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Yorodumi- PDB-1si3: Crystal structure of the PAZ domain of human eIF2c1 in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1si3 | ||||||
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Title | Crystal structure of the PAZ domain of human eIF2c1 in complex with a 9-mer siRNA-like duplex | ||||||
Components |
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Keywords | GENE REGULATION/RNA / PROTEIN-RNA COMPLEX / RNA INTERFERENCE / DOUBLE HELIX / OVERHANG / GENE REGULATION-RNA COMPLEX | ||||||
Function / homology | Function and homology information Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RNA secondary structure unwinding / RISC-loading complex / RISC complex assembly ...Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RNA secondary structure unwinding / RISC-loading complex / RISC complex assembly / miRNA-mediated gene silencing by inhibition of translation / miRNA processing / pre-miRNA processing / RISC complex / Regulation of RUNX1 Expression and Activity / miRNA binding / MicroRNA (miRNA) biogenesis / nuclear-transcribed mRNA catabolic process / RNA polymerase II complex binding / Regulation of MECP2 expression and activity / Transcriptional Regulation by VENTX / core promoter sequence-specific DNA binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of angiogenesis / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / P-body / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / double-stranded RNA binding / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / single-stranded RNA binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Ye, K. / Ma, J.B. / Patel, D. | ||||||
Citation | Journal: Nature / Year: 2004 Title: Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Authors: Ma, J.B. / Ye, K. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1si3.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1si3.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 1si3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/1si3 ftp://data.pdbj.org/pub/pdb/validation_reports/si/1si3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assemble consists of two PAZ domains bound to each end of a 9-mer siRNA-like duplex generated from the protein monomer and the 9-mer single stranded RNA in the asymmetric unit by the operation: -X+1,-Y+2,Z. |
-Components
#1: RNA chain | Mass: 2808.703 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 17377.562 Da / Num. of mol.: 1 / Fragment: PAZ domain (residues 225-369) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2C1 / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UL18 |
#3: 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: 2.49 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: PEG 1000, POTASSIUM CHLORIDE, HEPES-NAOH, DITHIOTHREITOL, pH 7.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9796 / Wavelength: 0.9796 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 18, 2003 |
Radiation | Monochromator: SI 111 / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 6431 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 59.2 Å2 / Rsym value: 0.115 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.663 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→19.83 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.0057 Å2 / ksol: 0.317842 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 10
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Xplor file |
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