+Open data
-Basic information
Entry | Database: PDB / ID: 3nna | ||||||
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Title | Crystal Structure of CUGBP1 RRM1/2-RNA Complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RRM / RNA binding / RNA / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information BRE binding / perinucleolar compartment / post-transcriptional gene silencing / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA splice site recognition / pre-mRNA binding / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / mRNA destabilization / regulation of RNA splicing ...BRE binding / perinucleolar compartment / post-transcriptional gene silencing / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA splice site recognition / pre-mRNA binding / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / mRNA destabilization / regulation of RNA splicing / germ cell development / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / mRNA processing / cytoplasmic stress granule / regulation of inflammatory response / ribonucleoprotein complex / negative regulation of cell population proliferation / negative regulation of gene expression / mRNA binding / positive regulation of gene expression / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.899 Å | ||||||
Authors | Teplova, M. / Song, J. / Gaw, H. / Teplov, A. / Patel, D.J. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Structural Insights into RNA Recognition by the Alternate-Splicing Regulator CUG-Binding Protein 1. Authors: Teplova, M. / Song, J. / Gaw, H.Y. / Teplov, A. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nna.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nna.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 3nna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/3nna ftp://data.pdbj.org/pub/pdb/validation_reports/nn/3nna | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20226.777 Da / Num. of mol.: 1 / Fragment: RRM1-RRM2 domain (UNP Residues 14-187) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRUNOL2, CELF1, CUGBP, CUGBP1, NAB50 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q92879 |
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#2: RNA chain | Mass: 3746.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M ammonium acetate, 45% MPD, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97920, 0.97880, 0.96360 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2008 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.899→50 Å / Num. obs: 33331 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 36.3 | ||||||||||||
Reflection shell | Resolution: 1.899→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3325 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.899→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.225 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.591 Å2
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Refinement step | Cycle: LAST / Resolution: 1.899→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.899→1.947 Å / Total num. of bins used: 20
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