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Yorodumi- PDB-6tqb: X-ray structure of Roquin ROQ domain in complex with a UCP3 CDE1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tqb | ||||||
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Title | X-ray structure of Roquin ROQ domain in complex with a UCP3 CDE1 SL RNA motif | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / roquin / ROQ domain / RNA binding / UCP1 | ||||||
Function / homology | Function and homology information negative regulation of germinal center formation / negative regulation of T-helper cell differentiation / regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CCR4-NOT complex binding / regulation of miRNA metabolic process / T follicular helper cell differentiation / regulation of T cell receptor signaling pathway / negative regulation of T-helper 17 cell differentiation / positive regulation of mRNA catabolic process / regulation of germinal center formation ...negative regulation of germinal center formation / negative regulation of T-helper cell differentiation / regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CCR4-NOT complex binding / regulation of miRNA metabolic process / T follicular helper cell differentiation / regulation of T cell receptor signaling pathway / negative regulation of T-helper 17 cell differentiation / positive regulation of mRNA catabolic process / regulation of germinal center formation / 3'-UTR-mediated mRNA destabilization / P-body assembly / miRNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / post-transcriptional regulation of gene expression / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / B cell homeostasis / nuclear-transcribed mRNA catabolic process / cellular response to interleukin-1 / lymph node development / T cell proliferation / spleen development / regulation of mRNA stability / mRNA 3'-UTR binding / P-body / RING-type E3 ubiquitin transferase / positive regulation of non-canonical NF-kappaB signal transduction / cytoplasmic stress granule / protein polyubiquitination / RNA stem-loop binding / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / double-stranded RNA binding / regulation of gene expression / T cell receptor signaling pathway / ubiquitin-dependent protein catabolic process / mRNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Binas, O. / Tants, J.-N. / Peter, S.A. / Janowski, R. / Davydova, E. / Braun, J. / Niessing, D. / Schwalbe, H. / Weigand, J.E. / Schlundt, A. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Structural basis for the recognition of transiently structured AU-rich elements by Roquin. Authors: Binas, O. / Tants, J.N. / Peter, S.A. / Janowski, R. / Davydova, E. / Braun, J. / Niessing, D. / Schwalbe, H. / Weigand, J.E. / Schlundt, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tqb.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tqb.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 6tqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tqb_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
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Full document | 6tqb_full_validation.pdf.gz | 473.3 KB | Display | |
Data in XML | 6tqb_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6tqb_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/6tqb ftp://data.pdbj.org/pub/pdb/validation_reports/tq/6tqb | HTTPS FTP |
-Related structure data
Related structure data | 6tqaC 6xwjC 6xwwC 6xxaC 6xxbC 4qi2S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / RNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 20528.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rc3h1, Gm551, Kiaa2025 / Production host: Escherichia coli (E. coli) References: UniProt: Q4VGL6, RING-type E3 ubiquitin transferase |
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#2: RNA chain | Mass: 6009.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) |
-Non-polymers , 5 types, 252 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.6 Å3/Da / Density % sol: 52.72 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 0.01 M Bis Tris Propane pH 6.5, 0.29 M Sodium Tartrate, 19 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 36355 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.16 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 2053 / CC1/2: 0.797 / % possible all: 75.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QI2 Resolution: 1.6→47.08 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.482 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 143.37 Å2 / Biso mean: 28.248 Å2 / Biso min: 16.39 Å2
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Refinement step | Cycle: final / Resolution: 1.6→47.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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