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Yorodumi- PDB-6sh7: Crystal structure of the human DEAH-helicase DHX15 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sh7 | |||||||||
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Title | Crystal structure of the human DEAH-helicase DHX15 in complex with the NKRF G-patch | |||||||||
Components |
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Keywords | HYDROLASE / G-patch / DEAH helicase / DExH helicase | |||||||||
Function / homology | Function and homology information U12-type spliceosomal complex / ATP-dependent activity, acting on RNA / response to alkaloid / ATPase activator activity / antiviral innate immune response / mRNA Splicing - Major Pathway / RNA splicing / helicase activity / spliceosomal complex / response to toxic substance ...U12-type spliceosomal complex / ATP-dependent activity, acting on RNA / response to alkaloid / ATPase activator activity / antiviral innate immune response / mRNA Splicing - Major Pathway / RNA splicing / helicase activity / spliceosomal complex / response to toxic substance / mRNA splicing, via spliceosome / mRNA processing / double-stranded RNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / RNA helicase activity / RNA helicase / nuclear speck / defense response to bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | |||||||||
Authors | Jonas, S. / Studer, M.K. / Ivanovic, L. | |||||||||
Funding support | Switzerland, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structural basis for DEAH-helicase activation by G-patch proteins. Authors: Studer, M.K. / Ivanovic, L. / Weber, M.E. / Marti, S. / Jonas, S. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sh7.cif.gz | 358 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sh7.ent.gz | 244.5 KB | Display | PDB format |
PDBx/mmJSON format | 6sh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/6sh7 ftp://data.pdbj.org/pub/pdb/validation_reports/sh/6sh7 | HTTPS FTP |
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-Related structure data
Related structure data | 6sh6C 5xdrS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 79063.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHX15, DBP1, DDX15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O43143, RNA helicase |
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#2: Protein | Mass: 7425.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NKRF, ITBA4, NRF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O15226 |
#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: 2.43 Å3/Da / Density % sol: 49.37 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M carboxylic acids, 0.1 M BICINE/Tris pH 8.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000041 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000041 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→46.23 Å / Num. obs: 39975 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 61.95 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.052 / Rrim(I) all: 0.187 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.21→2.29 Å / Redundancy: 13.5 % / Num. unique obs: 3912 / CC1/2: 0.38 / Rpim(I) all: 0.763 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XDR Resolution: 2.21→46.23 Å / SU ML: 0.3908 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7663 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→46.23 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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