+Open data
-Basic information
Entry | Database: PDB / ID: 4rcm | |||||||||
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Title | Crystal structure of the Pho92 YTH domain in complex with m6A | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / Structural Genomics / Structural Genomics Consortium / SGC / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information regulation of phosphate metabolic process / N6-methyladenosine-containing RNA reader activity / mRNA destabilization / positive regulation of translational initiation / regulation of mRNA stability / mRNA 3'-UTR binding / mRNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | |||||||||
Authors | Tempel, W. / Xu, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins. Authors: Xu, C. / Liu, K. / Ahmed, H. / Loppnau, P. / Schapira, M. / Min, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rcm.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rcm.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 4rcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/4rcm ftp://data.pdbj.org/pub/pdb/validation_reports/rc/4rcm | HTTPS FTP |
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-Related structure data
Related structure data | 4rciSC 4rcjC 4r3hS 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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Details | AS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN |
-Components
#1: Protein | Mass: 19313.057 Da / Num. of mol.: 2 / Fragment: UNP residues 141-306 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: PHO92, MRB1, YDR374C / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q06390 #2: RNA chain | Mass: 1560.995 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-UNX / #4: 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: 1.84 Å3/Da / Density % sol: 33.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG-3350, 0.2 M potassium isocyanate, vapor diffusion, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å | ||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 15, 2014 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.8→38.4 Å / Num. obs: 27985 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.3 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 4R3H AND 4RCI Resolution: 1.8→32.97 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.2485 / WRfactor Rwork: 0.1999 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.747 / SU B: 4.912 / SU ML: 0.143 / SU R Cruickshank DPI: 0.1674 / SU Rfree: 0.1578 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: AN ENSEMBLE OF CRYSTALLOGRAPHIC MODELS OF HUMAN YTHDC1 AND YTHDF1 WAS USED AS SEARCH MODEL FOR MOLECULAR REPLACEMENT. PARROT WAS USED FOR DENSITY MODIFICATION. ARP/WARP WAS USED FOR PHASE ...Details: AN ENSEMBLE OF CRYSTALLOGRAPHIC MODELS OF HUMAN YTHDC1 AND YTHDF1 WAS USED AS SEARCH MODEL FOR MOLECULAR REPLACEMENT. PARROT WAS USED FOR DENSITY MODIFICATION. ARP/WARP WAS USED FOR PHASE IMPROVEMENT AND AUTOMATED MODEL BUILDING. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY.
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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 max: 66.6 Å2 / Biso mean: 19.2124 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→32.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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