+Open data
-Basic information
Entry | Database: PDB / ID: 6f7p | ||||||
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Title | Crystal structure of Human ARS2 residues 147-270 + 408-763 | ||||||
Components | (Serrate RNA effector molecule homolog) x 2 | ||||||
Keywords | RNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information mRNA cap binding complex binding / neuronal stem cell population maintenance / primary miRNA processing / response to arsenic-containing substance / positive regulation of neurogenesis / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / mRNA processing / protein-macromolecule adaptor activity / nuclear body ...mRNA cap binding complex binding / neuronal stem cell population maintenance / primary miRNA processing / response to arsenic-containing substance / positive regulation of neurogenesis / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / mRNA processing / protein-macromolecule adaptor activity / nuclear body / ribonucleoprotein complex / regulation of DNA-templated transcription / protein-containing complex / DNA binding / RNA binding / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Cusack, S. / Schulze, W.M. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural analysis of human ARS2 as a platform for co-transcriptional RNA sorting. Authors: Schulze, W.M. / Stein, F. / Rettel, M. / Nanao, M. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f7p.cif.gz | 190.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f7p.ent.gz | 152.7 KB | Display | PDB format |
PDBx/mmJSON format | 6f7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/6f7p ftp://data.pdbj.org/pub/pdb/validation_reports/f7/6f7p | HTTPS FTP |
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-Related structure data
Related structure data | 6f7jSC 6f7sC 6f8dC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 14754.771 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Residues 147-270 and 408-763 were co-expressed.Residues 271-407 were deleted Source: (gene. exp.) Homo sapiens (human) / Gene: SRRT, ARS2, ASR2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q9BXP5 #2: Protein | Mass: 41169.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Residues 147-270 and 408-763 were co-expressed.Residues 271-407 were deleted Source: (gene. exp.) Homo sapiens (human) / Gene: SRRT, ARS2, ASR2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q9BXP5 |
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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: 3.83 Å3/Da / Density % sol: 67.86 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: Crystals were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution at 6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to ...Details: Crystals were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution at 6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to crystallisation solution. The crystallisation solution was 0.2 M lithium sulphate and 20% (w/v) PEG 3550. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→118.33 Å / Num. obs: 18658 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.33 % / CC1/2: 1 / Rsym value: 0.081 / Net I/σ(I): 12.11 |
Reflection shell | Resolution: 3.7→3.8 Å / Redundancy: 6.16 % / Mean I/σ(I) obs: 1.44 / CC1/2: 0.763 / Rsym value: 1.158 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F7J Resolution: 3.7→118.33 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.931 / SU B: 60.019 / SU ML: 0.767 / Cross valid method: THROUGHOUT / ESU R Free: 0.748 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 202.198 Å2
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Refinement step | Cycle: 1 / Resolution: 3.7→118.33 Å
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Refine LS restraints |
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