2024-04-24 REL PDBe PDBe PDBe 2024-01-29 2024-04-10 2024-04-10 2024-04-24 Alexander von Humboldt Foundation Germany German Research Foundation (DFG) BI 1998/2-1 Germany European Research Council (ERC) 856118 European Union Cryo-EM reconstruction of the formin Cdc12 bound to the barbed end of F-actin (without phalloidin) Oosterheert W Boiero Sanders M Funk J Prumbaum D Raunser S Bieling P actin, formin, Cdc12, actin assembly., STRUCTURAL PROTEIN Oosterheert W Boiero Sanders M Funk J Prumbaum D Raunser S Bieling P Molecular mechanism of actin filament elongation by formins. Science US 384 eadn9560 eadn9560 2024 38603491 doi:10.1126/science.adn9560 1095-9203 0038 SCIEAS EMD-19496 other EM volume
Reconstruction of the actin-Cdc12 complex in the presence of phalloidin
 Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the barbed end of F-actin. Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the barbed end of F-actin. 0 1 2
Human beta-actin and S. Pombe Cdc12 were purified separately. Both proteins were mixed to assemble the complex prior to cryo-EM grid preparation.
Homo sapiens Actin filament 1 1 Dimeric FH2 domain of S. Pombe Cdc12 1 2 Schizosaccharomyces pombe human cytoplasmic beta-actin Homo sapiens
Actin purified recombinantly from BTI-Tnao38 cells.
Trichoplusia ni LEVO MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIE(HIC)GIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESAGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF P60709 S. pombe Cdc12 Schizosaccharomyces pombe Escherichia coli LEVO SKDDLHKTTGLTRRPTRRLKQMHWEKLNSGLEFTFWTGPSDEANKILETLHTSGVLDELD ESFAMKEAKTLVKKTCARTDYMSSELQKLFGIHFHKLSHKNPNEIIRMILHCDDSMNECV EFLSSDKVLNQPKLKADLEPYRIDWANGGDLVNSEKDASELSRWDYLYVRLIVDLGGYWN QRMNALKVKNIIETNYENLVRQTKLIGRAALELRDSKVFKGLLYLILYLGNYMNDYVRQA KGFAIGSLQRLPLIKNANNTKSLLHILDITIRKHFPQFDNFSPELSTVTEAAKLNIEAIE QECSELIRGCQNLQIDCDSGALSDPTVFHPDDKILSVILPWLMEGTKKMDFLKEHLRTMN TTLNNAMRYFGEQPNDPNSKNLFFKRVDSFIIDYSKARSDNLKSEEEEASQHRRLNLVN Q10059 singleParticle particle 7.1 10.0 HEPES 100.0 NaCl sodium chloride 2.0 MgCl2 magnesium chloride 1.0 EGTA 0.5 TCEP
1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP)
 Quantifoil R2/1 GOLD 200 CARBON HOLEY GLOW DISCHARGE ETHANE-PROPANE 100 286 FEI VITROBOT MARK IV
3 seconds, force 0..
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 0.01 1.2 2.7 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. GIF Bioquantum 15
Gatan energy filter.
300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector.
GATAN K3 BIOQUANTUM (6k x 4k) 1 12009 64.3 1 2443647
Particles picked using SPHIRE-crYOLO.
 EMD-19496
Cdc12 bound to phalloidin-stabilized F-actin.
 C1 4.54 FSC 0.143 CUT-OFF RELION 3.1.0
Final reconstruction displays preferred orientation.
173582 MAXIMUM LIKELIHOOD cryoSPARC v3.3.2 MAXIMUM LIKELIHOOD RELION 3.1.0 4 RELION 3.1.0
3D classification in RELION.
 emd_19497.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.00765671 0.03492895 0.00026118013 0.0015996065 0.88 0.88 0.88 0.01 AUTHOR Sharpened cryo-EM density map of the formin Cdc12 bound to the barbed end of F-actin (without phalloidin). 8RTT PDB experimental model emd_19497_msk_1.map emd_19497_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.002707042 0.02432672 0.000059389884 0.0015475415 0.88 0.88 0.88 AUTHOR 3D-refined, unsharpened cryo-EM density map of the formin Cdc12 bound to the barbed end of F-actin (without phalloidin). emd_19497_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.008389283 0.041350674 0.000055230576 0.0015648304 0.88 0.88 0.88 AUTHOR Cryo-EM map Cdc12 bound to phalloidin-stabilized F-actin (EMD-19496), resampled on the cryo-EM reconstruction that was obtained without phalloidin. emd_19497_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.0026203892 0.025103675 0.000059389884 0.0015400988 0.88 0.88 0.88 AUTHOR Power-adjusted map of actin-Cdc12 with phalloidin(EMD-19496), resampled on the no-phalloidin map. Used to construct a difference map between the reconstructions with and without phalloidin. emd_19497_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.010022815 0.016656775 0.000000000000004 0.00038825173 0.88 0.88 0.88 AUTHOR Difference map between actin-Cdc12 reconstructions that were obtained in the absence (this entry) and presence (EMD-19496) of the toxin phalloidin. emd_19497_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.01315113 0.033332974 0.000059252612 0.0019441938 0.88 0.88 0.88 AUTHOR Unfiltered half map 1 of the formin Cdc12 bound to the barbed end of F-actin (without phalloidin). emd_19497_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.011344172 0.032282833 0.000059669153 0.0018832996 0.88 0.88 0.88 AUTHOR Unfiltered half map 2 of the formin Cdc12 bound to the barbed end of F-actin (without phalloidin).