+Open data
-Basic information
Entry | Database: PDB / ID: 7q65 | |||||||||
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Title | Cryo-em structure of the Nup98 fibril polymorph 2 | |||||||||
Components | Nuclear pore complex protein Nup98 | |||||||||
Keywords | PROTEIN FIBRIL / Nuclear pore complex protein Nup98 functional amyloid fibril PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / telomere tethering at nuclear periphery / 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 ...nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / telomere tethering at nuclear periphery / 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 / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of mRNA splicing, via spliceosome / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / promoter-specific chromatin binding / RHO GTPases Activate Formins / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.32 Å | |||||||||
Authors | Ibanez de Opakua, A. / Geraets, J.A. / Frieg, B. / Dienemann, C. / Savastano, A. / Rankovic, M. / Cima-Omori, M.-S. / Schroeder, G.F. / Zweckstetter, M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat Chem / Year: 2022 Title: Molecular interactions of FG nucleoporin repeats at high resolution. Authors: Alain Ibáñez de Opakua / James A Geraets / Benedikt Frieg / Christian Dienemann / Adriana Savastano / Marija Rankovic / Maria-Sol Cima-Omori / Gunnar F Schröder / Markus Zweckstetter / Abstract: Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear ...Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear pore complex and mislocalize in neurodegenerative diseases. Insights into the molecular interactions of FG-repeat nucleoporins have, however, remained largely elusive. Using a combination of NMR spectroscopy and cryoelectron microscopy, we have identified uniformly spaced segments of transient β-structure and a stable preformed α-helix recognized by messenger RNA export factors in the FG-repeat domain of human nucleoporin 98 (Nup98). In addition, we have determined at high resolution the molecular organization of reversible FG-FG interactions in amyloid fibrils formed by a highly aggregation-prone segment in Nup98. We have further demonstrated that amyloid-like aggregates of the FG-repeat domain of Nup98 have low stability and are reversible. Our results provide critical insights into the molecular interactions underlying the self-association and phase separation of FG-repeat nucleoporins in physiological and pathological cell activities. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q65.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q65.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 7q65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q65_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7q65_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7q65_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 7q65_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/7q65 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/7q65 | HTTPS FTP |
-Related structure data
Related structure data | 13852MC 7q64C 7q66C 7q67C M: map data used to model this data 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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1 |
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-Components
#1: Protein/peptide | Mass: 4005.211 Da / Num. of mol.: 22 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUP98, ADAR2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52948 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: The nuclear pore complex protein Nup98 fibril polymorph 2 Type: COMPLEX Details: The Nup98 polymorph 2 fibril is formed by two protofilaments, consisting of Nup98 monomers. Entity ID: all / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||
Buffer solution | pH: 7 | ||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 2.557 sec. / Electron dose: 41 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4180 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -2.33 ° / Axial rise/subunit: 4.68 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 356482 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11085 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.48 Å2 | ||||||||||||||||||||||||
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