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Yorodumi- PDB-5xjt: Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xjt | |||||||||
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Title | Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with SmD1(1-82)/D2.R61A/F/E/G from Human | |||||||||
Components |
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Keywords | SPLICING | |||||||||
Function / homology | Function and homology information negative regulation of RNA binding / Gemini of coiled bodies / SMN complex / U7 snRNP / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex ...negative regulation of RNA binding / Gemini of coiled bodies / SMN complex / U7 snRNP / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / Cajal body / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / DNA-templated transcription termination / spliceosomal complex / Z disc / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / mRNA processing / nervous system development / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / perikaryon / nuclear body / neuron projection / axon / nucleolus / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å | |||||||||
Authors | Yi, H. / Zhang, R. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Structures of 7S mutant complexes Authors: Yi, H. / Zhang, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xjt.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xjt.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xjt_validation.pdf.gz | 484 KB | Display | wwPDB validaton report |
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Full document | 5xjt_full_validation.pdf.gz | 502.5 KB | Display | |
Data in XML | 5xjt_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 5xjt_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/5xjt ftp://data.pdbj.org/pub/pdb/validation_reports/xj/5xjt | HTTPS FTP |
-Related structure data
Related structure data | 3s6n S: Starting model for refinement |
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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
-Small nuclear ribonucleoprotein ... , 5 types, 5 molecules ABEFG
#2: Protein | Mass: 9300.950 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62314 |
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#3: Protein | Mass: 13465.812 Da / Num. of mol.: 1 / Mutation: R61A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD2, SNRPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62316 |
#4: Protein | Mass: 10817.601 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPE / Production host: Escherichia coli (E. coli) / References: UniProt: P62304 |
#5: Protein | Mass: 9734.171 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPF, PBSCF / Production host: Escherichia coli (E. coli) / References: UniProt: P62306 |
#6: Protein | Mass: 8508.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPG, PBSCG / Production host: Escherichia coli (E. coli) / References: UniProt: P62308 |
-Protein / Protein/peptide , 2 types, 2 molecules 2M
#1: Protein | Mass: 31620.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN2, SIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14893 |
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#7: Protein/peptide | Mass: 4047.395 Da / Num. of mol.: 1 / Fragment: UNP residues 26-62 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMN1, SMN, SMNT, SMN2, SMNC / Production host: Escherichia coli (E. coli) / References: UniProt: Q16637 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1% PEG8000, 100mM Tris.HCl / PH range: 7.5-8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97846 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97846 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→66.98 Å / Num. obs: 13784 / % possible obs: 99.6 % / Redundancy: 12 % / Net I/σ(I): 8.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S6N 3s6n Resolution: 2.92→66.98 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.806 / SU B: 24.488 / SU ML: 0.424 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.602 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 183.82 Å2 / Biso mean: 63.778 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: final / Resolution: 2.92→66.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.922→2.998 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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