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- PDB-4kzz: Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kzz | ||||||
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Title | Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1A | ||||||
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![]() | RIBOSOME / translation initiation | ||||||
Function / homology | ![]() multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / ribosomal subunit / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mammalian oogenesis stage ...multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / ribosomal subunit / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Formation of a pool of free 40S subunits / phagocytic cup / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cytosolic ribosome / laminin binding / rough endoplasmic reticulum / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gastrulation / MDM2/MDM4 family protein binding / translational initiation / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / ribosome assembly / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / perikaryon / cytosolic small ribosomal subunit / mitochondrial inner membrane / tRNA binding / cytoplasmic translation / postsynaptic density / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell cycle / cell division / DNA repair / centrosome / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() Synthetic (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lomakin, I.B. / Steitz, T.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 4.1 MB | Display | ![]() |
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PDB format | ![]() | 3.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 839.8 KB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 267.6 KB | Display | |
Data in CIF | ![]() | 366.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kzxC ![]() 4kzyC ![]() 3j3a ![]() 3j3d S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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#35: RNA chain | Mass: 24231.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#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.) ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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