+Open data
-Basic information
Entry | Database: PDB / ID: 7per | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Model of the inner ring of the human nuclear pore complex | ||||||||||||
Components |
| ||||||||||||
Keywords | TRANSPORT PROTEIN / Nuclear Pore Complex / NPC | ||||||||||||
Function / homology | Function and homology information positive regulation of mitotic cytokinetic process / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / nuclear pore inner ring / protein localization to nuclear inner membrane / regulation of Ras protein signal transduction / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel ...positive regulation of mitotic cytokinetic process / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / nuclear pore inner ring / protein localization to nuclear inner membrane / regulation of Ras protein signal transduction / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / nuclear pore organization / nuclear pore complex assembly / atrial cardiac muscle cell action potential / Nuclear Pore Complex (NPC) Disassembly / positive regulation of protein localization to centrosome / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / miRNA processing / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / negative regulation of Ras protein signal transduction / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Flemming body / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / negative regulation of programmed cell death / mitotic centrosome separation / centrosome cycle / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / Viral Messenger RNA Synthesis / nuclear localization sequence binding / positive regulation of epidermal growth factor receptor signaling pathway / PTB domain binding / NLS-bearing protein import into nucleus / mitotic metaphase chromosome alignment / negative regulation of epidermal growth factor receptor signaling pathway / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / positive regulation of SMAD protein signal transduction / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / protein targeting / mRNA transport / regulation of signal transduction / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / regulation of mitotic spindle organization / Hsp70 protein binding / SH2 domain binding / nuclear periphery / SUMOylation of chromatin organization proteins / positive regulation of mitotic nuclear division / HCMV Late Events / ubiquitin binding / phospholipid binding / Transcriptional regulation by small RNAs / Hsp90 protein binding / mitotic spindle / ISG15 antiviral mechanism / spindle pole / HCMV Early Events / protein import into nucleus / cellular senescence / signaling receptor complex adaptor activity / protein transport / nuclear envelope / snRNP Assembly / positive regulation of canonical NF-kappaB signal transduction / nuclear membrane / cell surface receptor signaling pathway / ribonucleoprotein complex / negative regulation of cell population proliferation / centrosome / chromatin binding / protein-containing complex binding / negative regulation of apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / nucleoplasm / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 35 Å | ||||||||||||
Authors | Schuller, A.P. / Wojtynek, M. / Mankus, D. / Tatli, M. / Kronenberg-Tenga, R. / Regmi, S.G. / Dasso, M. / Weis, K. / Medalia, O. / Schwartz, T.U. | ||||||||||||
Funding support | Switzerland, 3items
| ||||||||||||
Citation | Journal: Nature / Year: 2021 Title: The cellular environment shapes the nuclear pore complex architecture. Authors: Anthony P Schuller / Matthias Wojtynek / David Mankus / Meltem Tatli / Rafael Kronenberg-Tenga / Saroj G Regmi / Phat V Dip / Abigail K R Lytton-Jean / Edward J Brignole / Mary Dasso / ...Authors: Anthony P Schuller / Matthias Wojtynek / David Mankus / Meltem Tatli / Rafael Kronenberg-Tenga / Saroj G Regmi / Phat V Dip / Abigail K R Lytton-Jean / Edward J Brignole / Mary Dasso / Karsten Weis / Ohad Medalia / Thomas U Schwartz / Abstract: Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE). These multi-megadalton structures are composed of about ...Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE). These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel. Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that-compared with previous human NPC models obtained from purified NEs-the inner ring in our model is substantially wider; the volume of the central channel is increased by 75% and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7per.cif.gz | 2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7per.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7per.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/7per ftp://data.pdbj.org/pub/pdb/validation_reports/pe/7per | HTTPS FTP |
---|
-Related structure data
Related structure data | 12814MC 7peqC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10700 (Title: Cryo electron tomography of FIB-milled lamella of human DLD-1 cells Data size: 8.0 Data #1: Un-aligned tilt series of FIB-lamella of human DLD-1 cells [tilt series]) EMPIAR-10701 (Title: Cryo electron tomography of FIB-milled lamella of human DLD-1 cells Data size: 8.0 Data #1: Un-aligned tilt series of FIB-milled lamella of Nup96-depleted human DLD-1 cells [tilt series]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 8
-Components
-Protein , 3 types, 12 molecules FXLRGYMSHZNT
#1: Protein | Mass: 55491.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z3B4 #2: Protein | Mass: 60941.480 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BVL2 #3: Protein | Mass: 53289.574 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P37198 |
---|
-Nuclear pore complex protein ... , 3 types, 12 molecules PVDJWKEQCIOU
#4: Protein | Mass: 228172.875 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92621 #5: Protein | Mass: 155357.281 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75694 #6: Protein | Mass: 93599.102 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N1F7 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: CELL / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Nup96::Neon-AID DLD-1 / Type: CELL / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: cryo-FIB milled sections of DLD1 cells |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE Details: Cells were grown on holey carbon, Au-mesh supports. Grids were rinsed briefly with PBS and manually blotted before plunging into liquid ethane. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 2.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software | Name: UCSF Chimera / Version: 1.14 / Category: model fitting |
---|---|
CTF correction | Type: PHASE FLIPPING ONLY |
Symmetry | Point symmetry: C8 (8 fold cyclic) |
3D reconstruction | Resolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1252 / Algorithm: BACK PROJECTION / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 54 / Num. of volumes extracted: 1552 |
Atomic model building | Protocol: RIGID BODY FIT |
Atomic model building | PDB-ID: 5IJN |