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- PDB-5xjl: Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xjl | |||||||||
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Title | Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with SmD1/D2/F/E/G from Human | |||||||||
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![]() | SPLICING | |||||||||
Function / homology | ![]() 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 spliceosomal complex / U2-type precatalytic spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / spliceosomal snRNP assembly / Cajal body / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / DNA-templated transcription termination / spliceosomal complex / mRNA processing / cytoplasmic ribonucleoprotein granule / Z disc / mRNA splicing, via spliceosome / 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a key intermediate of the SMN complex reveals Gemin2's crucial function in snRNP assembly Authors: Zhang, R. / So, B.R. / Li, P. / Yong, J. / Glisovic, T. / Wan, L. / Dreyfuss, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.8 KB | Display | ![]() |
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PDB format | ![]() | 103.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 490.9 KB | Display | ![]() |
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Full document | ![]() | 515.4 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Small nuclear ribonucleoprotein ... , 5 types, 5 molecules ABEFG
#2: Protein | Mass: 13310.653 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Protein | Mass: 13551.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 10817.601 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 9734.171 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#6: Protein | Mass: 8508.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein / Protein/peptide / Non-polymers , 3 types, 33 molecules 2M![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: Protein | Mass: 31620.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#7: Protein/peptide | Mass: 4047.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1%PEG8000, 100mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99993 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→59.19 Å / Num. obs: 19831 / % possible obs: 99.3 % / Redundancy: 6.3 % / Net I/σ(I): 13.7 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 125.65 Å2 / Biso mean: 52.21 Å2 / Biso min: 8.19 Å2
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Refinement step | Cycle: final / Resolution: 2.5→59.19 Å
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LS refinement shell | Resolution: 2.502→2.566 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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