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Yorodumi- PDB-6q6r: Recognition of different base tetrads by RHAU: X-ray crystal stru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q6r | |||||||||
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Title | Recognition of different base tetrads by RHAU: X-ray crystal structure of G4 recognition motif bound to the 3-end tetrad of a DNA G-quadruplex | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / G-quadruplex / X-ray crystallography / RHAU helicase / DHX36 / G4R1 / Mle1 / DEAH-box family. | |||||||||
Function / homology | Function and homology information positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / positive regulation of mRNA 3'-end processing / telomerase RNA stabilization / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / positive regulation of myeloid dendritic cell cytokine production / DEx/H-box helicases activate type I IFN and inflammatory cytokines production ...positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / positive regulation of mRNA 3'-end processing / telomerase RNA stabilization / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / positive regulation of myeloid dendritic cell cytokine production / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RNA secondary structure unwinding / G-quadruplex DNA binding / positive regulation of dendritic spine morphogenesis / regulation of transcription by RNA polymerase III / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / positive regulation of telomere maintenance / positive regulation of cytoplasmic translation / cellular response to arsenite ion / telomerase RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / response to exogenous dsRNA / positive regulation of interferon-alpha production / regulation of embryonic development / positive regulation of transcription initiation by RNA polymerase II / ATP-dependent activity, acting on DNA / regulation of mRNA stability / DNA helicase activity / ossification / mRNA 3'-UTR binding / mRNA 5'-UTR binding / cytoplasmic stress granule / histone deacetylase binding / cellular response to UV / single-stranded DNA binding / double-stranded RNA binding / cellular response to heat / perikaryon / G-quadruplex RNA binding / spermatogenesis / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / DNA helicase / negative regulation of translation / RNA helicase activity / chromosome, telomeric region / cell differentiation / transcription cis-regulatory region binding / RNA helicase / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / innate immune response / dendrite / positive regulation of gene expression / magnesium ion binding / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | unidentified (others) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Heddi, B. / Cheong, V.V. / Schmitt, E. / Mechulam, Y. / Phan, A.T. | |||||||||
Funding support | Singapore, 2items
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Citation | Journal: J.Struct.Biol. / Year: 2020 Title: Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3'-end tetrad of a DNA G-quadruplex. Authors: Heddi, B. / Cheong, V.V. / Schmitt, E. / Mechulam, Y. / Phan, A.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q6r.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q6r.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 6q6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/6q6r ftp://data.pdbj.org/pub/pdb/validation_reports/q6/6q6r | HTTPS FTP |
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-Related structure data
Related structure data | 2lk7S S: Starting model for refinement |
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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: DNA chain | Mass: 5122.284 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: synthetic construct (others) #2: Protein/peptide | Mass: 3443.912 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHX36, DDX36, KIAA1488, MLEL1, RHAU / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2U1, DNA helicase, RNA helicase #3: Chemical | ChemComp-K / #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: 2.11 Å3/Da / Density % sol: 41.61 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 55% methylpentanediol, 40 mM sodium cacodylate (pH 6.0), 80 mM potassium chloride and 12 mM spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→60.6 Å / Num. obs: 45681 / % possible obs: 99.35 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.827 % / CC1/2: 0.998 / Rsym value: 0.079 / Net I/σ(I): 8.68 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 3.62 % / Mean I/σ(I) obs: 1.62 / Num. unique obs: 7212 / CC1/2: 0.816 / Rsym value: 0.763 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LK7 Resolution: 1.5→60.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.057 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.597 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→60.6 Å
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