+Open data
-Basic information
Entry | Database: PDB / ID: 4kzx | ||||||
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Title | Rabbit 40S ribosomal subunit in complex with eIF1. | ||||||
Components |
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Keywords | RIBOSOME / translation initiation / preinitiation complex | ||||||
Function / homology | Function and homology information positive regulation of mRNA cis splicing, via spliceosome / multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / regulation of translational initiation / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator ...positive regulation of mRNA cis splicing, via spliceosome / multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / regulation of translational initiation / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / ribosomal small subunit binding / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / T cell proliferation involved in immune response / erythrocyte development / translation regulator activity / ribosomal small subunit export from nucleus / cytosolic ribosome / laminin binding / 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) / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / positive regulation of apoptotic signaling pathway / 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 / placenta development / small-subunit processome / translational initiation / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / glucose homeostasis / ribosome binding / 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 / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / cell differentiation / postsynaptic density / rRNA binding / mitochondrial inner membrane / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / positive regulation of apoptotic process / cell division / DNA repair / centrosome / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / negative regulation of apoptotic process / nucleolus / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.809 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 | 4kzx.cif.gz | 4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4kzx.ent.gz | 3.3 MB | Display | PDB format |
PDBx/mmJSON format | 4kzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kzx_validation.pdf.gz | 821.6 KB | Display | wwPDB validaton report |
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Full document | 4kzx_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4kzx_validation.xml.gz | 267.5 KB | Display | |
Data in CIF | 4kzx_validation.cif.gz | 365.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/4kzx ftp://data.pdbj.org/pub/pdb/validation_reports/kz/4kzx | HTTPS FTP |
-Related structure data
Related structure data | 4kzyC 4kzzC 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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Details | monomer |
-Components
+40S ribosomal protein ... , 33 types, 33 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
-RNA chain / Protein , 2 types, 2 molecules il
#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: Protein | Mass: 12752.498 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: K12 / Gene: EIF1, SUI1 / Plasmid: pET28a-heIF1tev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41567 |
-Details
Sequence details | The reference for chain A is XP_002712810.1 at NCBI which indicates Met at position 1 instead of Ala |
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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: 4.75 Å3/Da / Density % sol: 74.1 % |
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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: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 9→80 Å / Num. all: 18057 / Num. obs: 17938 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 667.15 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3J3A AND 3J3D Resolution: 7.809→58.112 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6088 / SU ML: 1.46 / σ(F): 1.33 / Phase error: 42.9 / 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: 480.27 Å2 / Biso mean: 216.9994 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 7.809→58.112 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: 9
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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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