+Open data
-Basic information
Entry | Database: PDB / ID: 4jhk | ||||||
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Title | Crystal structure of Danio rerio SLIP1 in complex with SLBP | ||||||
Components |
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Keywords | TRANSLATION / MRNA EXPORT / MRNA TRANSPORT / RNA BINDING / HISTONE MRNA PROCESSING / 3'-UTR / 3'-PROCESSING / SLBP / U7 snRNP / stem loop RNA | ||||||
Function / homology | Function and homology information histone mRNA stem-loop binding complex / photoreceptor cell differentiation / histone pre-mRNA stem-loop binding / mRNA 3'-end processing by stem-loop binding and cleavage / translation activator activity / cap-dependent translational initiation / histone pre-mRNA 3'end processing complex / neural retina development / brain morphogenesis / regulation of translational initiation ...histone mRNA stem-loop binding complex / photoreceptor cell differentiation / histone pre-mRNA stem-loop binding / mRNA 3'-end processing by stem-loop binding and cleavage / translation activator activity / cap-dependent translational initiation / histone pre-mRNA 3'end processing complex / neural retina development / brain morphogenesis / regulation of translational initiation / retinal ganglion cell axon guidance / mRNA transport / neuron differentiation / mRNA binding / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.507 Å | ||||||
Authors | von Moeller, H. / Conti, E. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: Structural and biochemical studies of SLIP1-SLBP identify DBP5 and eIF3g as SLIP1-binding proteins. Authors: von Moeller, H. / Lerner, R. / Ricciardi, A. / Basquin, C. / Marzluff, W.F. / Conti, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jhk.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jhk.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 4jhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jhk_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 4jhk_full_validation.pdf.gz | 444.4 KB | Display | |
Data in XML | 4jhk_validation.xml.gz | 11 KB | Display | |
Data in CIF | 4jhk_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/4jhk ftp://data.pdbj.org/pub/pdb/validation_reports/jh/4jhk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25794.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) Gene: MIF4G domain-containing protein B, mif4gdb, zgc:110826 Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q5EAQ1 | ||
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#2: Protein/peptide | Mass: 2595.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: sb:cb157, si:dkey-102m7.2, slbp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7SXI8 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.17 M K/Na-tartrate, 0.085 M Na-citrate pH 5.6, 1.7 M ammonium sulfate and 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→43.07 Å / Num. all: 13200 / Num. obs: 13244 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.507→43.069 Å / SU ML: 0.28 / σ(F): 2 / Phase error: 20.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.507→43.069 Å
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Refine LS restraints |
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LS refinement shell |
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