+Open data
-Basic information
Entry | Database: PDB / ID: 7w2p | ||||||
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Title | Tudor domain of SMN in complex with a small molecule | ||||||
Components | Survival motor neuron protein | ||||||
Keywords | RNA BINDING PROTEIN / SMN / Tudor / small molecule | ||||||
Function / homology | Function and homology information Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / Z disc / cytoplasmic ribonucleoprotein granule / nervous system development ...Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / Z disc / cytoplasmic ribonucleoprotein granule / nervous system development / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / perikaryon / nuclear body / neuron projection / axon / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Li, W. / Arrowsmith, C.H. / Edwards, A.M. / Liu, Y. / Min, J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II. Authors: Liu, Y. / Iqbal, A. / Li, W. / Ni, Z. / Wang, Y. / Ramprasad, J. / Abraham, K.J. / Zhang, M. / Zhao, D.Y. / Qin, S. / Loppnau, P. / Jiang, H. / Guo, X. / Brown, P.J. / Zhen, X. / Xu, G. / ...Authors: Liu, Y. / Iqbal, A. / Li, W. / Ni, Z. / Wang, Y. / Ramprasad, J. / Abraham, K.J. / Zhang, M. / Zhao, D.Y. / Qin, S. / Loppnau, P. / Jiang, H. / Guo, X. / Brown, P.J. / Zhen, X. / Xu, G. / Mekhail, K. / Ji, X. / Bedford, M.T. / Greenblatt, J.F. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w2p.cif.gz | 47 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w2p.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 7w2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w2p_validation.pdf.gz | 733.6 KB | Display | wwPDB validaton report |
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Full document | 7w2p_full_validation.pdf.gz | 733.7 KB | Display | |
Data in XML | 7w2p_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 7w2p_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/7w2p ftp://data.pdbj.org/pub/pdb/validation_reports/w2/7w2p | HTTPS FTP |
-Related structure data
Related structure data | 4qq6SC 4qqdC 6v9tC 7w30C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7352.253 Da / Num. of mol.: 1 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 | ||||||
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#2: Chemical | ChemComp-8AI / | ||||||
#3: Chemical | #4: Chemical | ChemComp-UNX / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8 M sodium acetate, pH 7.0, 0.1 M Bis-Tris propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→46 Å / Num. obs: 22319 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.15→1.17 Å / Num. unique obs: 1064 / CC1/2: 0.785 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QQ6 Resolution: 1.15→33.44 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.818 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.03 / 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: 57.12 Å2 / Biso mean: 11.864 Å2 / Biso min: 6.1 Å2
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Refinement step | Cycle: final / Resolution: 1.15→33.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.179 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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