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- PDB-3mmy: Structural and functional analysis of the interaction between the... -
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Basic information
Entry | Database: PDB / ID: 3mmy | ||||||
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Title | Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1 | ||||||
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![]() | NUCLEAR PROTEIN / Nuclear Pore Complex / mRNA export | ||||||
Function / homology | ![]() transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / 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 / telomere tethering at nuclear periphery / nuclear pore outer ring / 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 / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / 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 / 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 / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / molecular condensate scaffold activity / ubiquitin binding / RHO GTPases Activate Formins / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / fibrillar center / HCMV Early Events / Separation of Sister Chromatids / protein import into nucleus / nuclear envelope / snRNP Assembly / microtubule binding / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / cell cycle / cell division / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hoelz, A. / Ren, Y. | ||||||
![]() | ![]() Title: Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1. Authors: Ren, Y. / Seo, H.S. / Blobel, G. / Hoelz, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 338 KB | Display | ![]() |
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PDB format | ![]() | 276.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 497.7 KB | Display | ![]() |
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Full document | ![]() | 510.6 KB | Display | |
Data in XML | ![]() | 65.3 KB | Display | |
Data in CIF | ![]() | 92.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 41017.078 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 6273.065 Da / Num. of mol.: 4 / Fragment: UNP residues 158-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-MES / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.75 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.14014 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. obs: 188056 |
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Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.65→19.82 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.494 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.543 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→19.82 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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