[English] 日本語
![](img/lk-miru.gif)
- PDB-7f90: Crystal structure of SARS auxiliary protein in complex with human... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7f90 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SARS auxiliary protein in complex with human nuclear protein | ||||||
![]() |
| ||||||
![]() | VIRAL PROTEIN / immune system / auxiliary protein | ||||||
Function / homology | ![]() transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket ...transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / 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 / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / positive regulation of mRNA splicing, via spliceosome / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / mitotic spindle pole / Vpr-mediated nuclear import of PICs / host cell Golgi membrane / 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 / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / molecular condensate scaffold activity / HCMV Late Events / ubiquitin binding / promoter-specific chromatin binding / RHO GTPases Activate Formins / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / cell division / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, X. / Cui, S. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 505.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 382.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7f60C ![]() 4owrS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 7533.843 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P59634 #2: Protein | Mass: 41017.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P78406 #3: Protein | Mass: 197780.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P52948, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 0.47 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 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: 2.39→47.874 Å / Num. obs: 60024 / % possible obs: 99.7 % / Redundancy: 3.49 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.62 |
Reflection shell | Resolution: 2.39→2.54 Å / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 9702 / % possible all: 99.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4OWR Resolution: 2.39→47.87 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.06 / 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: 166.7 Å2 / Biso mean: 44.0392 Å2 / Biso min: 20.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.39→47.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -23.9906 Å / Origin y: -2.745 Å / Origin z: 10.8391 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|