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Yorodumi- PDB-7f60: Crystal structure of auxiliary protein in complex with human nucl... -
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-Basic information
Entry | Database: PDB / ID: 7f60 | ||||||
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Title | Crystal structure of auxiliary protein in complex with human nuclear protein | ||||||
Components |
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Keywords | VIRAL PROTEIN / immune system / auxiliary protein | ||||||
Function / homology | Function and homology information transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket ...transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / positive regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / mitotic spindle pole / host cell Golgi membrane / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / cellular response to organic cyclic compound / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / ubiquitin binding / RHO GTPases Activate Formins / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / fibrillar center / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / microtubule binding / nuclear membrane / transcription coactivator activity / host cell endoplasmic reticulum membrane / nuclear body / cell cycle / ribonucleoprotein complex / cell division / mRNA binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Gao, X. / Cui, S. | ||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport Authors: Gao, X. / Tian, H. / Zhu, K. / Li, Q. / Hao, W. / Wang, L. / Qin, B. / Deng, H. / Cui, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f60.cif.gz | 373.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f60.ent.gz | 266.9 KB | Display | PDB format |
PDBx/mmJSON format | 7f60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/7f60 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/7f60 | HTTPS FTP |
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-Related structure data
Related structure data | 7f90C 4owrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41017.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAE1, MRNP41 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P78406 #2: Protein | Mass: 197780.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUP98, ADAR2 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P52948, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #3: Protein | Mass: 7278.505 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P0DTC6 |
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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: 0.41 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1m Bis-tris ph5.5,45%PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→48.27 Å / Num. obs: 36291 / % possible obs: 99 % / Redundancy: 3.52 % / Rmerge(I) obs: 0.37 / Net I/σ(I): 3.47 |
Reflection shell | Resolution: 2.85→3.02 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5780 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OWR Resolution: 2.85→48.24 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.8 / Stereochemistry target values: ML
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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: 120.92 Å2 / Biso mean: 40.8356 Å2 / Biso min: 22.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→48.24 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: -24.3858 Å / Origin y: -2.8648 Å / Origin z: 10.1328 Å
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Refinement TLS group |
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