Cryo-EM structure of F-actin in the Mg2+-ADP-Pi nucleotide state.

2026-03-04 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION em_3d_fitting_list em_admin pdbx_initial_refinement_model _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update DATABASE_REFERENCES citation citation_author _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_3d_fitting_list em_admin pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update _pdbx_entry_details.has_protein_modification PDBe PDBe 2022-06-06 2022-08-10 2022-08-10 2026-03-04 European Research Council (ERC) 856118 European Union Alexander von Humboldt Foundation Germany European Molecular Biology Organization (EMBO) European Union Max Planck Society Germany Cryo-EM structure of F-actin in the Mg2+-ADP-Pi nucleotide state. Oosterheert W Klink BU Belyy A Pospich S Raunser S actin, cytoskeleton, filament, nucleotide state, STRUCTURAL PROTEIN Oosterheert W Klink BU Belyy A Pospich S Raunser S Structural basis of actin filament assembly and aging. Nature UK 611 374 379 2022 36289337 doi:10.1038/s41586-022-05241-8 1476-4687 0006 NATUAS EMD-15104 other EM volume

Cryo-EM structure of F-actin in the Mg2+-ADP-BeF3- nucleotide state.

8a2s FULLOVERLAP PDB 8A2R unspecified

Cryo-EM structure of F-actin in the Mg2+-ADP-BeF3- nucleotide state.

EMDB EMD-15104 other EM volume

Cryo-EM structure of F-actin in the Mg2+-ADP-BeF3- nucleotide state.

EMDB EMD-15105 associated EM volume

Cryo-EM structure of F-actin in the Mg2+-ADP-Pi nucleotide state.

rabbit skeletal alpha-actin in the filamentous state. rabbit skeletal alpha-actin in the filamentous state. 0 1

The helical rise of F-actin is 27.5 Angstrom, with a helical twist of ~166.5 degrees.

Oryctolagus cuniculus skeletal muscle 15.2 Actin, alpha skeletal muscle Oryctolagus cuniculus skeletal muscle 0.041875633 5 LEVO DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIE(HIC)GII TNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSG DGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSL EKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKE ITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF P68135 ADENOSINE-5'-DIPHOSPHATE 0.000427201 5 ADP MAGNESIUM ION 2.4305e-05 5 MG PHOSPHATE ION 9.4971e-05 5 PO4 water 1.8015e-05 591 HOH singleParticle filament 0.67 7.5 5.0 Tris 50.0 KCl potassium chloride 2.0 MgCl2 magnesium chloride 2.0 NaN3 sodium azide 1.0 dithiothreitol 50.0 potassium phosphate

F-phosphate buffer: 5 mM Tris, 100 mM KCl, 2 mM MgCl2, 2 mM NaN3, 1 mM DTT, 50 mM potassium phosphate pH 7.5

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

The Vitrobot was operated at 13 degrees celsius and the samples were blotted for 9 seconds with a blot force of -25..

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.7000000000000001 2.0 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 15 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1 9658 3.0 88.8

Images were collected in supperresolution mode.

1 2349979

We picked helical segments with a box distance of 40 pixels or 27.8 Angstrom and a minimum number of six boxes per filament.

CTFFIND 4.13 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-11787 C1 2.22 FSC 0.143 CUT-OFF RELION 3.1.0 1808554 MAXIMUM LIKELIHOOD SPHIRE 1.4 MAXIMUM LIKELIHOOD RELION 3.1.0 8 RELION 3.1.0 emd_15105.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 -0.18388304 0.31867424 0.0001377433 0.0076237414 0.695 0.695 0.695 0.045 AUTHOR ::::EMDATABANK.org::::EMD-15105:::: Sharpened, local-resolution filtered cryo-EM density map of F-actin in the Mg2 -ADP-Pi nucleotide state. 7AHN PDB experimental model FLEXIBLE FIT

The structures were then refined through a similar protocol of iterative cycles in Coot and phenix real-space refine. All solvent molecules (ions, waters) were placed manually in Coot in the central actin subunit, and were then placed in the other subunits using NCS. Because the local resolution of each F-actin reconstruction is highest in the center and lower at the periphery of the map, we inspected all waters in each structure manually before the final phenix refinement; water molecular with poor corresponding cryo-EM density were removed.

REAL emd_15105_msk_1.map emd_15105_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 -0.016594479 0.05462154 -0.000029893616 0.002067213 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15105:::: 3D-refined, unsharpened cryo-EM density map of F-actin in the Mg2 -ADP-Pi nucleotide state. emd_15105_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 -0.01938838 0.059297916 -0.000030003928 0.002334534 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15105:::: Unfiltered half map 1 of F-actin in the Mg2 -ADP-Pi nucleotide state. emd_15105_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 -0.022410378 0.057560224 -0.000029799427 0.0023360318 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15105:::: Unfiltered half map 2 of F-actin in the Mg2 -ADP-Pi nucleotide state.