[English] 日本語
Yorodumi- PDB-6f7s: Crystal structure of Human ARS2 residues 147-270 + 408-763 with d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f7s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Human ARS2 residues 147-270 + 408-763 with deletion of loop B | ||||||
Components |
| ||||||
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: 3.37 Å | ||||||
Authors | Cusack, S. / Schulze, W.M. | ||||||
Funding support | France, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6f7s.cif.gz | 186 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6f7s.ent.gz | 148.5 KB | Display | PDB format |
PDBx/mmJSON format | 6f7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f7s_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6f7s_full_validation.pdf.gz | 454.5 KB | Display | |
Data in XML | 6f7s_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 6f7s_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/6f7s ftp://data.pdbj.org/pub/pdb/validation_reports/f7/6f7s | HTTPS FTP |
-Related structure data
Related structure data | 6f7jSC 6f7pC 6f8dC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 14754.771 Da / Num. of mol.: 2 / Fragment: UNP residues 147-270 Source method: isolated from a genetically manipulated source Details: Residues 147-270 and 408-763 were co-expressed as separate pieces.Residues 271-407 were deleted.Residues 568-598 (denoted loop B) were replaced by GSGSGS 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: 38485.297 Da / Num. of mol.: 2 / Fragment: UNP residues 408-567,UNP residues 599-763 Source method: isolated from a genetically manipulated source Details: Residues 147-270 and 408-763 were co-expressed as separate pieces.Residues 271-407 were deleted.Residues 568-598 (denoted loop B) were replaced by GSGSGS,Residues 147-270 and 408-763 were co- ...Details: Residues 147-270 and 408-763 were co-expressed as separate pieces.Residues 271-407 were deleted.Residues 568-598 (denoted loop B) were replaced by GSGSGS,Residues 147-270 and 408-763 were co-expressed as separate pieces.Residues 271-407 were deleted.Residues 568-598 (denoted loop B) were replaced by GSGSGS 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 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.94 % |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: Crystals of human ARS2 were obtained at 4 C in 2 microliter hanging drops with a 1:1 ratio of protein solution (6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine, ...Details: Crystals of human ARS2 were obtained at 4 C in 2 microliter hanging drops with a 1:1 ratio of protein solution (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 potassium citrate tribasic monohydrate, 20 % (w/v) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 3.37→117.83 Å / Num. obs: 20293 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.12 % / CC1/2: 0.998 / Rsym value: 0.098 / Net I/σ(I): 12.62 |
Reflection shell | Resolution: 3.37→3.46 Å / Redundancy: 3.82 % / Mean I/σ(I) obs: 1.97 / CC1/2: 0.537 / Rsym value: 0.674 / % possible all: 67.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F7J Resolution: 3.37→117.83 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.862 / SU B: 38.314 / SU ML: 0.564 / Cross valid method: THROUGHOUT / ESU R Free: 0.647 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 124.446 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.37→117.83 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|