+Open data
-Basic information
Entry | Database: PDB / ID: 3nnh | ||||||
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Title | Crystal Structure of the CUGBP1 RRM1 with GUUGUUUUGUUU RNA | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RNA recognition motif / pre-mRNA splicing / RNA / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information BRE binding / perinucleolar compartment / post-transcriptional gene silencing / mRNA splice site recognition / regulatory ncRNA-mediated post-transcriptional gene silencing / pre-mRNA binding / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / mRNA destabilization / germ cell development ...BRE binding / perinucleolar compartment / post-transcriptional gene silencing / mRNA splice site recognition / regulatory ncRNA-mediated post-transcriptional gene silencing / pre-mRNA binding / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / mRNA destabilization / germ cell development / regulation of RNA splicing / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / cytoplasmic stress granule / mRNA processing / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7501 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 | 3nnh.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nnh.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 3nnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nnh_validation.pdf.gz | 486 KB | Display | wwPDB validaton report |
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Full document | 3nnh_full_validation.pdf.gz | 492.7 KB | Display | |
Data in XML | 3nnh_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3nnh_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/3nnh ftp://data.pdbj.org/pub/pdb/validation_reports/nn/3nnh | HTTPS FTP |
-Related structure data
Related structure data | 3nmrSC 3nnaC 3nncC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10109.561 Da / Num. of mol.: 4 / Fragment: RRM1 domain (UNP residues 14-100) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRUNOL2, CELF1, CUGBP, CUGBP1, NAB50 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q92879 #2: RNA chain | Mass: 3746.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) #3: Water | ChemComp-HOH / | |
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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: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M potassium sodium tartrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→40 Å / Num. all: 12400 / Num. obs: 12357 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1213 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NMR Resolution: 2.7501→19.596 Å / SU ML: 0.32 / σ(F): 0.27 / Phase error: 22.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.165 Å2 / ksol: 0.345 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7501→19.596 Å
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Refine LS restraints |
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LS refinement shell |
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