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Yorodumi- PDB-6ihj: Crystal structure of Drosophila Nxf1 NTF2 domain in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ihj | |||||||||
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Title | Crystal structure of Drosophila Nxf1 NTF2 domain in complex with Nxt1/p15 | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / Nuclear Export Factor / Drosophila / Nxf2 / NTF2 domain / p15 / Nxt1 | |||||||||
Function / homology | Function and homology information Transport of Mature mRNA derived from an Intron-Containing Transcript / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of RNA export from nucleus / nuclear pore central transport channel / nuclear export / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / ribonucleoprotein complex binding ...Transport of Mature mRNA derived from an Intron-Containing Transcript / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of RNA export from nucleus / nuclear pore central transport channel / nuclear export / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / ribonucleoprotein complex binding / negative regulation of innate immune response / transcription repressor complex / protein transport / nuclear envelope / nuclear membrane / defense response to Gram-negative bacterium / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Huang, Y. / Yuan, X. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat.Cell Biol. / Year: 2019 Title: A Pandas complex adapted for piRNA-guided transcriptional silencing and heterochromatin formation. Authors: Zhao, K. / Cheng, S. / Miao, N. / Xu, P. / Lu, X. / Zhang, Y. / Wang, M. / Ouyang, X. / Yuan, X. / Liu, W. / Lu, X. / Zhou, P. / Gu, J. / Zhang, Y. / Qiu, D. / Jin, Z. / Su, C. / Peng, C. / ...Authors: Zhao, K. / Cheng, S. / Miao, N. / Xu, P. / Lu, X. / Zhang, Y. / Wang, M. / Ouyang, X. / Yuan, X. / Liu, W. / Lu, X. / Zhou, P. / Gu, J. / Zhang, Y. / Qiu, D. / Jin, Z. / Su, C. / Peng, C. / Wang, J.H. / Dong, M.Q. / Wan, Y. / Ma, J. / Cheng, H. / Huang, Y. / Yu, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ihj.cif.gz | 126.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ihj.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ihj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ihj_validation.pdf.gz | 463.9 KB | Display | wwPDB validaton report |
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Full document | 6ihj_full_validation.pdf.gz | 476.1 KB | Display | |
Data in XML | 6ihj_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 6ihj_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/6ihj ftp://data.pdbj.org/pub/pdb/validation_reports/ih/6ihj | HTTPS FTP |
-Related structure data
Related structure data | 6iewC 1jkgS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22147.006 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sbr, nxf1, CG1664 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9U1H9 #2: Protein | Mass: 15340.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Nxt1, CG12752 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9V3H8 #3: Water | ChemComp-HOH / | |
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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: 2.22 Å3/Da / Density % sol: 44.65 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 16%(w/v) PEG 8000, 40mM Potassium phosphate dibasic and 20%(v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97854 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 18389 / % possible obs: 99.8 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 1822 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JKG Resolution: 2.7→28.764 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 24.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→28.764 Å
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Refine LS restraints |
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LS refinement shell |
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