KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
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| Deposited data | ||
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| Chemical Cross-linking with Mass Spectrometry readout datasets | Akey et al.7 | Zenodo (https://zenodo.org/) Accession#: 5721514 |
| Files and input data, scripts and results for integrative modeling of the Pom34-Pom152 tetramer | This paper | Zenodo (https://zenodo.org/) DOI-10.5281 Accession#: 8226857 |
| Integrative models for Pom152 rings | This paper | PDBDEV_00000213 |
| Full nuclear double outer ring of the yeast NPC | This paper | EMD-41114 |
| Double ring of Nup84 Y-complexes from the yeast NPC | This paper | EMD-41285 |
| Lumenal ring of the isolated yeast NPC | This paper | EMD-41116 |
| Pom34-152 membrane attachment site in the yeast NPC and preliminary model | This paper | EMD-41117 PDB: 8T9L |
| Inner ring spoke of the yeast NPC | This paper | EMD-41300 |
| Cytoplasmic outer ring of the yeast NPC | This paper | EMD-41119 |
| Central transporter/plug in 3D map of the yeast NPC | This paper | EMD-41120 |
| Connectors from the double outer ring of the yeast NPC | This paper | EMD-41121 |
| Connectors from the cytoplasmic outer ring of the yeast NPC | This paper | EMD-41122 |
| Composite multi-scale 3D structure of the yeast NPC | This paper | EMD-41123 |
| Molecular model of the inner ring protomer (spoke) | This paper, Akey et al.7; Jumper et al.26 | PDB: 8TIE PDB: 7N85 Alphafold CSMs |
| Molecular model of the double Nup84 Y-complex protomer | This paper, Akey et al.7; Jumper et al.26 | PDB: 8TJ5 PDB: 7N84 Alphafold CSMs |
| Crystal structures of domains of the Nup84 Y-complex | Stuwe et al.91; Brohawn and Schwartz92; Brohawn et al.111 | PDB: 3EWE, 3JRO PDB: 4XMM |
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| Experimental models: Cell lines | ||
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| S. cerevisiae strain W303 MATa ade2–1 ura3–1 his3–11,15 trp1–1 leu2–3,112 can1–100 MLP1-PPX-ProteinA::HIS5 | Kim et al.6 | N/A |
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| Software and algorithms | ||
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| UCSF Chimera, version 1.13 | Pettersen et al.112 | https://www.cgl.ucsf.edu/chimera/ |
| RELION 3.0.7 | Nakane and Scheres113 | https://github.com/3dem/relion |
| MotionCor2 v1.2.3 | Zheng et al.114 | https://msg.ucsf.edu/software |
| GCTF v1.18 | Zhang115 | https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/ |
| Gautomatch v0.55 | N/A | https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/ |
| CryoSPARC 3.3.2 | Punjani et al.39 | https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure |
| Coot 0.8.9.2 | Casanal et al.116 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
| NAMD/MDFF Molecular dynamics flexible fitting | Trabuco et al.38 |
https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD
https://github.com/ryanmcgreevy/mdff |
| EMAN2 | Tang et al.117 | https://blake.bcm.edu/emanwiki/EMAN2/Install |
| IMP, version 2.8 | Russel et al.82 | https://integrativemodeling.org/ |
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| Other | ||
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| Quantifoil holy carbon grids | Quantifoil Micro Tools | R2/2 400 mesh copper |