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- PDB-4rcj: Crystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rcj | |||||||||
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Title | Crystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA | |||||||||
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![]() | RNA BINDING PROTEIN/RNA / Structural Genomics / Structural Genomics Consortium / SGC / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | ![]() regulation of antigen processing and presentation / regulation of axon guidance / organelle assembly / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / immune system process / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability ...regulation of antigen processing and presentation / regulation of axon guidance / organelle assembly / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / immune system process / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability / learning / positive regulation of translation / P-body / memory / cytoplasmic stress granule / ribosome binding / mRNA binding / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Tempel, W. / Xu, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62 KB | Display | ![]() |
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PDB format | ![]() | 41.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.8 KB | Display | ![]() |
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Full document | ![]() | 443.8 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rciSC ![]() 4rcmC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22248.084 Da / Num. of mol.: 1 / Fragment: UNP residues 365-554 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: RNA chain | Mass: 1600.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 34.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG-3350, 0.2 M sodium chloride, 0.1 M bis-tris, pH 6.5, vapor diffusion, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2014 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791829 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.6→40.03 Å / Num. obs: 23138 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.4 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4RCI Resolution: 1.6→40.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.1607 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8468 / SU B: 2.042 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0988 / SU Rfree: 0.0988 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: ARP/WARP WAS USED IN DENSITY IMPROVEMENT MODE AFTER MOLECULAR REPLACEMENT. JLIGAND WAS USED FOR PREPARATION OF NUCLEOTIDE LINK RESTRAINT TARGETS. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. ...Details: ARP/WARP WAS USED IN DENSITY IMPROVEMENT MODE AFTER MOLECULAR REPLACEMENT. JLIGAND WAS USED FOR PREPARATION OF NUCLEOTIDE LINK RESTRAINT TARGETS. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY. WEAK ELECTRON DENSITY NEAR THE 3'-END OF THE MODELED OLIGONUCLEOTIDE SUGGESTS THE PRESENCE OF AN ADDITIONAL NUCLEOTIDE.
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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: 58.76 Å2 / Biso mean: 14.351 Å2 / Biso min: 4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→40.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.647 Å / Total num. of bins used: 20
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