Structure of nucleosome-bound Sirtuin 6 deacetylase

2024-06-19 REL RCSB RCSB RCSB 2023-02-11 2023-04-26 2023-04-26 2024-06-19 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) F32GM137463 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM127034 United States National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB) T32BM107000 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM127034 United States Structure of nucleosome-bound Sirtuin 6 deacetylase Chio US Rechiche O Bryll AR Zhu J Feldman JL Peterson CL Tan S Armache J-P Nucleosome, Sirt6, aging, DNA damage, repair, deacetylation, diacylation, apo, chromatin, heterochromatin, GENE REGULATION, TRANSFERASE-DNA complex Chio US Rechiche O Bryll AR Zhu J Leith EM Feldman JL Peterson CL Tan S Armache JP Cryo-EM structure of the human Sirtuin 6-nucleosome complex. Sci Adv US 9 eadf7586 eadf7586 2023 37058572 doi:10.1126/sciadv.adf7586 2375-2548 8g57 FULLOVERLAP Sirt6 deacetylase bound to a nucleosome assembled with 172-bp 601 Widom DNA Sirt6 deacetylase bound to a nucleosome assembled with 172-bp 601 Widom DNA 0 1 2 3 4 5 6 7 Homo sapiens 300 NAD-dependent protein deacylase sirtuin-6 Homo sapiens 0.039708507999999997 1 Escherichia coli LEVO GSMSVNYAAGLSPYADKGKCGLPEIFDPPEELERKVWELARLVWQSSNVVFHTGAGISTASGIPDFRGPHGVWTMEERGL APKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMG LKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVI VNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRINGSIPAGPKQE PCAQHNGSEPASPKRERPTSPAPHRPPKRVKAKAVPSKLN Q8N6T7 2.3.1.- Histone H3 Xenopus laevis 0.015004578999999999 2 Escherichia coli LEVO TKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDL RFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER A0A310TTQ1 Histone H4 Xenopus laevis 0.009704396 2 Escherichia coli LEVO HRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTL YGFGG P62799 Histone H2A type 1-B/E Homo sapiens 0.014034354999999998 2 Escherichia coli LEVO SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIP RHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK P04908 Histone H2B type 1-J Homo sapiens 0.013804045 2 Escherichia coli LEVO PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRL AHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P06899 DNA strand 1 synthetic construct 0.046541637000000004 1 (DT)(DG)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG) (DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT) (DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG) (DG)(DA)(DT)(DT)(DC)(DT)(DC)(DG)(DA)(DT) DNA DNA strand 2 synthetic construct 0.046061347999999995 1 (DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG)(DC)(DA) DNA singleParticle particle 1.2 7.5 60.0 KCl Potassium chloride 12.5 HEPES 2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid 1.0 Dithiothreitol (2S,3S)-1,4-Bis(sulfanyl)butane-2,3-diol 1.5 Glycerol Propane-1,2,3-triol

12.5 mM HEPES pH 7.5, 60 mM KCl, 1.5% glycerol, 1 mM DTT

Quantifoil R2/2 COPPER 200 CARBON HOLEY 1.0 GLOW DISCHARGE 10 AIR 0.2

Glass slides were wrapped with fresh parafilm. Tweezers were washed with ethanol, dried, and then used to pick grids from a grid box. Grids were carefully examined and placed on the parafilm-covered slides. These slides were then placed into the PelCO easyGLOW glow discharger, and treated there.

ETHANE 100 277.15 FEI VITROBOT MARK IV

SIRT6 deacetylase bound to asymmetrical nucleosome with 172 DNA base-pairs

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.2 1.0 2.5 2.2 81000.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 64.0 75.0 OTHER 20 GATAN K3 (6k x 4k) 5760 4092 2 11872 3.3 50.0

Data was collected in Super Resolution mode, thus the image size is 11520 (width) x 8184 (height)

1 12821862

Particles were selected using Blob Picker

Using Ab initio option, five starting models were selected; the most relevant was assessed based on its similarity to known nucleosome structures

C1 BACK PROJECTION 3.07 FSC 0.143 CUT-OFF cryoSPARC 3.32 71603 PROJECTION MATCHING

Using cryoSPARC Homogeneous Refinement

PROJECTION MATCHING cryoSPARC 3.32

Using cryoSPARC NonUniform Refinement

1 cryoSPARC 3.32 emd_29735.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 324.0 324.0 324.0 90.0 90.0 90.0 X Y Z -6.5175138 15.483361 0.0013880634 0.39455706 1.08 1.08 1.08 2.0 AUTHOR ::::EMDATABANK.org::::EMD-29735:::: Main map from cisTEM, aligned to the common point of reference with the PDB and cryoSPARC map 3LZ0 PDB experimental model 3PKI PDB experimental model 7CL0 PDB experimental model FLEXIBLE FIT

UCSF Chimera was used for manual fitting of the models; It was then used for optimizing the fit by using option Fit in Map. Then Coot was used to analyze the fits, build and adjust the models into the existing densities, and refine parts of the model. Once the model has been built, validated and adjusted, we used phenix.real_space_refine to fix and improve the fit into the densities

REAL 79.0 emd_29735_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 324.0 324.0 324.0 90.0 90.0 90.0 X Y Z -7.787305 17.763480999999999 0.0011918228 0.448365 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-29735:::: Main map from cisTEM in original position emd_29735_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 324.0 324.0 324.0 90.0 90.0 90.0 X Y Z -14.812745 25.607551999999998 -0.0009876818 0.81064016 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-29735:::: Sharpened main map from cisTEM, aligned to the common point of reference with the PDB and cryoSPARC map emd_29735_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 324.0 324.0 324.0 90.0 90.0 90.0 X Y Z -0.82873595 3.4917057 0.0086566005 0.062446192 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-29735:::: Sharpened and aligned main map from cryoSPARC emd_29735_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 324.0 324.0 324.0 90.0 90.0 90.0 X Y Z -6.570015 13.257858000000001 -0.031289164 0.3757463 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-29735:::: Half map 1 from cisTEM emd_29735_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 324.0 324.0 324.0 90.0 90.0 90.0 X Y Z -6.790064 13.627945 -0.03175438 0.37610528 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-29735:::: Half map 2 from cisTEM