+Open data
-Basic information
Entry | Database: PDB / ID: 6kug | ||||||
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Title | Crystal structure of YBX1 CSD with RNA | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / CSD / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / RNA transport / Noncanonical activation of NOTCH3 / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / messenger ribonucleoprotein complex / CRD-mediated mRNA stabilization ...tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / RNA transport / Noncanonical activation of NOTCH3 / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / messenger ribonucleoprotein complex / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule / histone pre-mRNA 3'end processing complex / embryonic morphogenesis / U12-type spliceosomal complex / positive regulation of cytoplasmic translation / mRNA stabilization / cellular response to interleukin-7 / miRNA binding / mRNA Splicing - Minor Pathway / negative regulation of cellular senescence / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of cell division / epidermis development / mRNA Splicing - Major Pathway / RNA splicing / P-body / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / mRNA processing / cytoplasmic stress granule / Interferon gamma signaling / sequence-specific double-stranded DNA binding / single-stranded DNA binding / GTPase binding / double-stranded DNA binding / regulation of gene expression / in utero embryonic development / negative regulation of translation / nucleic acid binding / ribonucleoprotein complex / mRNA binding / intracellular membrane-bounded organelle / synapse / chromatin binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Zou, F. / Li, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: DrosophilaYBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs. Authors: Zou, F. / Tu, R. / Duan, B. / Yang, Z. / Ping, Z. / Song, X. / Chen, S. / Price, A. / Li, H. / Scott, A. / Perera, A. / Li, S. / Xie, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kug.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kug.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/6kug ftp://data.pdbj.org/pub/pdb/validation_reports/ku/6kug | HTTPS FTP |
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-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: 8710.782 Da / Num. of mol.: 1 / Fragment: CSD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YBX1, NSEP1, YB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P67809 |
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#2: RNA chain | Mass: 1216.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#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: 2.21 Å3/Da / Density % sol: 44.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.4 M Ammonium sulfate, 0.1M citric acid pH 5.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→40 Å / Num. obs: 17335 / % possible obs: 100 % / Redundancy: 19.2 % / Rsym value: 0.073 / Net I/σ(I): 44.4 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.8 / Num. unique obs: 1715 / CC1/2: 0.912 / Rsym value: 1.286 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→21.758 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→21.758 Å
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Refine LS restraints |
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LS refinement shell |
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