB ENTRIES 3J3A AND 3J3D. THIS RESULTS IN CLOSE CONTACTS BETWEEN SIDECHAINS
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Solvent computation | Shrinkage radii: 1.2 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 100 Å2 / ksol: 0.334 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 529.05 Å2 / Biso mean: 179.8919 Å2 / Biso min: 12.79 Å2
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Refinement step | Cycle: LAST / Resolution: 7.0305→77.529 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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