Cryo-EM of the SLFN12-PDE3A complex: PDE3A body refinement

2026-04-15 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin entity _chem_comp.name _em_admin.last_update _entity.formula_weight _entity.pdbx_description REFINEMENT_DESCRIPTION chem_comp_atom chem_comp_bond database_2 em_3d_fitting_list 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 STRUCTURE_SUMMARY chem_comp em_admin entity pdbx_entity_nonpoly pdbx_entry_details _chem_comp.formula _chem_comp.formula_weight _chem_comp.name _em_admin.last_update _entity.formula_weight _entity.pdbx_description _pdbx_entity_nonpoly.name _pdbx_entry_details.has_protein_modification RCSB RCSB 2021-02-16 2021-06-09 2021-06-09 2026-04-15 Cryo-EM of the SLFN12-PDE3A complex: PDE3A body refinement Fuller JR Garvie CW Lemke CT complex, velcrin, molecular glue, DNMDP, HYDROLASE 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 7lrc FULLOVERLAP EMDB EMD-23494 associated EM volume

SLFN12-PDE3A complex, PDE3A body with interacting peptide from SLFN12 SLFN12-PDE3A complex, PDE3A body with interacting peptide from SLFN12 0 1 2 Homo sapiens cGMP-inhibited 3',5'-cyclic phosphodiesterase A Homo sapiens 0.057352995999999996 2 Escherichia coli LEVO GEDETECLREPLRKASACSTYAPETMMFLDKPILAPEPLVMDNLDSIMEQLNTWNFPIFDLVENIGRKCGRILSQVSYRL FEDMGLFEAFKIPIREFMNYFHALEIGYRDIPYHNRIHATDVLHAVWYLTTQPIPGLSTVINDHGSTSDSDSDSGFTHGH MGYVFSKTYNVTDDKYGCLSGNIPALELMALYVAAAMHDYDHPGRTNAFLVATSAPQAVLYNDRSVLENHHAAAAWNLFM SRPEYNFLINLDHVEFKHFRFLVIEAILATDLKKHFDFVAKFNGKVNDDVGIDWTNENDRLLVCQMCIKLADINGPAKCK ELHLQWTDGIVNEFYEQGDEEASLGLPISPFMDRSAPQLANLQESFISHIVGPLCNSYDSAGLMPGKWVEDSDESGDTDD PEEEEEEAPAPNEEETCENNESPKKKTFKRRKIYCQITQHLLQNHKMWKKVIEEEQRLAGIENQSLDQTPQSHSSEQIQA IKEEEEEKGKPRGEEIPTQKPDQ Q14432 3.1.4.17 Schlafen family member 12 Homo sapiens 0.06738373399999999 2 unidentified baculovirus LEVO GGGGSMNISVDLETNYAELVLDVGRVTLGENSRKKMKDCKLRKKQNESVSRAMCALLNSGGGVIKAEIENEDYSYTKDGI GLDLENSFSNILLFVPEYLDFMQNGNYFLIFVKSWSLNTSGLRITTLSSNLYKRDITSAKVMNATAALEFLKDMKKTRGR LYLRPELLAKRPCVDIQEENNMKALAGVFFDRTELDRKEKLTFTESTHVEIKNFSTEKLLQRIKEILPQYVSAFANTDGG YLFIGLNEDKEIIGFKAEMSDLDDLEREIEKSIRKMPVHHFCMEKKKINYSCKFLGVYDKGSLCGYVCALRVERFCCAVF AKEPDSWHVKDNRVMQLTRKEWIQFMVEAEPKFSSSYEEVISQINTSLPAPHSWPLLEWQRQRHHCPGLSGRITYTPENL CRKLFLQHEGLKQLICEEMDSVRKGSLIFSRSWSVDLGLQENHKVLCDALLISQDSPPVLYTFHMVQDEEFKGYSTQTAL TLKQKLAKIGGYTKKVCVMTKIFYLSPEGMTSCQYDLRSQVIYPESYYFTRRKYLLKALFKALKRLKSLRDQFSFAENLY QIIGIDCFQKNDKKMFKSCRRLT Q8IYM2 MANGANESE (II) ION 5.4938e-05 2 MN MAGNESIUM ION 2.4305e-05 2 MG (5R,6P)-6-[4-(diethylamino)-3-nitrophenyl]-5-methyl-4,5-dihydropyridazin-3(2H)-one 0.00030434399999999996 2 X5M 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 45 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 CTFFIND 4.1.13

CTF correction was applied throughout the entire processing workflow, beginning with particle picking

PHASE FLIPPING AND AMPLITUDE CORRECTION

The initial startup model was calculated de novo from the data using the method implemented in cisTEM v1.0.0-beta

C2 FOURIER SPACE 2.97 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_23494.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 -0.019649941 0.052426178 0.000091294554 0.0014236004 1.063 1.063 1.063 0.0175 AUTHOR ::::EMDATABANK.org::::EMD-23494:::: 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_23494_msk_1.map emd_23494_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 -0.20192806 0.35954687 0.000090031215 0.0043297294 1.063 1.063 1.063 AUTHOR ::::EMDATABANK.org::::EMD-23494:::: Sharpened by an automatically-determined B-factor (-117.379) and filtered to local resolution, using the Relion local resolution implementation. Model was primarily refined against this map. emd_23494_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 -0.02113917 0.05905707 0.000021791662 0.0014993765 1.063 1.063 1.063 AUTHOR ::::EMDATABANK.org::::EMD-23494:::: Body half-map 2 from Relion Multibody refinement emd_23494_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 -0.021467865 0.056993935 0.000021219397 0.001498618 1.063 1.063 1.063 AUTHOR ::::EMDATABANK.org::::EMD-23494:::: Body half-map 1 from Relion Multibody refinement