Key Resource Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| E. coli DH5α | Invitrogen | Cat#: 18–265-017 |
| E. coli LOBSTR-BL21(DE3)-RIL | Andersen, Leksa, & Schwartz33; Vector Laboratories |
Cat#: NC1789768 |
| Chemicals, peptides, and recombinant proteins | ||
| DNAse I | Roche | Cat#: 10104159001 |
| Human Rhinovirus B14 3C (3CRV) protease (purified in-house) |
Gifted from Kevin D. Corbett, PhD | N/A |
| Synthetic Orf9b (44–70) peptide: IILRLGSPLSLNMARKTLNSLEDKAFQ |
VWR (custom synthesis) | N/A |
| 99.96% D2O | Cambridge Isotope Laboratories, Inc. | Cat#: DLM-1172–10 |
| Deposited data | ||
| HsTom70c raw diffraction data | This paper | SBGrid-DB: 1186 |
| HsTom70c model coordinates and maps | This paper | PDB: 9PKQ |
|
HsTom70c, HsTom70c + Orf9b (44–70), and HsTom70c + FL-Orf9b raw spectra and HDX-MS analysis files |
This paper | MassIVE: MSV000098542 |
| HsTom70c all atom molecular dynamics simulations system and parameter files | This paper | Zenodo: https://doi.org/10.5281/zenodo.14014935 |
| Oligonucleotides | ||
| HsTom70c_ctag_fwd: TTTGTTTAACTTTAAGAAGGAGATATACAT ATGAATAGTCTGGATCGTGCCCAA |
This paper | N/A |
| HsTom70c_ctag_rvs: GGGCCCCTGGAACAGAACTTCCAGGCCACC GATCAATGTTGGTGGTTTCAGTCCG |
This paper | N/A |
| HsTom70c_ntag_fwd: CGCAGACTCTGGAAGTTCTGTTCCAGGGGC CCATGAATAGTCTGGATCGTGCCCAAGCCG |
This paper | N/A |
| HsTom70c_ntag_rvs: CGGGCTTTGTTAGCAGCCGGATCCTCGAGT CACAATGTTGGTGGTTTCAGTCCGTATTTCT TGGCAACC |
This paper | N/A |
| pDUET1_Orf9b_fwd: CCTCTAGAAATAATTTTGTTTAACTTTAAGA AGGAGATATACCATGGACCCGAAGATCAGC GAGATGC |
This paper | N/A |
| pDUET1_Orf9b_rvs: GCAGGCGCGCCGAGCTCGAATTCGGATCCT TATTTCACGGTCACAACCACAAATTCATCC |
This paper | N/A |
| pDUET1_HsTom70c_fwd: CCCCATCTTAGTATATTAGTTAAGTATAAGA AGGAGATATACATATGAATAGTCTGGATCG TGCCCAAGCC |
This paper | N/A |
| pDUET1_HsTom70c_rvs: AAATTTCGCAGCAGCGGTTTCTTTACCAGA CTCGAGTTAGTGGGTGGTGGTGGTGGTGGG C |
This paper | N/A |
| Recombinant DNA | ||
| Codon-optimized gene synthesis of Homo Sapiens Tom70 (NCBI Reference Sequence: NP_055635.3) (BioBasic) |
This paper | N/A |
| Codon-optimized gene synthesis of SARS CoV-2 Orf9b (UniProtKB/SwissProt: P0DTD2.1) | This paper | N/A |
| pET24a | BioBasic | Cat#: 69749–3 |
| pET-DUET | BioBasic | Cat#: 71146 |
| Software and algorithms | ||
| RAPD version 2.0.1 | Northeastern | https://github.com/RAPD |
| Collaborative Access Team (NE-CAT), Advanced Photon Source, Argonne National Laboratory | ||
| XDS version June 30, 2024 | Kabsch34 | https://xds.mr.mpg.de |
| AIMLESS version 2.3.3 | Evans & Murshudov35 | https://github.com/ccp4 |
| TRUNCATE version 2.3.3 | Evans36 | https://github.com/ccp4 |
| PHASER version 2.5.0 | McCoy37 | https://github.com/ccp4 |
| Alphafold2 version 2.3.2 | Jumper et al.38 | https://github.com/google-deepmind/alphafold |
| Alphafold3 version 3.0.1 | Abramson et al.45 | https://github.com/google-deepmind/alphafold |
| COOT version 1.1.19 | Emsley, Lohkamp, Scott, & Cowtan39 | https://github.com/pemsley/coot |
| PHENIX version 1.19 | Afonine et al.40 | https://github.com/phenix-project |
| ProteinLynx Global Server version 3.0.3 | Waters Corporation | https://www.waters.com |
| DynamX version 3.0 | Waters Corporation | https://www.waters.com |
| DECA version 1.16 | Lumpkin and Komives44 | https://github.com/komiveslab/DECA |
| ChimeraX version 1.9 | Meng et al46 | https://github.com/RBVI/ChimeraX |
| NAMD version 2.14 | Phillips et al.47 | https://github.com/nbcrrolls/namd |
| CHARMM36m | Brooks, B. R. et al.48 | https://github.com/openmm |
| ProDy version 2.4.1 | Bakan, Meireles, & Bahar50; Zhang et al.51 | https://github.com/prody/ProDy |
| Python version 3.9 | Python Software Foundation | https://github.com/python |
| DNA package version 2.0 | Michaud‐Agrawal, Denning, Woolf, & Beckstein52 |
https://github.com/melomcr/dynetan |
| MDAnalysis version 2.9.0 | Gowers et al.53 | https://github.com/MDAnalysis |
| NumPy version 2.3.1 | NumPy Developers | https://github.com/numpy |
| Numba version 0.61.2 | Lam, Pitrou, & Seibert54 | https://github.com/numba |
| VMD version 1.9.4 | Humphrey, Dalke, & Schulten55 | https://github.com/nbcrrolls/vmd |
| NetworkView version 2.0 | Humphrey, Dalke, & Schulten55 | https://github.com/nbcrrolls/vmd |
| HDXer version 1.2 | Bradshaw, Marinelli, Faraldo-Gómez, & Forrest30 |
https://github.com/Lucy-ForrestLab/HDXer |
| MDTraj version 1.9.9 | McGiboon et al.56 | https://github.com/mdtraj |
| Custom code | This paper | https://doi.org/10.5281/zenodo.15882339 |
| Other | ||
| 5 mL HisTrap™ HP columns | Cytiva | Cat#: 17524801 |
| Strep-Tactin Superflow resin | IBA | product no longer available |
| 5 mL HiTrap Q HP anion exchange column | Cytiva | Cat#: 17115401 |
| HiLoad™ 16/600 Superdex™ 200 pg sizeexclusion column | Cytiva | Cat#: 28989335 |
| Immobilized Pepsin Agarose | Pierce | Cat#: 20343 |
| BEH C18 Vanguard precolumn | Waters Corporation | Cat#: 186003975 |