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Open data
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Basic information
Entry | Database: PDB / ID: 5a9q | ||||||
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Title | Human nuclear pore complex | ||||||
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![]() | TRANSPORT PROTEIN | ||||||
Function / homology | ![]() GATOR2 complex / nephron development / Seh1-associated complex / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-coated vesicle budding / nuclear envelope organization / nuclear pore inner ring / 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 envelope organization / nuclear pore inner ring / 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 / SUMOylation of chromatin organization proteins / 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 / neurogenesis / 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 / HCMV Late Events / nuclear periphery / molecular condensate scaffold activity / chromosome segregation / promoter-specific chromatin binding / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / HCMV Early Events / ER to Golgi transport vesicle membrane / kinetochore / ISG15 antiviral mechanism / spindle / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / protein transport / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / defense response to Gram-positive bacterium Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 23 Å | ||||||
![]() | von Appen, A. / Kosinski, J. / Sparks, L. / Ori, A. / DiGuilio, A. / Vollmer, B. / Mackmull, M. / Banterle, N. / Parca, L. / Kastritis, P. ...von Appen, A. / Kosinski, J. / Sparks, L. / Ori, A. / DiGuilio, A. / Vollmer, B. / Mackmull, M. / Banterle, N. / Parca, L. / Kastritis, P. / Buczak, K. / Mosalaganti, S. / Hagen, W. / Andres-Pons, A. / Lemke, E.A. / Bork, P. / Antonin, W. / Glavy, J.S. / Bui, K.H. / Beck, M. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 2.7 MB | Display | ![]() |
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PDB format | ![]() | 1.7 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 941.8 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 349.2 KB | Display | |
Data in CIF | ![]() | 612.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3103MC ![]() 3104C ![]() 3105C ![]() 3106C ![]() 3107C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 16 molecules 09IR2KTb6FOX7GPY
#1: Protein | Mass: 42195.652 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 36748.512 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 35578.438 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | Mass: 39700.566 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-NUCLEAR PORE COMPLEX PROTEIN ... , 6 types, 22 molecules 1JSa3CLU4DMV5ENW8HQZAB
#2: Protein | Mass: 162280.203 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 129108.461 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 106504.969 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 106039.656 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 75105.266 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 155357.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: electron tomography |
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Sample preparation
Component | Name: HUMAN NUCLEAR PORE COMPLEX / Type: ORGANELLE OR CELLULAR COMPONENT |
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Buffer solution | Name: 20MM TRIS, 0.2-0.4% TREHALOSE / pH: 7.5 / Details: 20MM TRIS, 0.2-0.4% TREHALOSE |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, INSTRUMENT- HOMEMADE PLUNGER, |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Oct 17, 2014 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 42000 X / Calibrated magnification: 42000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm |
Specimen holder | Tilt angle max: 60 ° / Tilt angle min: -45 ° |
Image recording | Electron dose: 110 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
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Processing
EM software |
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CTF correction | Details: PHASE FLIPPING OF TILT SERIES | ||||||||||||
Symmetry | Point symmetry: C8 (8 fold cyclic) | ||||||||||||
3D reconstruction | Method: SUBTOMOGRAM AVERAGING / Resolution: 23 Å Details: THIS PDB STRUCTURE INCLUDES UNAMBIGUOUS FITS ONLY. THE STRUCTURE WITH LESS CONFIDENT FITS CAN BE OBTAINED FROM AUTHORS. PROTEIN-PROTEIN INTERFACES SHALL NOT BE INTERPRETED AT RESIDUE-LEVEL ...Details: THIS PDB STRUCTURE INCLUDES UNAMBIGUOUS FITS ONLY. THE STRUCTURE WITH LESS CONFIDENT FITS CAN BE OBTAINED FROM AUTHORS. PROTEIN-PROTEIN INTERFACES SHALL NOT BE INTERPRETED AT RESIDUE-LEVEL RESOLUTION. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3103. (DEPOSITION ID: 13616). Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 23 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 23 Å
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