2023-11-22 REL PDBe PDBe PDBe 2023-03-22 2023-08-16 2023-08-16 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 R183W 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 8oi8 FULLOVERLAP Actin filament harboring the R183W mutation. Actin filament harboring the R183W mutation. 0 1
Actin was purified as monomer from insect cells. It was then polymerized into a filament in vitro.
Homo sapiens Actin, cytoplasmic 1 Homo sapiens 0.041792633 5 Trichoplusia ni LEVO MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIE(HIC)GIV TNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSG DGVTHTVPIYEGYALPHAILRLDLAGWDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSL EKSYELPDGQVITIGNERFRCPEALFQPSFLGMESAGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKE ITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF P60709 3.6.4.- ADENOSINE-5'-DIPHOSPHATE 0.000427201 5 ADP MAGNESIUM ION 2.4305e-05 5 MG water 1.8015e-05 585 HOH singleParticle filament 2.3 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 ETHANE 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 7916 70.0 1
K3 operated in super-resolution mode.
1569882 EMD-15109 C1 2.28 FSC 0.143 CUT-OFF RELION 3.1.0
Refinement from Local searches in RELION.
1386604 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_16888.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 -0.12874886 0.36157265 0.00017974104 0.0063069593 0.695 0.695 0.695 0.038 AUTHOR Sharpened, local-resolution filtered cryo-EM density map of filamentous beta-actin harboring the R183W mutation. 8a2t PDB experimental model FLEXIBLE FIT
The structure was refined using phenix-real-space refine.
REAL emd_16888_msk_1.map emd_16888_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 -0.011294154 0.065294534 -0.0000073557726 0.0019157351 0.695 0.695 0.695 AUTHOR 3D refined, unsharpened cryo-EM density map of filamentous beta-actin harboring the R183W mutation. emd_16888_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 -0.016666982 0.06896294 -0.0000075081166 0.0022212141 0.695 0.695 0.695 AUTHOR Half map 1 of the refinement of filamentous beta-actin harboring the R183W mutation. emd_16888_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 -0.017806327 0.073953636 -0.000007928486 0.0022154725 0.695 0.695 0.695 AUTHOR Half map 2 of the refinement of filamentous beta-actin harboring the R183W mutation.