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Yorodumi- PDB-5h1m: Crystal structure of WD40 repeat domains of Gemin5 in complex with M7G -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h1m | |||||||||||||||||||||
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Title | Crystal structure of WD40 repeat domains of Gemin5 in complex with M7G | |||||||||||||||||||||
Components | Gem-associated protein 5 | |||||||||||||||||||||
Keywords | SPLICING / WD repeat / Gemin5 / SMN | |||||||||||||||||||||
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 / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.492 Å | |||||||||||||||||||||
Authors | Jin, W. / Wang, Y. / 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 | 5h1m.cif.gz | 149.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h1m.ent.gz | 113.3 KB | Display | PDB format |
PDBx/mmJSON format | 5h1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h1m_validation.pdf.gz | 806.6 KB | Display | wwPDB validaton report |
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Full document | 5h1m_full_validation.pdf.gz | 814.2 KB | Display | |
Data in XML | 5h1m_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 5h1m_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/5h1m ftp://data.pdbj.org/pub/pdb/validation_reports/h1/5h1m | HTTPS FTP |
-Related structure data
Related structure data | 5h1jSC 5h1kC 5h1lC 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: Chemical | ChemComp-M7G / |
#3: 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: 2.44 Å3/Da / Density % sol: 49.67 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES (pH 7.5), 14% PEG 8000, 25mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 26965 / % possible obs: 99.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 64.24 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.045 / Rrim(I) all: 0.084 / Χ2: 1.035 / Net I/av σ(I): 15.937 / Net I/σ(I): 11.2 / Num. measured all: 89686 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H1J Resolution: 2.492→29.341 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.91 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.91 Å2 / Biso mean: 70.8732 Å2 / Biso min: 35.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.492→29.341 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: 10
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