KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
| ||
| Rabbit IgG Protein A Purified | Innovative Research | Cat.# IR-RB-GF; RRID:AB_1501660 |
|
| ||
| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| PreScission protease | GE Healthcare Life Sciences | Cat.# 27–0843-01 |
| GelCode Blue Stain Reagent | Thermo Fisher Scientific | Cat.# 24592 |
| DSS(DiSuccinimidylSuberate)-H12 | Creative molecules | Cat.# 001S |
| Trypsin Sequencing Grade, modified | Thermo Fisher Scientific | Cat.# 25200072 |
| Iodoacetamide | Sigma | Cat.# I6125–10 g |
| Nupage LDS Sample buffer | Thermo Fisher Scientific | Cat.# NP0007 |
| Fibronectin | Sigma-Aldrich, Inc. | Cat.# 341631 |
| Dulbecco’s modified Eagle’s medium | Thermo Fisher Scientific | Cat# 11995073 |
| Antibiotic-Antimycotic | Thermo Fisher Scientific | Cat# 15240062 |
| Calf serum | Colorado Serum Company | Cat# 31332 |
| Fetal Bovine Serum | Thermo Fisher Scientific | Cat# A3840002 |
| Jasplakinolide | Thermo Fisher Scientific | Cat# J7473 |
| 50% Ethane Balance Propane | Airgas | Cat# X02PR50C33A0000 |
|
| ||
| Critical commercial assays | ||
|
| ||
| Dynabeads M270 Epoxy | Thermo Fisher Scientific | Cat # 143.02D |
|
| ||
| Deposited data | ||
|
| ||
| Yeast NPC: Full C8 NPC’s composite of double NR | This paper | EMD-44377 |
| Yeast NPC: Full C8 NPC’s composite of single NR | This paper | EMD-44372 |
| Yeast NPC: Full C8 NPC’s consensus | This paper | EMD-45255 |
| Yeast NPC: C1 asymmetric subunit’s composite of double NR | This paper | EMD-45197 |
| Yeast NPC: C1 asymmetric subunit’s composite of single NR | This paper | EMD-45198 |
| Yeast NPC: C1 asymmetric subunit’s consensus | This paper | EMD-45256 |
| Yeast NPC: Focused CR’s subunit | This paper | EMD-45199 |
| Yeast NPC: Focused IR’s subunit | This paper | EMD-45200 |
| Yeast NPC: Focused NR’s subunit of single NR | This paper | EMD-45201 |
| Yeast NPC: Focused NR’s subunit of double NR | This paper | EMD-45202 |
| Yeast NPC: Focused basket’s subunit | This paper | EMD-45203 |
| Yeast NPC: Focused membrane’s subunit (single NR) | This paper | EMD-45204 |
| Yeast NPC: Focused membrane’s subunit (double NR) | This paper | EMD-45205 |
| Mammalian NPC: Full C8 NPC’s composite | This paper | EMD-44379 |
| Mammalian NPC: Full C8 NPC’s consensus | This paper | EMD-45257 |
| Mammalian NPC: C1 asymmetric subunit’s composite | This paper | EMD-45216 |
| Mammalian NPC: C1 asymmetric subunit’s consensus | This paper | EMD-45258 |
| Mammalian NPC: Focused CR’s subunit | This paper | EMD-45219 |
| Mammalian NPC: Focused IR’s subunit | This paper | EMD-45220 |
| Mammalian NPC: Focused NR’s subunit | This paper | EMD-45222 |
| Mammalian NPC: Focused basket’s subunit | This paper | EMD-45223 |
| Mammalian NPC: Focused membrane’s subunit | This paper | EMD-45227 |
| Protozoan NPC: Full C8 NPC’s composite | This paper | EMD-44381 |
| Protozoan NPC: Full C8 NPC’s consensus | This paper | EMD-45259 |
| Protozoan NPC: C1 asymmetric subunit’s composite | This paper | EMD-45228 |
| Protozoan NPC: C1 asymmetric subunit’s consensus | This paper | EMD-45260 |
| Protozoan NPC: Focused CR’s subunit | This paper | EMD-45229 |
| Protozoan NPC: Focused IR’s subunit | This paper | EMD-45230 |
| Protozoan NPC: Focused NR’s subunit | This paper | EMD-45231 |
| Protozoan NPC: Focused membrane’s subunit | This paper | EMD-45232 |
| Protozoan NPC: Focused lumenal ring’s subunit | This paper | EMD-45233 |
| Single collection of all (yeast + mammalian) basket models | This paper | PDBDEV: PDBDEV_G_1000004 |
| Yeast NPC: C1 asymmetric subunit basket model | This paper | PDBDEV: PDBDEV_00000386 |
| Yeast NPC: Full C8 basket model | This paper | PDBDEV: PDBDEV_00000387 |
| Mammalian NPC: C1 asymmetric subunit basket model | This paper | PDBDEV: PDBDEV_00000384 |
| Mammalian NPC: Full C8 basket model | This paper | PDBDEV: PDBDEV_00000385 |
| Yeast NPC: Chemical Cross-linking with Mass Spectrometry readout datasets | This paper; Akey et al.5; Kim et al.6 | Zenodo: 10892434 |
| Protozoan NPC: Some Tilt-series of S. cerevisiae NPC | Allegretti et al.8 | EMPIAR-104661 |
