#empiar — Public Fediverse posts on home.social

Guillaume Gaullier @[email protected] · 2026-01-02 · 13:18 UTC

In 2021, I was involved in a study of the #chromatin remodeler ALC1, a protein involved in the early events of the DNA damage response. This led to a paper summarized in a previous thread: https://fediscience.org/@Guillawme/111534984107819771

We had deposited the raw #cryoEM data to #EMPIAR (dataset EMPIAR-10739), which is the primary reason this new preprint could come to exist at all.

This figure shows the structural knowledge available on ALC1 up to the point of the new structure we report in the preprint. An AlphaFold2 prediction, a structure of the auto-inhibited conformation, and a few structures of ALC1-nucleosome complexes. Notably, none of the structures of nucleosome complexes resolved the macro domain. This is a significant gap, because the macro domain is key in regulating ALC1: it is responsible for auto-inhibition and recruitment to PARylated nucleosomes, and these two things are exclusive, which is why recruitment also causes release of the auto-inhibition. So at this point we know what the protein looks like when auto-inhibited and when active, but how it transitions from the former to the latter is unclear.

2/5

#chromatin #cryoem #empiar

Guillaume Gaullier @[email protected] · 2026-01-02 · 13:18 UTC

In 2021, I was involved in a study of the #chromatin remodeler ALC1, a protein involved in the early events of the DNA damage response. This led to a paper summarized in a previous thread: https://fediscience.org/@Guillawme/111534984107819771

We had deposited the raw #cryoEM data to #EMPIAR (dataset EMPIAR-10739), which is the primary reason this new preprint could come to exist at all.

This figure shows the structural knowledge available on ALC1 up to the point of the new structure we report in the preprint. An AlphaFold2 prediction, a structure of the auto-inhibited conformation, and a few structures of ALC1-nucleosome complexes. Notably, none of the structures of nucleosome complexes resolved the macro domain. This is a significant gap, because the macro domain is key in regulating ALC1: it is responsible for auto-inhibition and recruitment to PARylated nucleosomes, and these two things are exclusive, which is why recruitment also causes release of the auto-inhibition. So at this point we know what the protein looks like when auto-inhibited and when active, but how it transitions from the former to the latter is unclear.

2/5

#chromatin #cryoem #empiar

Guillaume Gaullier @[email protected] · 2026-01-02 · 13:18 UTC

In 2021, I was involved in a study of the #chromatin remodeler ALC1, a protein involved in the early events of the DNA damage response. This led to a paper summarized in a previous thread: https://fediscience.org/@Guillawme/111534984107819771

We had deposited the raw #cryoEM data to #EMPIAR (dataset EMPIAR-10739), which is the primary reason this new preprint could come to exist at all.

This figure shows the structural knowledge available on ALC1 up to the point of the new structure we report in the preprint. An AlphaFold2 prediction, a structure of the auto-inhibited conformation, and a few structures of ALC1-nucleosome complexes. Notably, none of the structures of nucleosome complexes resolved the macro domain. This is a significant gap, because the macro domain is key in regulating ALC1: it is responsible for auto-inhibition and recruitment to PARylated nucleosomes, and these two things are exclusive, which is why recruitment also causes release of the auto-inhibition. So at this point we know what the protein looks like when auto-inhibited and when active, but how it transitions from the former to the latter is unclear.

2/5

#chromatin #cryoem #empiar

Guillaume Gaullier @[email protected] · 2026-01-02 · 13:18 UTC

In 2021, I was involved in a study of the #chromatin remodeler ALC1, a protein involved in the early events of the DNA damage response. This led to a paper summarized in a previous thread: https://fediscience.org/@Guillawme/111534984107819771

We had deposited the raw #cryoEM data to #EMPIAR (dataset EMPIAR-10739), which is the primary reason this new preprint could come to exist at all.

