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Reply to: Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase

The Original Article was published on 22 July 2021

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Fig. 1: Cryo-EM density of acetyl-CoA and OAA in the ACLY active site.
Fig. 2: Cryo-EM density of a reaction intermediate in the ACLY active site.

Data availability

A revised cryo-EM map of the ACLY ASH domain of the ACLY–OAA–acetyl-CoA complex and the associated coordinates were generated from micrographs corresponding to ACLY–OAA–acetyl-CoA–D2 (PDB 6UI9) and EMD-20783, reported in Wei et al.2, and were deposited with local refinement under accession codes PDB 7LJ9 and EMD-23389 and without local refinement under accession codes PDB 7LLA and EMD-23413 to the wwPDB and EMDB, respectively. A revised cryo-EM map of the ACLY ASH domain of the ACLY-E599Q–ATP–citrate–CoA complex and the associated coordinates were generated from micrographs corresponding to ACLY-E599Q–ATP–citrate–CoA–D2 (PDB 6UUW) and EMD-20902, reported in Wei et al.2 and deposited with accession codes PDB 7LIW and EMD-23387 to the wwPDB and EMDB, respectively.

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Acknowledgements

Molecular graphics and structural analyses were performed with UCSF Chimera, developed by the Resource for Biocomputing. This work was supported by National Institutes of Health grant nos. R35 GM118090 and P01 AG031862 to R.M.

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Authors

Contributions

X.W. and R.M. conceptualized the study. Methodology was designed by X.W. and R.M. The investigation was carried out by X.W. Formal analysis was done by X.W. The original draft was written by R.M. Visualization was done by X.W. X.W. and R.M. wrote the paper. Funding and resources were acquired by R.M., who also supervised the study.

Corresponding author

Correspondence to Ronen Marmorstein.

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The authors declare no competing interests.

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Peer review information Anke Sparmann was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 Revised Cryo-EM density for ACLY with products.

Comparison of cryo-EM density of acetyl-CoA in ACLY–OAA–acetyl-CoA (PDB-7LJ9/EMD-23389) and electron density of ACLY-bound CoA and citrate in PDB 6QFB reported in Verschueren et al.3. The figure was made in Pymol with a contour level of 2 σ applied.

Extended Data Fig. 2 Workflow of data analysis.

Particle symmetry expansion, particle subtraction and autorefinement on the CSH-tetramer + ASH monomer. (a) Generation of ACLY-E599Q–ATP–citrate–CoA (PDB 7LJW/EMD-23387) is shown as an example. (b) FSC curves illustration the improvement of ASH domain following local refinement in cryospac. The local resolution of the ASH domain was improved from 3.93.0 Å to 3.3–3.0 Å. Although the local resolution map for ACLY–OAA–acetyl-CoA (PDB 7LJ9/EMD-23389) showed a more modest improvement (4.0–2.8 Å to 3.9–2.7 Å), the map showed clearer density for the acetyl-CoA and OAA ligands (Fig. 1).

Supplementary information

Supplementary Information

Supplementary Table 1 and Note.

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Wei, X., Marmorstein, R. Reply to: Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase. Nat Struct Mol Biol 28, 639–641 (2021). https://doi.org/10.1038/s41594-021-00625-2

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