- EMDB-3104: The human Nuclear Pore Complex with nucleoporin 358 knockdown -
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Basic information
Entry
Database: EMDB / ID: EMD-3104
Title
The human Nuclear Pore Complex with nucleoporin 358 knockdown
Map data
Reconstruction of human nuclear pore complex after Nup358 knockdown
Sample
Sample: Human nuclear pore complex with nucleoporin 358 knockdown
Protein or peptide: nuclear pore complex
Keywords
nuclear pore complex / Nup358 knockdown
Function / homology
Function and homology information
GATOR2 complex / nephron development / Seh1-associated complex / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-coated vesicle budding / nuclear pore inner ring / nuclear envelope organization / COPII-coated vesicle cargo loading / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...GATOR2 complex / nephron development / Seh1-associated complex / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-coated vesicle budding / nuclear pore inner ring / nuclear envelope organization / COPII-coated vesicle cargo loading / 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 / atrial cardiac muscle cell action potential / nuclear pore organization / somite development / COPII vesicle coat / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / paraxial mesoderm development / 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) / Amino acids regulate mTORC1 / miRNA processing / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / protein-containing complex localization / 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 / neural tube development / COPII-mediated vesicle transport / lamellipodium assembly / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / mitotic metaphase chromosome alignment / female gonad development / SUMOylation of ubiquitinylation proteins / macrophage chemotaxis / 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 / positive regulation of TOR signaling / mRNA transport / cellular response to nutrient levels / 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 / negative regulation of TORC1 signaling / Resolution of Sister Chromatid Cohesion / positive regulation of TORC1 signaling / MHC class II antigen presentation / serine-type peptidase activity / cellular response to amino acid starvation / neurogenesis / SUMOylation of chromatin organization proteins / nuclear periphery / molecular condensate scaffold activity / HCMV Late Events / chromosome segregation / promoter-specific chromatin binding / RHO GTPases Activate Formins / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / intracellular protein transport / ER to Golgi transport vesicle membrane / kinetochore / ISG15 antiviral mechanism / spindle / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / protein transport / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / defense response to Gram-positive bacterium Similarity search - Function
Journal: Nature / Year: 2015 Title: In situ structural analysis of the human nuclear pore complex. Authors: Alexander von Appen / Jan Kosinski / Lenore Sparks / Alessandro Ori / Amanda L DiGuilio / Benjamin Vollmer / Marie-Therese Mackmull / Niccolo Banterle / Luca Parca / Panagiotis Kastritis / ...Authors: Alexander von Appen / Jan Kosinski / Lenore Sparks / Alessandro Ori / Amanda L DiGuilio / Benjamin Vollmer / Marie-Therese Mackmull / Niccolo Banterle / Luca Parca / Panagiotis Kastritis / Katarzyna Buczak / Shyamal Mosalaganti / Wim Hagen / Amparo Andres-Pons / Edward A Lemke / Peer Bork / Wolfram Antonin / Joseph S Glavy / Khanh Huy Bui / Martin Beck / Abstract: Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and ...Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations.
History
Deposition
Jul 21, 2015
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Header (metadata) release
Aug 12, 2015
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Map release
Sep 30, 2015
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Update
Oct 7, 2015
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Current status
Oct 7, 2015
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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