| Yeast NPC modeling: yNup84 complex dimer | Akey et al.5 | PDB: 7N84 |
| Yeast NPC modeling: Fitted yNup84 complex dimer on input map | This paper | Zenodo: 12561838 |
| Yeast NPC modeling: Derived from yNup2 AlphaFold model | This paper; Jumper et al.90 | Zenodo: 12561838 |
| Yeast NPC modeling: Generic Mlps coiled-coil segments models | This paper; Soni and Madhusudhan91 | Zenodo: 12561838 |
| Yeast NPC modeling: Files with input data, scripts, and output resultsfor the integrative modeling of yBasket | This paper | Zenodo: 12561838 and https://github.com/integrativemodeling/NPC_Basket |
| Mammalian NPC modeling: mNup107 complex dimer model | This paper | Zenodo: 12561838 |
| Mammalian NPC modeling: Fitted mNup107 complex dimer on input map | This paper | Zenodo: 12561838 |
| Mammalian NPC modeling: Derived from mNup50 AlphaFold model | This paper; Jumper et al.90 | Zenodo: 12561838 |
| Mammalian NPC modeling: Tprs coiled-coil segments models | This paper; Soni and Madhusudhan91 | Zenodo: 12561838 |
| Mammalian NPC modeling: Files with input data, scripts, and output resultsfor the integrative modeling of mBasket | This paper | Zenodo: 12561838 and https://github.com/integrativemodeling/NPC_Basket |
|
| ||
| Experimental models: Cell lines | ||
|
| ||
| NIH3T3 Cell line | ATCC | CRL-1658 |
| Toxoplasma gondii RH strain | Readily available strain | Toxoplasma gondii RH strain |
| Human foreskin fibroblasts | Readily available strain | Human foreskin fibroblasts (HFF) |
|
| ||
| Experimental models: Organisms/strains | ||
|
| ||
| MATa ade2–1 ura3–1 his3–11,15 trp1–1 leu2–3,112 can1–100 | Kim et al.6 | W303 |
| MATa ade2–1 ura3–1 his3–11,15 trp1–1 leu2–3,112 can1–100 MLP1-PPX-ProteinA::HIS5 | Kim et al.6 | Mlp1-PPX-PrA |
| MATa his3Δ200 trp1Δ63 leu2Δ0 met15Δ0 ura3Δ0 | Brachmann et al.92 | BY4733 |
| MATa his3Δ200 trp1Δ63 leu2Δ0 met15Δ0 ura3Δ0 Dbp5-PPX-GFP::TRP1 | This paper | Dbp5-PPX-GFP |
| MATα ade2–1 ura3–1 his3–11,15 trp1–1 leu2–3,112 can1–100 Gle1-PPX-ProteinA::HIS5 | This paper | Gle1-PPX-PrA |
|
| ||
| Software and algorithms | ||
|
| ||
| SerialEM | Mastronarde93 | https://bio3d.colorado.edu/SerialEM/ |
| PACE-Tomo | Eisenstein et al.94 | https://github.com/eisfabian/PACEtomo |
| WARP | Tegunov and Cramer95 | http://www.warpem.com/warp/ |
| Relion 3.1 | Nakane et al.96 | https://github.com/3dem/relion |
| IMP, version 2.19 | Russel et al.50 | https://integrativemodeling.org/ |
| PCOILS | McDonnell et al.97; Gabler et al.98 | https://toolkit.tuebingen.mpg.de/tools/pcoils |
| chimera/Chimerax | Pettersen et al.99; Pettersen et al.100 | https://www.cgl.ucsf.edu/chimerax/ |
| COCONUT, version 1.0 | Soni and Madhusudhan91 | https://github.com/neeleshsoni21/coconut |
| IMOD Package | Kremer et al.101 | https://bio3d.colorado.edu/imod/ |
| AreTomo | Zheng et al.102 | https://msg.ucsf.edu/software |
| EMAN2 | Chen et al.103 | https://blake.bcm.edu/emanwiki/EMAN2 |
| AlphaFold2 | Jumper et al.90 | https://github.com/google-deepmind/alphafold |
| Dynamo | Castaño-Díez et al.104 | https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Main_Page |
| pLink and pLink2 | Yang et al.105; Chen et al.106 | http://pfind.ict.ac.cn/software/pLink/ |
|
| ||
| Other | ||
|
| ||
| Custom made plunger | Max-Planck-Institute for Biochemistry | N/A |
| Mass Spectrometer | Thermo Fisher Scientific | Orbitrap Fusion Lumos Tribrid |
| Liquid Chromatograph | Thermo Fisher Scientific | Easy-nLC 1200 |
| Easy-Spray column | Thermo Fisher Scientific | ES800 |
| NuPage 4–12% Bis-Tris Gel 1.0mm × 10 well | Thermo Fisher Scientific | Cat.# NP0321Box |
| Quantifoil R 2/1 200 Mesh, Cu | Electron Microscopy Sciences | Q2100CR1 |
| Quantifoil R 1/4, 200 Mesh, Au | Electron Microscopy Sciences | Q210AR-14 |
| Titan Krios G3 (300 kV Cryo-transmission electron microscope) | Thermo Fisher Scientific | Titan Krios G3. |
| Energy filter and direct electron detector | Gatan | K2 detector and Quantum 968 LS post-column energy filter or a K3 Summit detector with 1067HD BioContinuum post-column |
| Aquilos cryo-FIB Dual-Beam | Thermo Fisher Scientific | Aquilos cryo-FIB |
| Whatman filter paper #1 | Whatman | Cat# 1001 090 |