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Yorodumi- PDB-6f9s: Crystal structure of the C-terminal RecA domain of DDX6 in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f9s | ||||||||||||||||||
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Title | Crystal structure of the C-terminal RecA domain of DDX6 in complex with a conserved peptide from LSM14 | ||||||||||||||||||
Components |
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Keywords | RNA / mRNA turnover / translational repression / decapping | ||||||||||||||||||
Function / homology | Function and homology information : / mitotic spindle midzone / mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / RISC complex / P granule / stem cell population maintenance / pericentriolar material ...: / mitotic spindle midzone / mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / RISC complex / P granule / stem cell population maintenance / pericentriolar material / negative regulation of neuron differentiation / RNA polymerase II core promoter sequence-specific DNA binding / stress granule assembly / helicase activity / P-body / neuron differentiation / mitotic spindle / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / mRNA processing / RNA helicase activity / negative regulation of translation / RNA helicase / cadherin binding / ribonucleoprotein complex / protein domain specific binding / mRNA binding / positive regulation of gene expression / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) Caenorhabditis elegans (invertebrata) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å | ||||||||||||||||||
Authors | Jinek, M. / Brandmann, T. | ||||||||||||||||||
Funding support | Switzerland, Canada, 5items
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Citation | Journal: EMBO J. / Year: 2018 Title: Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes. Authors: Brandmann, T. / Fakim, H. / Padamsi, Z. / Youn, J.Y. / Gingras, A.C. / Fabian, M.R. / Jinek, M. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f9s.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f9s.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 6f9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f9s_validation.pdf.gz | 426.2 KB | Display | wwPDB validaton report |
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Full document | 6f9s_full_validation.pdf.gz | 426.6 KB | Display | |
Data in XML | 6f9s_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 6f9s_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/6f9s ftp://data.pdbj.org/pub/pdb/validation_reports/f9/6f9s | HTTPS FTP |
-Related structure data
Related structure data | 6f9wC 2wayS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 20008.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX6, HLR2, RCK / Plasmid: pML-2MT Addgene #29708 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26196, RNA helicase | ||
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#2: Protein | Mass: 10429.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: car-1, CELE_Y18D10A.17, Y18D10A.17 / Plasmid: pGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9XW17 | ||
#3: Chemical | #4: 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: 3.06 Å3/Da / Density % sol: 59.83 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1.55 M Li2SO4, 0.1 M Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 3.03→46.07 Å / Num. obs: 7824 / % possible obs: 99.8 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 3.03→3.14 Å / Redundancy: 19.7 % / Rmerge(I) obs: 1.118 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 763 / CC1/2: 0.875 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WAY Resolution: 3.03→46.07 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.03→46.07 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: -27.4166 Å / Origin y: 17.3755 Å / Origin z: 6.1882 Å
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Refinement TLS group | Selection details: all |