+Open data
-Basic information
Entry | Database: PDB / ID: 8v1h | ||||||
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Title | Crystal structure of human pre-mascRNA | ||||||
Components | pre-mascRNA | ||||||
Keywords | RNA / non-coding RNAs / cancer / mascRNA | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.89 Å | ||||||
Authors | Skeparnias, I. / Zhang, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2024 Title: Structural basis of MALAT1 RNA maturation and mascRNA biogenesis. Authors: Skeparnias, I. / Bou-Nader, C. / Anastasakis, D.G. / Fan, L. / Wang, Y.X. / Hafner, M. / Zhang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8v1h.cif.gz | 90.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v1h.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 8v1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8v1h_validation.pdf.gz | 387 KB | Display | wwPDB validaton report |
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Full document | 8v1h_full_validation.pdf.gz | 387.4 KB | Display | |
Data in XML | 8v1h_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 8v1h_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/8v1h ftp://data.pdbj.org/pub/pdb/validation_reports/v1/8v1h | HTTPS FTP |
-Related structure data
Related structure data | 8v1iC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 24332.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-NA / |
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: 2.3 Å3/Da / Density % sol: 46.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M sodium chloride, 0.1 M lithium chloride, 0.01 M magnesium chloride hexahydrate, 0.05 M MES (pH 6.5) and 35% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 29, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40.83 Å / Num. obs: 5028 / % possible obs: 94.5 % / Redundancy: 11.6 % / CC1/2: 0.998 / Net I/σ(I): 9.26 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 491 / CC1/2: 0.99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.89→40.83 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.3 / 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 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→40.83 Å
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Refine LS restraints |
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Refinement TLS params. | Method: refined / Origin x: -0.5873 Å / Origin y: 6.2369 Å / Origin z: 33.2639 Å
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Refinement TLS group | Selection details: all |