Bovine Cardiac Myosin in Complex with Chicken Skeletal Actin and Human Cardiac Tropomyosin in the Rigor State

2024-03-06 REL RCSB RCSB RCSB 2020-05-27 2020-07-22 2020-07-22 2024-03-06 National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) R01HL036153 United States National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) R01HL123774 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) S10RR25434 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) U24 GM129541 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM029090 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) U24GM116787 United States Horizon 2020 Research and Innovation Programme 777204 SILICOFCM European Union Bovine Cardiac Myosin in Complex with Chicken Skeletal Actin and Human Cardiac Tropomyosin in the Rigor State Doran MH Lehman W Bullitt E myosin, tropomyosin, actin, cardiac, CONTRACTILE PROTEIN Doran MH Pavadai E Rynkiewicz MJ Walklate J Bullitt E Moore JR Regnier M Geeves MA Lehman W Cryo-EM and Molecular Docking Shows Myosin Loop 4 Contacts Actin and Tropomyosin on Thin Filaments. Biophys.J. US 119 821 830 2020 32730789 doi:10.1016/j.bpj.2020.07.006 1542-0086 0030 BIOJAU 6x5z FULLOVERLAP Helical complex of bovine S1 cardiac myosin and human cardiac tropomyosin-decorated chicken skeletal actin filaments Helical complex of bovine S1 cardiac myosin and human cardiac tropomyosin-decorated chicken skeletal actin filaments 0 1 2 3

Bovine myosin was isolated from the masseter muscle and the S1 fragment was generated through proteolytic cleavage.

0.40322 skeletal actin filaments 1 1 Gallus gallus Breast Skeletal Muscle S1 cardiac myosin 1 2 Bos taurus Masseter Muscle cardiac tropomyosin 1 3 Homo sapiens Actin, alpha skeletal muscle Gallus gallus Breast Skeletal Muscle 0.042096953

Residues 1-9 and 377 were disordered and were not modeled.

3 LEVO MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITN WDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDG VTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEIT ALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF P68139 Tropomyosin alpha-1 chain Homo sapiens 0.032763621

Only the central section (residues 45-210) was modeled.

2 Escherichia coli LEVO MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATD AEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADR KYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDRYEEEIKVLSDKLKEAETRAE FAERSVTKLEKSIDDLEDELYAQKLKYKAISEELDHALNDMTSI P09493 Myosin-7 Bos taurus Masseter Muscle 0.09744689799999999

Residues 1-35, 200-216, 624-641, and 777-850 were disordered and not modeled.

3 LEVO MVDAEMAAFGEAAPYLRKSEKERLEAQTRPFDLKKDVFVPDDKEEFVKATILSREGGKVTAETEHGKTVTVKEDQVLQQN PPKFDKIEDMAMLTFLHEPAVLYNLKERYASWMIYTYSGLFCVTINPYKWLPVYNAEVVAAYRGKKRSEAPPHIFSISDN AYQYMLTDRENQSILITGESGAGKTVNTKRVIQYFAVIAAIGDRSKKEQATGKGTLEDQIIQANPALEAFGNAKTVRNDN SSRFGKFIRIHFGATGKLASADIETYLLEKSRVIFQLKAERDYHIFYQILSNKKPELLDMLLITNNPYDYAFISQGETTV ASIDDAEELMATDNAFDVLGFTTEEKNSMYKLTGAIMHFGNMKFKLKQREEQAEPDGTEEADKSAYLMGLNSADLLKGLC HPRVKVGNEYVTKGQNVQQVVYAKGALAKAVYERMFNWMVTRINATLETKQPRQYFIGVLDIAGFEIFDFNSFEQLCINF TNEKLQQFFNHHMFVLEQEEYKKEGIEWEFIDFGMDLQACIDLIEKPMGIMSILEEECMFPKATDMTFKAKLFDNHLGKS SNFQKPRNIKGKPEAHFSLIHYAGTVDYNIIGWLQKNKDPLNETVVDLYKKSSLKMLSSLFANYAGFDTPIEKGKGKAKK GSSFQTVSALHRENLNKLMTNLRSTHPHFVRCIIPNETKSPGVIDNPLVMHQLRCNGVLEGIRICRKGFPNRILYGDFRQ RYRILNPAAIPEGQFIDSRKGAEKLLGSLDIDHNQYKFGHTKVFFKAGLLGLLEEMRDERLSRIITRIQAQSRGVLSRME FKKLLERRDSLLIIQWNIRAFMGVKNWPWMKLYFKIKPLLKSAETEKEIA Q9BE39 ADENOSINE-5'-DIPHOSPHATE 0.000427201 3 ADP MAGNESIUM ION 2.4305e-05 3 MG helical helicalArray .525 7.0 50.0 CH3COONa Sodium Acetate 3.0 MgCl2 Magnesium Chloride 1.0 Dithiothreitol 10.0 HEPES Quantifoil R2/1 COPPER 200 CARBON HOLEY GLOW DISCHARGE 25 AIR

Glow discharged using a PELCO easiGlow station

ETHANE 100 283 FEI VITROBOT MARK III

Thin filaments were reconstituted by first mixing F-actin and tropomyosin to final concentrations of 10 uM actin and 7 uM tropomyosin. Just before applying 1.5 uL actin-tropomyosin to a freshly glow discharged holey-carbon grid, the surfactant octyl B-D-glucopyranoside was added to the protein solution to a concentration of 12 nM. The grid sample was manually blotted for 1 second and a 1.5 uL drop of 7.5 uM myosin-S1 sub-fragment was then applied to the blotted grid sample. The sample was immediately blotted for 4 seconds and plunge-frozen in liquid ethane..

FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 1.5 2.5 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER In-column Omega Filter 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1-35 1 2496 7.0 53.0 1 27.5 -166.4 C1 4.24 FSC 0.143 CUT-OFF RELION

Performed in the Relion post-processing step

32158 45040 RELION 3.0.7

200 Angstrom Featureless Cylinder

NOT APPLICABLE RELION 3.0.7 emd_22067.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 271.36 271.36 271.36 90.0 90.0 90.0 X Y Z -0.03484657 0.058786064 0.00039920956 0.0025944682 1.06 1.06 1.06 0.007 AUTHOR ::::EMDATABANK.org::::EMD-22067:::: Cryo-EM map of the cardiac actin-myosin-tropomyosin complex. 6KN8 PDB experimental model

The F-actin structure was taken from the Yamada et al. map (PDB ID: 6KN8), fitted within its corresponding density of the masseter S1-decorated actin-tropomyosin reconstruction. A homology model of the beta-myosin S1 was then built based on the rigor-state crystal structure of squid muscle myosin S1 (PDB ID: 3I5G). These models were fit using molecular dynamics flexible fitting in order to align secondary structure elements using VMD 1.9.3. Next, we used Phenix’s Cryo-EM Real Space Refinement in order to refine the MDFF result. Finally, Coot was used to manually refine side chain orientations to reduce clashes, Ramachandran outliers, and sidechain outliers. The tropomyosin backbone was fit into its respective density using UCSF Chimera’s Fit in Map tool. The side chains of tropomyosin included in this structure are based on our extensive protein-protein docking studies found in the associated publication.

3I5G PDB experimental model FLEXIBLE FIT

version 1.9.3; initial flexible fitting to align secondary structure using MDFF

REAL OTHER

version 1.18-3861

REAL 70.879999999999995 OTHER

manual refinement of residues to match backbone and sidechain density and to limit clashes, sidechain outliers, and Ramachandran outliers

REAL