+Open data
-Basic information
Entry | Database: PDB / ID: 5tef | ||||||
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Title | Crystal structure of Gemin5 WD40 repeats in complex with m7GpppG | ||||||
Components | Gem-associated protein 5 | ||||||
Keywords | SPLICING / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 / SMN-Sm protein complex / U4 snRNA binding / 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 / SMN-Sm protein complex / U4 snRNA binding / 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: 1.95 Å | ||||||
Authors | Chao, X. / Tempel, W. / Bian, C. / He, H. / Cerovina, T. / Seitova, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Genes Dev. / Year: 2016 Title: Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly. Authors: Xu, C. / Ishikawa, H. / Izumikawa, K. / Li, L. / He, H. / Nobe, Y. / Yamauchi, Y. / Shahjee, H.M. / Wu, X.H. / Yu, Y.T. / Isobe, T. / Takahashi, N. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tef.cif.gz | 154.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tef.ent.gz | 116 KB | Display | PDB format |
PDBx/mmJSON format | 5tef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/5tef ftp://data.pdbj.org/pub/pdb/validation_reports/te/5tef | 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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Details | Authors did not specify the biological assembly |
-Components
#1: Protein | Mass: 84170.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN5 / Plasmid: pFBOH-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEQ6 | ||||
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#2: Chemical | ChemComp-GTG / | ||||
#3: Chemical | #4: Chemical | ChemComp-UNX / #5: 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: 2.35 Å3/Da / Density % sol: 47.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 15% PEG4000, 0.2 M ammonium acetate, 0.1 sodium citrate, 0.0005-0.001 M m7GpppG |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97944 Å | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2011 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97944 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→48.02 Å / Num. obs: 55703 / % possible obs: 98.6 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.046 / Rrim(I) all: 0.092 / Net I/σ(I): 11 / Num. measured all: 216124 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: "apo" GEMIN5 WD40 repeats Resolution: 1.95→48.02 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.781 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.14 Details: A nearly isomorphous crystal structure was used as the search model for molecular replacement. Model coordinates where transformed with PDBSET to facilitate comparison with other, nearly ...Details: A nearly isomorphous crystal structure was used as the search model for molecular replacement. Model coordinates where transformed with PDBSET to facilitate comparison with other, nearly isomorphous Gemin5 crystal structures. Restraints for the partially resolved GTG residue were prepared on the GRADE server. Not all expected atoms of the GTG ligand were resolved in the electron density. Sulfhydryl groups of some cystyl residue appear chemically modified, based on peaks in the electron density maps. Coot was used for interactive model building. PHENIX.molprobity was used for geometry validation.
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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 max: 108.72 Å2 / Biso mean: 34.097 Å2 / Biso min: 12.57 Å2
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Refinement step | Cycle: final / Resolution: 1.95→48.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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