+Open data
-Basic information
Entry | Database: PDB / ID: 7bbl | ||||||
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Title | Structure of human Gemin6/Gemin7/Gemin8 trimeric complex | ||||||
Components |
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Keywords | SPLICING / UsnRNP / Biogenesis / SMN-complex / Gemin8 | ||||||
Function / homology | Function and homology information Sm-like protein family complex / Gemini of coiled bodies / SMN complex / import into nucleus / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery ...Sm-like protein family complex / Gemini of coiled bodies / SMN complex / import into nucleus / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / nuclear body / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.521 Å | ||||||
Authors | Viswanathan, A. / Grimm, C. / Fischer, U. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Identification and structural analysis of the Schizosaccharomyces pombe SMN complex. Authors: Veepaschit, J. / Viswanathan, A. / Bordonne, R. / Grimm, C. / Fischer, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bbl.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bbl.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 7bbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/7bbl ftp://data.pdbj.org/pub/pdb/validation_reports/bb/7bbl | HTTPS FTP |
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-Related structure data
Related structure data | 7bb3C 1y96S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10537.991 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WXD5 #2: Protein | Mass: 9733.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H840 #3: Protein/peptide | Mass: 4900.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN8, FAM51A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NWZ8 #4: 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: 2.1 Å3/Da / Density % sol: 41.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 100 mM 2-(N-morpholino) ethanesulfonic acid, 200 mM NaCl, 30 % Jeffamine ED2003 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2016 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.521→48.494 Å / Num. obs: 58263 / % possible obs: 93.55 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.61 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06668 / Rpim(I) all: 0.03546 / Rrim(I) all: 0.07609 / Net I/σ(I): 10.83 |
Reflection shell | Resolution: 1.521→1.576 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.7935 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 4340 / CC1/2: 0.197 / CC star: 0.574 / Rpim(I) all: 0.5227 / Rrim(I) all: 0.9596 / % possible all: 70.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y96 Resolution: 1.521→48.494 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.85 / 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: 98.27 Å2 / Biso mean: 27.442 Å2 / Biso min: 10 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.521→48.494 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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