+Open data
-Basic information
Entry | Database: PDB / ID: 7byf | ||||||
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Title | The crystal structure of mouse ORF10-Rae1-Nup98 complex | ||||||
Components |
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Keywords | PROTEIN BINDING / complex | ||||||
Function / homology | Function and homology information Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response ...Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / RNA export from nucleus / structural constituent of nuclear pore / mitotic spindle pole / cellular response to organic cyclic compound / mRNA transport / mRNA export from nucleus / nuclear pore / regulation of mitotic spindle organization / ubiquitin binding / fibrillar center / protein transport / nuclear envelope / cell cycle / cell division / RNA binding / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Murid herpesvirus 4 (Murine herpesvirus 68) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Gao, P. / Feng, H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Molecular mechanism underlying selective inhibition of mRNA nuclear export by herpesvirus protein ORF10. Authors: Feng, H. / Tian, H. / Wang, Y. / Zhang, Q. / Lin, N. / Liu, S. / Yu, Y. / Deng, H. / Gao, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7byf.cif.gz | 325.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7byf.ent.gz | 267.8 KB | Display | PDB format |
PDBx/mmJSON format | 7byf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/7byf ftp://data.pdbj.org/pub/pdb/validation_reports/by/7byf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
-Protein , 3 types, 6 molecules ADBEFC
#1: Protein | Mass: 39054.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rae1, Mrnp41 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q8C570 #2: Protein | Mass: 6370.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nup98 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q3TPG3 #3: Protein | Mass: 46268.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68) Gene: GAMMAHV.ORF10, 10, ORF10 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: O41931 |
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-Non-polymers , 3 types, 449 molecules
#4: Chemical | ChemComp-HG / #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.64 Å3/Da / Density % sol: 53.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M di-Sodium tartrate, 20% PEG 3350, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.903 Å / Num. obs: 63997 / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.597 / Num. unique obs: 12416 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→48.903 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.03 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.16 Å2 / Biso mean: 41.4789 Å2 / Biso min: 16.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→48.903 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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