+Open data
-Basic information
Entry | Database: PDB / ID: 6rol | ||||||
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Title | Structure of IMP2 KH34 domains | ||||||
Components | Insulin-like growth factor 2 mRNA-binding protein 2 | ||||||
Keywords | RNA BINDING PROTEIN / Specificity | ||||||
Function / homology | Function and homology information translation regulator activity, nucleic acid binding / cold-induced thermogenesis / Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / anatomical structure morphogenesis / mRNA transport / translation regulator activity / energy homeostasis / regulation of cytokine production ...translation regulator activity, nucleic acid binding / cold-induced thermogenesis / Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA / CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / anatomical structure morphogenesis / mRNA transport / translation regulator activity / energy homeostasis / regulation of cytokine production / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding / cytoplasmic stress granule / nervous system development / cytoskeleton / negative regulation of translation / RNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Bhaskar, V. / Biswas, J. / Singer, R.H. / Chao, J.A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: The structural basis for RNA selectivity by the IMP family of RNA-binding proteins. Authors: Biswas, J. / Patel, V.L. / Bhaskar, V. / Chao, J.A. / Singer, R.H. / Eliscovich, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rol.cif.gz | 259.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rol.ent.gz | 215.4 KB | Display | PDB format |
PDBx/mmJSON format | 6rol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/6rol ftp://data.pdbj.org/pub/pdb/validation_reports/ro/6rol | HTTPS FTP |
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-Related structure data
Related structure data | 3krmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 18199.803 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2BP2, IMP2, VICKZ2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6M1 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 23% PEG-3350, 200mM Ammonium sulfate, 100mM Tris pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→37.8 Å / Num. obs: 46202 / % possible obs: 96.89 % / Redundancy: 1.9 % / Biso Wilson estimate: 32.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.0566 / Rpim(I) all: 0.0566 / Rrim(I) all: 0.08005 / Net I/σ(I): 8.05 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4114 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 4632 / CC1/2: 0.725 / Rpim(I) all: 0.4114 / Rrim(I) all: 0.5819 / % possible all: 98.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KRM Resolution: 2.1→37.8 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.1→37.8 Å
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LS refinement shell | Resolution: 2.1→2.175 Å
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