+Open data
-Basic information
Entry | Database: PDB / ID: 6rns | ||||||
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Title | Crystal structure of the dimerization domain of Gemin5 at 2.7 A | ||||||
Components | Gem-associated protein 5 | ||||||
Keywords | RNA BINDING PROTEIN / Dimerization / translation / Tetratricopeptide repeat (TPR) / SMN 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 / SAD / Resolution: 2.69 Å | ||||||
Authors | Moreno-Morcillo, M. / Ramon-Maiques, S. / Martinez-Salas, E. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Structural basis for the dimerization of Gemin5 and its role in protein recruitment and translation control. Authors: Moreno-Morcillo, M. / Francisco-Velilla, R. / Embarc-Buh, A. / Fernandez-Chamorro, J. / Ramon-Maiques, S. / Martinez-Salas, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rns.cif.gz | 222.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rns.ent.gz | 152.5 KB | Display | PDB format |
PDBx/mmJSON format | 6rns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/6rns ftp://data.pdbj.org/pub/pdb/validation_reports/rn/6rns | HTTPS FTP |
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-Related 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: 28003.029 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN5 / Plasmid: pOPINM / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 Rosetta(DE3)pLys / References: UniProt: Q8TEQ6 #2: Chemical | ChemComp-IOD / #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: 3.34 Å3/Da / Density % sol: 63.18 % / Description: Plates |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 200 mM NaI, 25% PEG 3350 and 100 mM BisTris Methane pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 2.033 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→97.53 Å / Num. obs: 20115 / % possible obs: 97.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 62.46 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.1401 / Rpim(I) all: 0.09073 / Rrim(I) all: 0.1675 / Net I/σ(I): 6.61 |
Reflection shell | Resolution: 2.691→2.787 Å / Redundancy: 3.1 % / Num. unique obs: 1946 / CC1/2: 0.745 / % possible all: 96.71 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.69→64.22 Å / SU ML: 0.4295 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3508
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.69→64.22 Å
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Refine LS restraints |
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LS refinement shell |
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