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. Author manuscript; available in PMC: 2024 Sep 23.
Published in final edited form as: Mol Cell. 2023 Dec 13;83(24):4586–4599.e5. doi: 10.1016/j.molcel.2023.11.007

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Bacterial and Virus Strains
E. coli DH5α Chemically Competent Cell NEB C2987P
E. coli BL21 (DE3) Chemically Competent Cell NEB C2527H
Escherichia phage T5 DSMZ DSM 16353
Deposited Data
SIR2_HerA complex 1 (12:6) map This study EMDB: EMD-40762
SIR2_HerA complex 1 (12:6) model This study PDB: 8SU9
SIR2_HerA complex 2 (12:5) map This study EMDB: EMD-40763
SIR2_HerA complex 2 (12:5) model This study PDB: 8SUB
SIR2_HerA complex 3 (12:4) map This study EMDB: EMD-40778
SIR2_HerA complex 3 (12:4) model This study PDB: 8SUW
SIR2 Dodecamer map This study EMDB: EMD-40860
SIR2 Dodecamer model This study PDB: 8SXX
SIR2_HerA complex 1 (12:6) bound with ATPγS map This study EMDB: EMD-42061
SIR2_HerA complex 1 (12:6) bound with ATPγS model This study PDB: 8UAE
SIR2_HerA complex 1 (12:6) bound with NAD+ map This study EMDB: EMD-42062
SIR2_HerA complex 1 (12:6) bound with NAD+ model This study PDB: 8UAF
Chemicals, Peptides, and Recombinant Proteins
ε-NAD+ sodium salt Sigma-Aldrich N2630-5MG
beta-NAD+ sodium salt Sigma-Aldrich N0632-1G
NTP (ATP, UTP, CTP, GTP) NEB N0450S
dNTP (dATP, dTTP, dCTP, dGTP) NEB N0447S
ATPγS Roche 11162306001
HerA recombinant protein This paper N/A
SIR2 recombinant protein This paper N/A
SIR2-HerA complex recombinant protein This paper N/A
Critical commercial assays
ATPase/GTPase Activity Assay Kit Sigma-Aldrich MAK113
Oligonucleotides
5’Cy3-ssRNA1 /cy3/rArCrArCrArCrUrArUrArCrArArCrCrUrArCrUrArCrCrUrCrArArCrC This paper Figure 6F, 6H, 6I
Complementary_ssRNA2 rUrGrArGrGrUrArGrUrArGrGrUrUrGrUrArUrArGrU This paper Figure 6F
5’Cy3-ssDNA4 /cy3/TACTTTACATAAATTGTAAAATTTATTTAATTAACAAC This paper Figure 6A, 6B, 6D, 6E, 6G, 6I, 6J, S7A, S7C, S7D, S7E
Complementary_blunt_ssDNA5 GTTGTTAATTAAATAAATTTTACAATTTATGTAAAGTA This paper Figure 6A, 6B, 6E, S7A, S7C
Complementary_5’_Overhang_ssDNA6 TTTTTTGAACTTTTTTTGTCAAGTTGTTAATTAAATAAATTTTACAATTTATGTAAAGTA This paper Figure 6A, 6B, 6E, S7A, S7E
Complementary_3’ Overhang_ssDNA7 GTTGTTAATTAAATAAATTTTACAATTTATGTAAAGTAAATTGAGATCTCTTTTTTTGTCA This paper Figure 6A, 6B, 6E, S7A
Complementary_dual_forked_ssDNA8 TTTTTTTTTTTTTTTTTTTTTTAATTTTACAATTTATGTAAAGTA This paper Figure 6A, 6B, S7A, S7D
Complementary_dual_forked_3’overhand_ssDNA9 TTTTTTTTTTTTTTTTTTTTTTAATTTTACAATTTATGTAAAGTATTTTTTTTTTTTTTT This paper Figure S7D
Recombinant DNA
pET28a-His×6-HerA This paper N/A
pDB-His×6-MBP-TEV-SIR2 This paper N/A
pDB-His×6-MBP-TEV-SIR2H227A This paper N/A
pDB-His×6-MBP-TEV-SIR2D311A This paper N/A
pDB-His×6-MBP-TEV-SIR2H313A This paper N/A
pET28a-SIR2-HerA-His×6 This paper N/A
pET28a-SIR2-HerA H227A-His×6 This paper N/A
pET28a-SIR2-HerA D311A-His×6 This paper N/A
pET28a-SIR2-HerA H313A-His×6 This paper N/A
Software and Algorithms
cryoSPARC (v4.1.1) Punjani et al. 24 https://cryosparc.com
AlphaFold v2 John Jumper et al.25 https://github.com/deepmind/alphafold
UCSF Chimera Pettersen et al. 26 https://www.cgl.ucsf.edu/chimera/
Coot Emsley and Cowtan 27 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
PHENIX Adams et al.28 https://phenix-online.org
Molprobity Williams et al. 29 http://molprobity.manchester.ac.uk
ChimeraX v1.5 Pettersen et al. 30 https://www.rbvi.ucsf.edu/chimerax/
PyMOL 2.3.0 Schrödinger 31 https://pymol.org/2/
Analyst_1.7.2 AB Sciex https://sciex.com/support/software-support/software-downloads
SCIEX OS 2.0 AB Sciex https://sciex.com/products/software/sciex-os-software
Other
Superose™ 6 Increase 10/300 GL Cytiva 29-0915-96
HiTrap Heparin HP affinity column Cytiva GE17-0407-01
Black 96-well plates Thermo Fisher Scientific 237105
HSS T3 column Waters Cat#186003539
Quantifoil R 1.2/1.3, 400 mesh, Gold Electron Microscopy Sciences Cat#Q4100AR1.3