2024-03-06 REL RCSB RCSB RCSB 2021-02-16 2021-06-09 2021-06-09 2024-03-06 Cryo-EM of the SLFN12-PDE3A complex: SLFN12 body refinement Fuller JR Garvie CW Lemke CT complex, velcrin, molecular glue, DNMDP, RNA BINDING PROTEIN Garvie CW Wu X Papanastasiou M Lee S Fuller J Schnitzler GR Horner SW Baker A Zhang T Mullahoo JP Westlake L Hoyt SH Toetzl M Ranaghan MJ de Waal L McGaunn J Kaplan B Piccioni F Yang X Lange M Tersteegen A Raymond D Lewis TA Carr SA Cherniack AD Lemke CT Meyerson M Greulich H Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase. Nat Commun UK 12 4375 4375 2021 34272366 doi:10.1038/s41467-021-24495-w 2041-1723 7lre FULLOVERLAP SLFN12-PDE3A complex, SLFN12 body SLFN12-PDE3A complex, SLFN12 body 0 1 Homo sapiens Schlafen family member 12 Homo sapiens 0.06738373399999999 2 Spodoptera frugiperda LEVO GGGGSMNISVDLETNYAELVLDVGRVTLGENSRKKMKDCKLRKKQNESVSRAMCALLNSGGGVIKAEIENEDYSYTKDGI GLDLENSFSNILLFVPEYLDFMQNGNYFLIFVKSWSLNTSGLRITTLSSNLYKRDITSAKVMNATAALEFLKDMKKTRGR LYLRPELLAKRPCVDIQEENNMKALAGVFFDRTELDRKEKLTFTESTHVEIKNFSTEKLLQRIKEILPQYVSAFANTDGG YLFIGLNEDKEIIGFKAEMSDLDDLEREIEKSIRKMPVHHFCMEKKKINYSCKFLGVYDKGSLCGYVCALRVERFCCAVF AKEPDSWHVKDNRVMQLTRKEWIQFMVEAEPKFSSSYEEVISQINTSLPAPHSWPLLEWQRQRHHCPGLSGRITYTPENL CRKLFLQHEGLKQLICEEMDSVRKGSLIFSRSWSVDLGLQENHKVLCDALLISQDSPPVLYTFHMVQDEEFKGYSTQTAL TLKQKLAKIGGYTKKVCVMTKIFYLSPEGMTSCQYDLRSQVIYPESYYFTRRKYLLKALFKALKRLKSLRDQFSFAENLY QIIGIDCFQKNDKKMFKSCRRLT Q8IYM2 ZINC ION 6.5409e-05 2 ZN singleParticle particle 0.6 7.4 150.0 NaCl sodium chloride 1.0 MgCl2 magnesium chloride 20.0 C8H18N2O4S HEPES 0.5 C9H15O6P TCEP
0.0038% NP-40s detergent (CAS 9016-45-9) added immediately prior to plunge freezing
 C-flat GOLD 400 CARBON HOLEY ARRAY GLOW DISCHARGE AIR ETHANE 100 291 FEI VITROBOT MARK IV
4.5 second blot time.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1 3163 50.0
Exposures were collected in super-resolution mode, as movies fractionated over 40 frames
 1 2160426
The initial startup model was calculated de novo from the data using the method implemented in cisTEM v1.0.0-beta
 C2 FOURIER SPACE 2.76 FSC 0.143 CUT-OFF RELION 3.1
Multi-body refinement in Relion
247402 MAXIMUM LIKELIHOOD cisTEM 1.0.0-beta MAXIMUM LIKELIHOOD RELION 3.1 9 RELION 3.1 emd_23496.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 344.412 344.412 344.412 90.0 90.0 90.0 X Y Z -0.02046164 0.0635099 0.000011518381 0.0015845727 1.063 1.063 1.063 0.0175 AUTHOR Body output from Relion Multibody refinement 5YD0 PDB experimental model
The atomic model (including per-residue ADP/B-factors) was refined in Phenix against the sharpened/local resolution-filtered map
REAL emd_23496_msk_1.map emd_23496_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 344.412 344.412 344.412 90.0 90.0 90.0 X Y Z -0.18815903 0.4022038 0.00009442897 0.005068592 1.063 1.063 1.063 AUTHOR Sharpened by an automatically-determined B-factor (-100.32) and filtered to local resolution, using the Relion local resolution implementation. Model was primarily refined against this map. emd_23496_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 344.412 344.412 344.412 90.0 90.0 90.0 X Y Z -0.020204563 0.063844964 0.000018125791 0.001652828 1.063 1.063 1.063 AUTHOR Body half-map 2 from Relion Multibody refinement emd_23496_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 344.412 344.412 344.412 90.0 90.0 90.0 X Y Z -0.02166876 0.06619204 0.000017736436 0.0016513322 1.063 1.063 1.063 AUTHOR Body half-map 1 from Relion Multibody refinement