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

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY 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 EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update 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 REMEDIATION REPOSITORY Metalloprotein remediation DERIVED_CALCULATIONS em_admin pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update PDBe PDBe 2022-06-06 2022-08-10 2022-08-10 2026-09-02 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-BeF3- 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 8a2r FULLOVERLAP EMDB EMD-15104 associated EM volume

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 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 BERYLLIUM TRIFLUORIDE ION 6.600700000000001e-05 5 BEF water 1.8015e-05 480 HOH singleParticle filament 0.13 7.5 5.0 Tris 100.0 KCl potassium chloride 2.0 MgCl2 magnesium chloride 2.0 NaN3 sodium azide 1.0 dithiothreitol 0.75 BeF2 beryllium fluoride 5.0 NaF sodium fluoride

F-buffer: 5 mM Tris pH 7.5, 100 mM KCl, 2 mM MgCl2, 2 mM NaN3, 1 mM DTT, 0.75 mM BeF2, 5 mM NaF.

Quantifoil R2/1 COPPER 300 GLOW DISCHARGE 90 ETHANE 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 10822 3.0 78.9

Images were collected in supperresolution mode.

1 2897679 CTFFIND 4.13 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-11787 C1 2.17 FSC 0.143 CUT-OFF RELION 3.1.0 2228553 MAXIMUM LIKELIHOOD SPHIRE 1.4 MAXIMUM LIKELIHOOD RELION 3.1.0 8 RELION 3.1.0 emd_15104.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 -0.14504097 0.41138676 0.00007222443 0.0066346317 0.695 0.695 0.695 0.036 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: Sharpened, local-resolution filtered cryo-EM density map of F-actin in the ADP-BeF3- nucleotide state. 7AHN PDB experimental model FLEXIBLE FIT REAL emd_15104_msk_1.map emd_15104_msk_2.map emd_15104_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 -0.01277671 0.06874959 -0.000068252135 0.0019753801 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: 3D-refined, unsharpened cryo-EM density map of F-actin in the ADP-BeF3- nucleotide state. emd_15104_additional_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 -0.1834607 0.45769057 0.00008240319 0.0070131524 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: Sharpened, local-resolution filtered cryo-EM density map of F-actin in the ADP-BeF3- nucleotide state with a closed D-loop in the central subunit. emd_15104_additional_3.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 -0.012498937 0.06578501 -0.000060539605 0.0019251321 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: 3D-refined, unsharpened cryo-EM density map of F-actin in the ADP-BeF3- nucleotide state with a closed D-loop in the central subunit. emd_15104_additional_4.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 -0.021999044 0.0697756 -0.000057993497 0.0024819928 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: Unfiltered half map 1 of F-actin in the ADP-BeF3- nucleotide state with a closed D-loop in the central subunit. emd_15104_additional_5.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 -0.018162744 0.07025285 -0.000057962698 0.002484644 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: Unfiltered half map 2 of F-actin in the ADP-BeF3- nucleotide state with a closed D-loop in the central subunit. emd_15104_additional_6.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 -0.19932917 0.50409406 0.0000777676 0.007486944 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: Sharpened, local-resolution filtered cryo-EM density map of F-actin in the ADP-BeF3- nucleotide state with an open D-loop in the central subunit. emd_15104_additional_7.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 -0.02644945 0.06770946 -0.000056965855 0.0019863662 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: 3D-refined, unsharpened cryo-EM density map of F-actin in the ADP-BeF3- nucleotide state with an open D-loop in the central subunit. emd_15104_additional_8.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 -0.026709996 0.07306554 -0.000059290764 0.002505105 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: Unfiltered half map 1 of F-actin in the ADP-BeF3- nucleotide state with an open D-loop in the central subunit. emd_15104_additional_9.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 -0.029367996 0.0709822 -0.00005953439 0.0025056286 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: Unfiltered half map 2 of F-actin in the ADP-BeF3- nucleotide state with an open D-loop in the central subunit. emd_15104_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 -0.017592723 0.070776455 -0.00006326995 0.0021784997 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: Unfiltered half map 1 of F-actin in the ADP-BeF3- nucleotide state. emd_15104_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 -0.016984798 0.072358124 -0.00006329467 0.0021785216 0.695 0.695 0.695 AUTHOR ::::EMDATABANK.org::::EMD-15104:::: Unfiltered half map 2 of F-actin in the ADP-BeF3- nucleotide state.