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Yorodumi- PDB-7sxp: G-quadruplex structure formed in the NRAS mRNA with a G8U substitution -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sxp | ||||||
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Title | G-quadruplex structure formed in the NRAS mRNA with a G8U substitution | ||||||
Components | NRAS mRNA | ||||||
Keywords | RNA / G-quadruplex / NRAS | ||||||
Function / homology | CACODYLIC ACID / : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Banco, M.T. / Ferre-D'Amare, A.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Chem Biol / Year: 2023 Title: Investigating the NRAS 5' UTR as a target for small molecules. Authors: Balaratnam, S. / Torrey, Z.R. / Calabrese, D.R. / Banco, M.T. / Yazdani, K. / Liang, X. / Fullenkamp, C.R. / Seshadri, S. / Holewinski, R.J. / Andresson, T. / Ferre-D'Amare, A.R. / ...Authors: Balaratnam, S. / Torrey, Z.R. / Calabrese, D.R. / Banco, M.T. / Yazdani, K. / Liang, X. / Fullenkamp, C.R. / Seshadri, S. / Holewinski, R.J. / Andresson, T. / Ferre-D'Amare, A.R. / Incarnato, D. / Schneekloth Jr., J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sxp.cif.gz | 23.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sxp.ent.gz | 13.4 KB | Display | PDB format |
PDBx/mmJSON format | 7sxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sxp_validation.pdf.gz | 407.8 KB | Display | wwPDB validaton report |
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Full document | 7sxp_full_validation.pdf.gz | 408.3 KB | Display | |
Data in XML | 7sxp_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 7sxp_validation.cif.gz | 3.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/7sxp ftp://data.pdbj.org/pub/pdb/validation_reports/sx/7sxp | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 7242.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
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#2: Chemical | #3: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20 - 25 % PEG 3350, 80 mM sodium chloride and 100 mM BIS-TRIS pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.104 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.104 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→31.53 Å / Num. obs: 2556 / % possible obs: 99.6 % / Redundancy: 17.4 % / Biso Wilson estimate: 88.13 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.058 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.32→2.42 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 305 / CC1/2: 0.468 / Rpim(I) all: 0.678 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→31.53 Å / SU ML: 0.1496 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.7152 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: 83.24 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→31.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→31.53 Å
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