This figure shows the structural knowledge available on ALC1 up to the point of the new structure we report in the preprint. An AlphaFold2 prediction, a structure of the auto-inhibited conformation, and a few structures of ALC1-nucleosome complexes. Notably, none of the structures of nucleosome complexes resolved the macro domain. This is a significant gap, because the macro domain is key in regulating ALC1: it is responsible for auto-inhibition and recruitment to PARylated nucleosomes, and these two things are exclusive, which is why recruitment also causes release of the auto-inhibition. So at this point we know what the protein looks like when auto-inhibited and when active, but how it transitions from the former to the latter is unclear.

2/5

#empiar #cryoem #chromatin

Guillaume Gaullier @[email protected] · 2026-01-02 · 13:18 UTC

In 2021, I was involved in a study of the #chromatin remodeler ALC1, a protein involved in the early events of the DNA damage response. This led to a paper summarized in a previous thread: https://fediscience.org/@Guillawme/111534984107819771

We had deposited the raw #cryoEM data to #EMPIAR (dataset EMPIAR-10739), which is the primary reason this new preprint could come to exist at all.

This figure shows the structural knowledge available on ALC1 up to the point of the new structure we report in the preprint. An AlphaFold2 prediction, a structure of the auto-inhibited conformation, and a few structures of ALC1-nucleosome complexes. Notably, none of the structures of nucleosome complexes resolved the macro domain. This is a significant gap, because the macro domain is key in regulating ALC1: it is responsible for auto-inhibition and recruitment to PARylated nucleosomes, and these two things are exclusive, which is why recruitment also causes release of the auto-inhibition. So at this point we know what the protein looks like when auto-inhibited and when active, but how it transitions from the former to the latter is unclear.

2/5

#chromatin #cryoem #empiar

Guillaume Gaullier @[email protected] · 2025-06-01 · 13:27 UTC

When depositing #cryoEM data to #EMPIAR, I can never remember how to determine the "voxel type" requested in the metadata entry form.

Over the years, I have asked about it on CCPEM, bookmarked the permalink to the answer I received back then (probably in multiple browser profiles) and written similar notes at different places in my system.

Here is one more note about it, this time public: https://www.gaullier.org/en/blog/2025/06/01/voxel-type-empiar-deposition/

#cryoem #empiar

Guillaume Gaullier @[email protected] · 2025-06-01 · 13:27 UTC

When depositing #cryoEM data to #EMPIAR, I can never remember how to determine the "voxel type" requested in the metadata entry form.

Over the years, I have asked about it on CCPEM, bookmarked the permalink to the answer I received back then (probably in multiple browser profiles) and written similar notes at different places in my system.

Here is one more note about it, this time public: https://www.gaullier.org/en/blog/2025/06/01/voxel-type-empiar-deposition/

#cryoem #empiar

Guillaume Gaullier @[email protected] · 2025-06-01 · 13:27 UTC

When depositing #cryoEM data to #EMPIAR, I can never remember how to determine the "voxel type" requested in the metadata entry form.

Over the years, I have asked about it on CCPEM, bookmarked the permalink to the answer I received back then (probably in multiple browser profiles) and written similar notes at different places in my system.

Here is one more note about it, this time public: https://www.gaullier.org/en/blog/2025/06/01/voxel-type-empiar-deposition/

#cryoem #empiar

Guillaume Gaullier @[email protected] · 2025-06-01 · 13:27 UTC

When depositing #cryoEM data to #EMPIAR, I can never remember how to determine the "voxel type" requested in the metadata entry form.

Over the years, I have asked about it on CCPEM, bookmarked the permalink to the answer I received back then (probably in multiple browser profiles) and written similar notes at different places in my system.

Here is one more note about it, this time public: https://www.gaullier.org/en/blog/2025/06/01/voxel-type-empiar-deposition/

#empiar #cryoem

Guillaume Gaullier @[email protected] · 2025-06-01 · 13:27 UTC

When depositing #cryoEM data to #EMPIAR, I can never remember how to determine the "voxel type" requested in the metadata entry form.

Over the years, I have asked about it on CCPEM, bookmarked the permalink to the answer I received back then (probably in multiple browser profiles) and written similar notes at different places in my system.

Here is one more note about it, this time public: https://www.gaullier.org/en/blog/2025/06/01/voxel-type-empiar-deposition/

#cryoem #empiar