Structure of the F-actin-tropomyosin complex (reprocessed, tropomyosin filtered to 7 Angstrom)

2025-04-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION database_2 em_3d_fitting_list em_admin pdbx_initial_refinement_model _database_2.pdbx_DOI _database_2.pdbx_database_accession _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 EXPERIMENTAL_PREPARATION em_sample_support em_software pdbx_database_related struct_conn _em_sample_support.grid_type _em_software.name _em_software.version STRUCTURE_SUMMARY cell em_entity_assembly em_entity_assembly_naturalsource em_entity_assembly_recombinant pdbx_database_related refine refine_hist refine_ls_restr refine_ls_restr_ncs refine_ls_shell _cell.Z_PDB _pdbx_database_related.content_type _refine.pdbx_refine_id _refine_hist.pdbx_refine_id _refine_ls_restr.pdbx_refine_id _refine_ls_restr_ncs.pdbx_refine_id _refine_ls_shell.pdbx_refine_id OTHER atom_sites _atom_sites.fract_transf_matrix[1][1] _atom_sites.fract_transf_matrix[2][1] _atom_sites.fract_transf_matrix[2][2] _atom_sites.fract_transf_matrix[3][2] _atom_sites.fract_transf_matrix[3][3] STRUCTURE_SUMMARY struct _struct.title STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_3d_fitting_list em_admin pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature _database_2.pdbx_DOI _database_2.pdbx_database_accession _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 RCSB PDBe 2016-04-27 2016-05-25 2016-06-15 2025-04-09 Max Planck Society Germany Behrens-Weise foundation Germany Structure of the F-actin-tropomyosin complex (reprocessed, tropomyosin filtered to 7 Angstrom) von der Ecken J Raunser S CONTRACTILE FILAMENT, MUSCLE, THIN FILAMENT, CYTOSKELETON, STRUCTURAL PROTEIN, HYDROLASE COMPLEX, F-actin, tropomyosin, filament, protein polymers, cryo EM, Contractile protein Ecken JV Heissler SM Pathan-Chhatbar S Manstein DJ Raunser S Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution. Nature UK 534 724 728 2016 27324845 doi:10.1038/nature18295 1476-4687 0006 NATUAS von der Ecken J Mueller M Lehman W Manstein DJ Penczek PA Raunser S Structure of the F-actin-tropomyosin complex. Nature UK 519 114 117 2015 25470062 doi:10.1038/nature14033 1476-4687 0006 NATUAS EMD-8162 FULLOVERLAP

The EM volume is the same reconstruction after post-processing with RELION with filtering of tropomyosin to 7 Angstrom.

EMD-8163 FULLOVERLAP

The EM volume is the same reconstruction after post-processing with RELION without filtering of tropomyosin to 7 Angstrom.

EMD-8163 other EM volume

The EM volume is the same reconstruction after post-processing with RELION without filtering of tropomyosin to 7 Angstrom.

5jlf FULLOVERLAP

The PDB model belongs to both entries.

F-actin-tropomyosin complex F-actin-tropomyosin complex 0 1 2

Filament

0.2 F-actin 1 1 Oryctolagus cuniculus tropomyosin 1 2 Mus musculus Actin, alpha skeletal muscle Oryctolagus cuniculus 0.041875633 5 LEVO DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIE(HIC)GII TNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSG DGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSL EKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKE ITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF P68135 Tropomyosin Alpha-1 Mus musculus 0.011507176

MOUSE TROPOMYSIN WAS USED (UNP P58771, RESIDUES 97-231). DUE TO THE LIMITED RESOLUTION OF THE CRYO-EM DENSITY IN THE REGION OF TROPOMYOSIN, TROPOMYOSIN HAS BEEN REPRESENTED AS POLY(UNK).

2 Escherichia coli LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) ADENOSINE-5'-DIPHOSPHATE 0.000427201 5 ADP MAGNESIUM ION 2.4305e-05 5 MG singleParticle filament 7.5 5.0 Tris-HCl 1.0 DTT 100.0 KCl 2.0 MgCl2

5 mM Tris-HCl pH 7.5, 1 mM DTT, 100 mM KCl, and 2 mM MgCl2

C-flat-2/1 COPPER 300 CARBON HOLEY GLOW DISCHARGE ETHANE 90 GATAN CRYOPLUNGE 3

Sample was applied to a glow-discharged holey carbon grid, incubated for 10 s and manually blotted for 3 s from the backside with filter paper..

FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.6 59000.0

Cs corrected microscope

FEI FALCON II (4k x 4k) COUNTING 2-8 0.475 16.0 1 119000 EMD-6124 27.5 166.9 C1 3.6 FSC 0.143 CUT-OFF RELION 1.3

THE TROPOMYOSIN MAP FILTERED TO 6.5 ANGSTROM WAS MERGED WITH THE FINAL F-ACTIN MAP (3.6 ANGSTROM) TO OBTAIN A MAP OF THE ENTIRE F-ACTIN-TROPOMYOSIN COMPLEX.

91000 NOT APPLICABLE RELION 1.3 NOT APPLICABLE RELION 1.3 emd_8162.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 -128 -129 -123 256 256 256 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.09427254 0.23495093 0.0012265167 0.009904748 1.1 1.1 1.1 0.1 AUTHOR ::::EMDATABANK.org::::D_1000219857:::: None 3J8A PDB experimental model BACKBONE TRACE RECIPROCAL 98.0 RIGID BODY FIT

tropomyosin fitting