Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution (tropomyosin filtered to 7 Angstrom)

2024-07-10 REL PDBe RCSB PDBe 2016-04-27 2016-05-25 2016-06-15 2024-07-10 Max Planck Society Germany Behrens-Weise foundation Germany Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution (tropomyosin filtered to 7 Angstrom) von der Ecken J Heissler SM Pathan-Chhatbar S Manstein DJ Raunser S CONTRACTILE FILAMENT, MUSCLE, THIN FILAMENT, CYTOSKELETON, STRUCTURAL PROTEIN, HYDROLASE COMPLEX, F-actin, tropomyosin, filament, myosin, 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 EMD-8164 FULLOVERLAP

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

EMD-8165 FULLOVERLAP

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

EMD-8165 other EM volume

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

5jlh FULLOVERLAP

The PDB model belongs to both entries.

F-actin-myosin-tropomyosin complex F-actin-myosin-tropomyosin complex 0 1 2 3

Filament

0.44 actin, myosin 1 1 2 Homo sapiens tropomyosin 1 3 Homo sapiens Actin, cytoplasmic 2 Homo sapiens 0.04170757 5 Spodoptera frugiperda LEVO EEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDD MEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTH TVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYE LPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALA PSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF P63261 Myosin-14,Alpha-actinin A Dictyostelium discoideum 0.117570633

NON MUSCLE MYOSIN 2C HEAVY CHAIN, MOTOR DOMAIN RESIDUES 1-799 LINKED TO ALPHA-ACTININ 3, REPEATS 1 AND 2 RESIDUES 800-1039 FRAGMENT: UNP Q7Z406-1 RESIDUES 1-799, UNP P05095 RESIDUES 265-502

2 Spodoptera frugiperda LEVO MAAVTMSVPGRKAPPRPGPVPEAAQPFLFTPRGPSAGGGPGSGTSPQVEWTARRLVWVPSELHGFEAAALRDEGEEEAEV ELAESGRRLRLPRDQIQRMNPPKFSKAEDMAELTCLNEASVLHNLRERYYSGLIYTYSGLFCVVINPYKQLPIYTEAIVE MYRGKKRHEVPPHVYAVTEGAYRSMLQDREDQSILCTGESGAGKTENTKKVIQYLAHVASSPKGRKEPGVPGELERQLLQ ANPILEAFGNAKTVKNDNSSRFGKFIRINFDVAGYIVGANIETYLLEKSRAIRQAKDECSFHIFYQLLGGAGEQLKADLL LEPCSHYRFLTNGPSSSPGQERELFQETLESLRVLGFSHEEIISMLRMVSAVLQFGNIALKRERNTDQATMPDNTAAQKL CRLLGLGVTDFSRALLTPRIKVGRDYVQKAQTKEQADFALEALAKATYERLFRWLVLRLNRALDRSPRQGASFLGILDIA GFEIFQLNSFEQLCINYTNEKLQQLFNHTMFVLEQEEYQREGIPWTFLDFGLDLQPCIDLIERPANPPGLLALLDEECWF PKATDKSFVEKVAQEQGGHPKFQRPRHLRDQADFSVLHYAGKVDYKANEWLMKNMDPLNDNVAALLHQSTDRLTAEIWKD VEGIVGLEQVSSLGDGPPGGRPRRGMFRTVGQLYKESLSRLMATLSNTNPSFVRCIVPNHEKRAGKLEPRLVLDQLRCNG VLEGIRICRQGFPNRILFQEFRQRYEILTPNAIPKGFMDGKQACEKMIQALELDPNLYRVGQSKIFFRAGVLAQLEEERA SEQTKSDYLKRANELVQWINDKQASLESRDFGDSIESVQSFMNAHKEYKKTEKPPKGQEVSELEAIYNSLQTKLRLIKRE PFVAPAGLTPNEIDSTWSALEKAEQEHAEALRIELKRQKKIAVLLQKYNRILKKLENWATTKSVYLGSNETGDSITAVQA KLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTERKDTFFAQQWTGVKSSAETYKNTLLAELERLQKIED Q7Z406 P05095 Tropomyosin alpha-3 chain Homo sapiens 0.011507176

Human TROPOMYSIN WAS USED (UNP P06753-2,TPM3_HUMAN, RESIDUES 62-196). DUE TO THE LIMITED RESOLUTION OF THE CRYO-EM DENSITY IN THE REGION OF TROPOMYOSIN, TROPOMYOSIN HAS BEEN REPRESENTED AS POLY(UNK).

4 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

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

Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter paper. Afterwards 1.5 uL of myosin solution (3 uM without nucleotide) were added directly on the grid, incubated for 10 s and then manually blotted for 5 s from the backside with filter paper..

FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 0.7000000000000001 2.8000000000000003 59000.0

Cs corrected microscope

FEI FALCON II (4k x 4k) COUNTING 2-8 6300 0.475 16.0 1 138000 EMD-6124 27.5 166.9 C1 3.9 FSC 0.143 CUT-OFF RELION 1.3

THE TROPOMYOSIN MAP FILTERED TO 7.0 ANGSTROM WAS MERGED WITH THE FINAL F-ACTIN-MYOSIN MAP (3.9 ANGSTROM) TO OBTAIN A MAP OF THE ENTIRE F-ACTIN-MYOSIN-TROPOMYOSIN COMPLEX.

118000 NOT APPLICABLE RELION 1.3 NOT APPLICABLE RELION 1.3 emd_8164.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 -0.06937454 0.17635544 0.0011794708 0.0077009643 1.1 1.1 1.1 0.049 AUTHOR ::::EMDATABANK.org::::D_1000219896:::: None 3J8A A PDB experimental model 4PD3 A PDB experimental model 3J8A B PDB experimental model 3J8A C PDB experimental model 3J8A D PDB experimental model 3J8A E PDB experimental model BACKBONE TRACE 180.0 4A7F B PDB experimental model 4A7F H PDB experimental model RIGID BODY FIT

tropomyosin fitting