Cryo-EM structure of ADP-bound, filamentous beta-actin harboring the N111S mutation

2023-11-22 REL PDBe PDBe PDBe 2023-03-22 2023-08-09 2023-08-09 2023-11-22 Max Planck Society Germany Alexander von Humboldt Foundation Germany European Research Council (ERC) 856118 European Union Cryo-EM structure of ADP-bound, filamentous beta-actin harboring the N111S mutation Oosterheert W Blanc FEC Roy A Belyy A Hofnagel O Hummer G Bieling P Raunser S Actin filament, cytoskeletal protein, ATPase, STRUCTURAL PROTEIN Oosterheert W Blanc FEC Roy A Belyy A Sanders MB Hofnagel O Hummer G Bieling P Raunser S Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Nat.Struct.Mol.Biol. US 30 1774 1785 2023 37749275 doi:10.1038/s41594-023-01101-9 1545-9985 EMD-16887 other EM volume EMD-16888 other EM volume 8oid FULLOVERLAP Actin filament harboring the N111S mutation. Actin filament harboring the N111S mutation. 0 1

Beta-actin was expressed as fusion protein, with thymosin beta4 and a deca-His-tag fused to the actin C-terminus. During the purification, thymosin beta-4 and the deca-His-tag were removed. Actin was purified as monomer from insect cells. It was then polymerized into a filament in vitro.

Homo sapiens Actin, cytoplasmic 1, N-terminally processed Homo sapiens 0.04173659 5 Trichoplusia ni LEVO MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIE(HIC)GIV TNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLSPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSG DGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSL EKSYELPDGQVITIGNERFRCPEALFQPSFLGMESAGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKE ITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF P60709 ADENOSINE-5'-DIPHOSPHATE 0.000427201 5 ADP MAGNESIUM ION 2.4305e-05 5 MG water 1.8015e-05 616 HOH singleParticle filament 2.5 7.1 10.0 HEPES 100.0 KCl potassium chloride 2.0 MgCl2 magnesium chloride 1.0 EGTA 0.02 Tween20

1x KMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA) supplemented with 0.02% Tween20 (v/v)

Quantifoil R2/1 COPPER 300 CARBON HOLEY GLOW DISCHARGE 90 ETHANE-PROPANE 100 286 FEI VITROBOT MARK IV

Actin filaments were reconstituted by adding salt to monomeric actin.

FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 2.0 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 15

Titan Krios G3 microscope was aligned using Sherpa (FEI). Data collected in superresolution mode.

GATAN K3 BIOQUANTUM (6k x 4k) 1 9516 70.0 1

K3 operated in super-resolution mode.

2001281

crYOLO in filament mode.

EMD-15109 C1 2.3 FSC 0.143 CUT-OFF RELION 3.1.0

The final refinement was performed from local searches in RELION.

1756928 MAXIMUM LIKELIHOOD SPHIRE 1.4

First 3D refinement was performed in helical SPHIRE with meridien alpha, which imposes helical restraints to limit particle shifts to the helical rise to prevent particle duplication, but does not apply helical symmetry

MAXIMUM LIKELIHOOD RELION 3.1.0 8 RELION 3.1.0

3D classification without image alignment was performed in RELION to remove particles that did not contain high-resolution information.

emd_16889.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 266.88 266.88 266.88 90.0 90.0 90.0 X Y Z -0.16569497 0.39300117 0.00015015746 0.0064122896 0.695 0.695 0.695 0.0375 AUTHOR ::::EMDATABANK.org::::EMD-16889:::: Sharpened, local-resolution filtered cryo-EM density map of filamentous beta-actin harboring the N111S mutation. 8a2t PDB experimental model FLEXIBLE FIT

chain C of pdb 8A2T (including all water molecules) was fit in the central actin subunit of the density map. After substitution of all alpha-actin specific amino-acids to the corresponding beta-actin residues, introducing the N111S mutation, and further manual model building in Coot, the resulting model was fitted in four more actin subunits (chains A, B, D, E) in the density map. The filament was modeled as a pentamer to capture the full interaction interface of the central subunit with its four neighboring subunits. All water molecules were first manually built, inspected and adjusted in the central subunit, and were then copied to the other chains with non-crystallographic symmetry (NCS). Because the local resolution was worse at the periphery of the reconstruction, we removed water molecules that displayed poor corresponding cryo-EM density in the non-central actin chains. The model was refined in Phenix real-space refine with NCS restraints but without Ramachandran and rotamer restraints.

REAL emd_16889_msk_1.map emd_16889_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 266.88 266.88 266.88 90.0 90.0 90.0 X Y Z -0.011609006 0.059952408 -0.00002128602 0.0017785551 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-16889:::: 3D refined, unsharpened cryo-EM density map of filamentous beta-actin harboring the N111S mutation. emd_16889_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 266.88 266.88 266.88 90.0 90.0 90.0 X Y Z -0.016197138 0.0636588 -0.00002293685 0.0019740635 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-16889:::: Half map 1 of the refinement of filamentous beta-actin harboring the N111S mutation. emd_16889_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 266.88 266.88 266.88 90.0 90.0 90.0 X Y Z -0.015184741 0.06366411 -0.000022507023 0.0019749806 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-16889:::: Half map 2 of the refinement of filamentous beta-actin harboring the N111S mutation.