KEY RESOURCES TABLE
REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Bacterial and virus strains | ||
Staphylococcus aureus RN4220 | N/A | N/A |
Escherichia coli Rosetta 2 (DE3) - Novagen | Millipore Sigma | 71400–3 |
PhiNM1gamma6-GFP | Baca et al.12 | N/A |
Phi80alpha-vir | Banh et al.29 | N/A |
PhiNM4gamma4 | Banh et al.29 | N/A |
PhiJ1 | Banh et al.29 | N/A |
PhiJ2 | Banh et al.29 | N/A |
PhiJ4 | Banh et al.29 | N/A |
Chemicals, peptides, and recombinant proteins | ||
ATP | NEB | P0756S |
dATP | NEB | N0440S |
ITP | Sigma Aldrich | I0879–50MG |
dITP | Thermo Fisher | R1191 |
Adenosine | Sigma Aldrich | A9251–1G |
Inosine | Sigma Aldrich | I4125–1G |
AMP | Sigma Aldrich | 01930–5G |
UTP | NEB | N0450L |
CTP | NEB | N0450L |
cA2 | Biolog | C 088 |
cA3 | Biolog | C 362 |
cA4 | Biolog | C 335 |
cA6 | Biolog | C 332 |
Deposited data | ||
Cad1 apo | This study | EMDB: 45241 and PDB: 9C67 |
Cad1 ATP asymmetric | This study | EMDB: 45245 and PDB: 9C6F |
Cad1 ATP symmetric | This study | EMDB: 45244 and PDB: 9C6C |
Cad1 cA4 ATP | This study | EMDB: 45277 and PDB: 9C77 |
Cad1 cA6 ATP | This study | EMDB: 45466 and PDB: 9CDB |
Cad1 RNA-seq raw reads | This study | Deposited in NCBI Sequence Read Archive with BioProject: PRJNA1152273 |
apo-Cad1-CARF | This study | PDB: 9C6A |
Cad1-CARF + cA6 | This study | PDB: 9C68 |
Cad1-CARF-cA4 | This study | PDB: 9C69 |
Oligonucleotides | ||
See Data S1 | N/A | N/A |
Recombinant DNA | ||
See Data S1 | N/A | N/A |
Software and algorithms | ||
CCP4i2 Suite | Winn et al.42 | https://www.ccp4.ac.uk |
Foldseek | van Kempen et al.18 | https://search.foldseek.com/search |
CRISPRCasTyper | Russel et al.43 | https://crisprcastyper.crispr.dk/#/submit |
UCSF Chimera | Pettersen et al.44 | https://www.cgl.ucsf.edu/chimera/ |
cryoSPARC | Punjani et al.45 | https://cryosparc.com |
HISAT2 | Kim et al.46 | http://daehwankimlab.github.io/hisat2/ |
Coot | Emsley and Cowtan47 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
REDItools V2 | Flati et al.48 | https://github.com/BioinfoUNIBA/REDItools |
Alphafold 3 | Abramson et al.49 | https://alphafoldserver.com |
Python 3.9 | Python | https://www.python.org/downloads/release/python-390/ |
Prism 10.1.1 | GraphPad | https://www.graphpad.com |
Prism 9.4.0 | GraphPad | https://www.graphpad.com |