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Yorodumi- PDB-8qmh: Crystal structure of RNA G2C4 repeats in complex with small synth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qmh | ||||||||||||||||||||||||||||
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Title | Crystal structure of RNA G2C4 repeats in complex with small synthetic molecule ANP77 | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / G2C4 repeats / ALS / FTD / hexanucleotide repeats | Function / homology | : / RNA | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | Authors | Kiliszek, A. / Ryczek, M. / Blaszczyk, L. | Funding support | Poland, 1items |
Citation | Journal: Nucleic Acids Res. / Year: 2024 | Title: Antisense RNA C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms a triplex-like structure and binds small synthetic ligand. Authors: Blaszczyk, L. / Ryczek, M. / Das, B. / Mateja-Pluta, M. / Bejger, M. / Sliwiak, J. / Nakatani, K. / Kiliszek, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qmh.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qmh.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 8qmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qmh_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8qmh_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8qmh_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 8qmh_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/8qmh ftp://data.pdbj.org/pub/pdb/validation_reports/qm/8qmh | HTTPS FTP |
-Related structure data
Related structure data | 8qmiC 9en6C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.18150/AJNJBE / Data set type: diffraction image 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: RNA chain | Mass: 1866.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-W53 / | Mass: 430.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26N8O / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.92 Å3/Da / Density % sol: 35.78 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.08 M NaCl, 0.04 M Na cacodylate trihydrate pH 6.0, 45% v/v MPD, 0.012 M Spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5406 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→21.85 Å / Num. obs: 23771 / % possible obs: 99.9 % / Redundancy: 16.3 % / Biso Wilson estimate: 8.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.025 / Rrim(I) all: 0.081 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.1→1.16 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3417 / CC1/2: 0.894 / Rpim(I) all: 0.254 / Rrim(I) all: 0.617 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→21.85 Å / SU ML: 0.0885 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9432 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.03 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→21.85 Å
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Refine LS restraints |
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LS refinement shell |
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