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Yorodumi- PDB-1vec: Crystal structure of the N-terminal domain of rck/p54, a human DE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vec | ||||||
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Title | Crystal structure of the N-terminal domain of rck/p54, a human DEAD-box protein | ||||||
Components | ATP-dependent RNA helicase p54 | ||||||
Keywords | RNA BINDING PROTEIN / RNA HELICASE / DEAD-BOX PROTEIN | ||||||
Function / homology | Function and homology information mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / P-body assembly / miRNA-mediated gene silencing by inhibition of translation / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity / P-body ...mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / P-body assembly / miRNA-mediated gene silencing by inhibition of translation / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity / P-body / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / negative regulation of translation / RNA helicase activity / RNA helicase / cadherin binding / protein domain specific binding / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Hogetsu, K. / Matsui, T. / Yukihiro, Y. / Tanaka, M. / Sato, T. / Kumasaka, T. / Tanaka, N. | ||||||
Citation | Journal: Genes Cells / Year: 2006 Title: Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes Authors: Matsui, T. / Hogetsu, K. / Usukura, J. / Sato, T. / Kumasaka, T. / Akao, Y. / Tanaka, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vec.cif.gz | 100.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vec.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1vec ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1vec | HTTPS FTP |
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-Related structure data
Related structure data | 1qdeS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 23113.076 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HUMRCK / Plasmid: PTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P26196 #2: Chemical | ChemComp-ZN / | #3: Chemical | ChemComp-TLA / | #4: 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: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG3350, di-sodium tartrate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 15, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→29.9 Å / Num. all: 52406 / Num. obs: 52054 / % possible obs: 99.3 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.01→2.08 Å / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5271 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QDE Resolution: 2.01→29.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 116477.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.4738 Å2 / ksol: 0.335418 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.01→29.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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