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Yorodumi- PDB-5h1l: Crystal structure of WD40 repeat domains of Gemin5 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h1l | ||||||||||||||||||
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Title | Crystal structure of WD40 repeat domains of Gemin5 in complex with 7-nt U4 snRNA fragment | ||||||||||||||||||
Components |
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Keywords | SPLICING/RNA / WD repeat / Gemin5 / SMN / U4 snRNA / RNA binding / SPLICING-RNA complex | ||||||||||||||||||
Function / homology | Function and homology information SMN-Gemin2 complex / Gemini of coiled bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / U4 snRNA binding / SMN-Sm protein complex / spliceosomal snRNP assembly / U1 snRNA binding ...SMN-Gemin2 complex / Gemini of coiled bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / U4 snRNA binding / SMN-Sm protein complex / spliceosomal snRNP assembly / U1 snRNA binding / mRNA 3'-UTR binding / mRNA splicing, via spliceosome / ribosome binding / regulation of translation / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / protein-containing complex assembly / nuclear body / translation / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||||||||
Authors | Jin, W. / Wang, Y. / Liu, C.P. / Yang, N. / Jin, M. / Cong, Y. / Wang, M. / Xu, R.M. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Genes Dev. / Year: 2016 Title: Structural basis for snRNA recognition by the double-WD40 repeat domain of Gemin5 Authors: Jin, W. / Wang, Y. / Liu, C.P. / Yang, N. / Jin, M. / Cong, Y. / Wang, M. / Xu, R.M. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h1l.cif.gz | 166.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h1l.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 5h1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/5h1l ftp://data.pdbj.org/pub/pdb/validation_reports/h1/5h1l | HTTPS FTP |
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-Related structure data
Related structure data | 5h1jSC 5h1kC 5h1mC 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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Unit cell |
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-Components
#1: Protein | Mass: 81428.109 Da / Num. of mol.: 1 / Fragment: UNP residues 1-726 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN5 / Plasmid: pFastBac-HTC / Cell (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEQ6 |
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#2: RNA chain | Mass: 2160.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: NR_003925 |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.64 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Sodium malonate (pH 7.0), 12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 45763 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.059 / Rrim(I) all: 0.108 / Χ2: 1.072 / Net I/av σ(I): 13.024 / Net I/σ(I): 7.2 / Num. measured all: 153633 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H1J Resolution: 2.1→40.784 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.16 Å2 / Biso mean: 35.3017 Å2 / Biso min: 11.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→40.784 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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