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Yorodumi- PDB-4qmg: The Structure of MTDH-SND1 Complex Reveals Novel Cancer-Promoting... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qmg | ||||||
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Title | The Structure of MTDH-SND1 Complex Reveals Novel Cancer-Promoting Interactions | ||||||
Components |
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Keywords | TRANSCRIPTION / SN domains / oligonucleotide/oligosaccharide binding-fold (OB-fold) / DNA/RNA-binding / miRNA-mediated silencing / nuclease / breast cancer / tumorigenesis / SND1 / MTDH | ||||||
Function / homology | Function and homology information RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / regulation of cell cycle process / miRNA catabolic process / RISC complex binding / nuclease activity / dense body / bicellular tight junction assembly / intercellular canaliculus / regulatory ncRNA-mediated gene silencing / RISC complex ...RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / regulation of cell cycle process / miRNA catabolic process / RISC complex binding / nuclease activity / dense body / bicellular tight junction assembly / intercellular canaliculus / regulatory ncRNA-mediated gene silencing / RISC complex / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / mRNA catabolic process / NF-kappaB binding / bicellular tight junction / positive regulation of autophagy / lipopolysaccharide-mediated signaling pathway / RNA endonuclease activity / transcription coregulator activity / fibrillar center / osteoblast differentiation / positive regulation of angiogenesis / Signaling by BRAF and RAF1 fusions / double-stranded RNA binding / melanosome / positive regulation of NF-kappaB transcription factor activity / nuclear membrane / endonuclease activity / positive regulation of canonical NF-kappaB signal transduction / membrane => GO:0016020 / transcription coactivator activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear body / cadherin binding / apical plasma membrane / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / extracellular exosome / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.701 Å | ||||||
Authors | Guo, F. / Stanevich, V. / Wan, L. / Satyshur, K. / Kang, Y. / Xing, Y. | ||||||
Citation | Journal: Cell Rep / Year: 2014 Title: Structural Insights into the Tumor-Promoting Function of the MTDH-SND1 Complex. Authors: Guo, F. / Wan, L. / Zheng, A. / Stanevich, V. / Wei, Y. / Satyshur, K.A. / Shen, M. / Lee, W. / Kang, Y. / Xing, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qmg.cif.gz | 648.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qmg.ent.gz | 553.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qmg_validation.pdf.gz | 541.6 KB | Display | wwPDB validaton report |
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Full document | 4qmg_full_validation.pdf.gz | 556.1 KB | Display | |
Data in XML | 4qmg_validation.xml.gz | 58.9 KB | Display | |
Data in CIF | 4qmg_validation.cif.gz | 80.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/4qmg ftp://data.pdbj.org/pub/pdb/validation_reports/qm/4qmg | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 36918.207 Da / Num. of mol.: 5 / Fragment: SND1, UNP residues 16-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: Metadherin (MTDH) and Staphylococcal nuclease domain containing 1 (SND1), SND1, TDRD11 Plasmid: pQlink / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q7KZF4 #2: Protein/peptide | Mass: 4392.189 Da / Num. of mol.: 5 / Fragment: MTDH, UNP residues 386-407 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AEG1, LYRIC, Metadherin (MTDH), MTDH / Plasmid: pQlink / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q86UE4 |
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-Non-polymers , 4 types, 304 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CS / #5: Chemical | ChemComp-GOL / #6: 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: 2.62 Å3/Da / Density % sol: 52.99 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Mix 275nl of 15mg/ml SeMet-SND1(16-339)-L21-MTDH(386-407) with 250nl of well buffer (21.6% pEG3350, 0.1M Sodium Citrate, PH8.0, 0.1M CsCl )+50nl of micro seeds., VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97849 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97849 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 59029 / Num. obs: 59029 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 46.34 Å2 / Rsym value: 0.151 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.65 / Num. unique all: 5813 / Rsym value: 0.791 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.701→45.071 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 26.28 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.701→45.071 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -24.591 Å / Origin y: -14.9862 Å / Origin z: -35.4751 Å
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Refinement TLS group | Selection details: all |