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Yorodumi- PDB-5h1k: Crystal structure of WD40 repeat domains of Gemin5 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h1k | |||||||||||||||||||||
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Title | Crystal structure of WD40 repeat domains of Gemin5 in complex with 13-nt U4 snRNA fragment | |||||||||||||||||||||
Components |
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Keywords | SPLICING/RNA / WD repeat / Gemin5 / SMN / RNA binding / U4 snRNA / 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: 1.9 Å | |||||||||||||||||||||
Authors | Wang, Y. / Jin, W. / Liu, C.P. / Yang, N. / Jin, M. / Cong, Y. / Wang, M. / Xu, R.M. | |||||||||||||||||||||
Funding support | China, 6items
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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 | 5h1k.cif.gz | 328.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h1k.ent.gz | 257.3 KB | Display | PDB format |
PDBx/mmJSON format | 5h1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/5h1k ftp://data.pdbj.org/pub/pdb/validation_reports/h1/5h1k | HTTPS FTP |
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-Related structure data
Related structure data | 5h1jSC 5h1lC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 81428.109 Da / Num. of mol.: 2 / 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 #2: RNA chain | Mass: 4103.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: NR_003925 #3: Water | ChemComp-HOH / | |
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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: 2.34 Å3/Da / Density % sol: 47.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 4% Tacsimate (pH 8.0), 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2016 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 126392 / % possible obs: 99.7 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.8 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H1J Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.968 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.131 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.954 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→50 Å
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Refine LS restraints |
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