+Open data
-Basic information
Entry | Database: PDB / ID: 7zhr | ||||||
---|---|---|---|---|---|---|---|
Title | Complex structure of drosophila Unr CSD789 and pAbp RRM3 | ||||||
Components |
| ||||||
Keywords | RNA BINDING PROTEIN / drosophila Unr / CSD / cold-shock domain / protein complex / PPI / drosophila pAbp / RRM / Unr / pAbp | ||||||
Function / homology | Function and homology information : / regulation of compound eye photoreceptor development / male meiosis cytokinesis / AUF1 (hnRNP D0) binds and destabilizes mRNA / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation / dosage compensation complex assembly / : ...: / regulation of compound eye photoreceptor development / male meiosis cytokinesis / AUF1 (hnRNP D0) binds and destabilizes mRNA / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation / dosage compensation complex assembly / : / spermatid nucleus differentiation / protein-RNA adaptor activity / RISC complex binding / male meiotic nuclear division / sex differentiation / oocyte development / poly(A) binding / dorsal/ventral pattern formation / poly(U) RNA binding / lncRNA binding / precatalytic spliceosome / oogenesis / negative regulation of translational initiation / catalytic step 2 spliceosome / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / positive regulation of translation / mRNA splicing, via spliceosome / cytoplasmic stress granule / spermatogenesis / chemical synaptic transmission / cell differentiation / ribonucleoprotein complex / mRNA binding / synapse / RNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Hollmann, N.M. / Jagtap, P.K.A. / Hennig, J. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein. Authors: Hollmann, N.M. / Jagtap, P.K.A. / Linse, J.B. / Ullmann, P. / Payr, M. / Murciano, B. / Simon, B. / Hub, J.S. / Hennig, J. #1: Journal: Nucleic Acids Res. / Year: 2023 Title: Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein. Authors: Hollmann, N.M. / Jagtap, P.K.A. / Linse, J.B. / Ullmann, P. / Payr, M. / Murciano, B. / Simon, B. / Hub, J.S. / Hennig, J. #2: Journal: Biorxiv / Year: 2022 Title: Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein during translation regulation Authors: Hollmann, N.M. / Jagtap, P.K.A. / Linse, J.B. / Ullmann, P. / Payr, M. / Murciano, B. / Simon, B. / Hub, J.S. / Hennig, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7zhr.cif.gz | 127.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7zhr.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 7zhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/7zhr ftp://data.pdbj.org/pub/pdb/validation_reports/zh/7zhr | HTTPS FTP |
---|
-Related structure data
Related structure data | 7zhhSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26166.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: Unr, BcDNA:LD13080, CR32028, Dmel\CG7015, dUNR, dUnr, dunr, MRE30, UNR, unr, CG7015, Dmel_CG7015 Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9VSK3 |
---|---|
#2: Protein | Mass: 9948.186 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: pAbp, CG5119 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21187 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.66 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M sodium formate 0.1 M bis-tris propane 20 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 31, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.99→42.36 Å / Num. obs: 7836 / % possible obs: 98.1 % / Redundancy: 6.262 % / Biso Wilson estimate: 44.16 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.26 / Rrim(I) all: 0.283 / Χ2: 0.853 / Net I/σ(I): 6.61 / Num. measured all: 49067 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZHH Resolution: 2.99→42.36 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.73 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.52 Å2 / Biso mean: 40.3117 Å2 / Biso min: 26.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.99→42.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|