2026-03-04 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION em_3d_fitting_list em_admin pdbx_initial_refinement_model _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 _em_admin.last_update STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_3d_fitting_list em_admin pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature _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 _em_admin.last_update _pdbx_entry_details.has_protein_modification RCSB RCSB 2021-09-13 2021-11-03 2021-11-03 2026-03-04 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM136258 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1R01GM138990 United States National Science Foundation (NSF, United States) DMR-1719875 United States CryoEM structure of modular PKS holo-Lsd14 stalled at the condensation step and bound to antibody fragment 1B2, composite structure Bagde SR Kim C-Y Fromme JC Modular polyketide synthase, ketosynthase, ketoreductase, acyl carrier protein, BIOSYNTHETIC PROTEIN Bagde SR Mathews II Fromme JC Kim CY Modular polyketide synthase contains two reaction chambers that operate asynchronously. Science US 374 723 729 2021 34735234 doi:10.1126/science.abi8532 1095-9203 0038 SCIEAS EMD-24862 other EM volume EMD-24863 other EM volume EMD-24864 other EM volume EMD-24865 other EM volume EMD-24866 other EM volume EMD-24867 other EM volume 7s6c FULLOVERLAP EMDB EMD-24862 other EM volume EMDB EMD-24863 other EM volume EMDB EMD-24864 other EM volume EMDB EMD-24865 other EM volume EMDB EMD-24866 other EM volume EMDB EMD-24867 other EM volume EMDB EMD-24868 associated EM volume
CryoEM structure of modular PKS holo-Lsd14 bound to antibody fragment 1B2, composite structure
 Dimeric holo-Lsd14 containing docking domains from DEBS module 3 (holo-Lsd14-DD*) bound to two copies each of Fab 1B2 light and heavy chains and NADP, treated with 2-Acetaminoethyl-thio-3-oxobutanoate Dimeric holo-Lsd14 containing docking domains from DEBS module 3 (holo-Lsd14-DD*) bound to two copies each of Fab 1B2 light and heavy chains and NADP, treated with 2-Acetaminoethyl-thio-3-oxobutanoate 0 1 2 3 0.45 Polyketide synthase 1 Streptomyces lasalocidi Fab 1B2 heavy chain, Fab 1B2 light chain 1 Homo sapiens 6-deoxyerythronolide-B synthase EryA2, modules 3 and 4, Lsd14 Polyketide synthase fusion Streptomyces lasalocidi 0.174085734 4 Escherichia coli LEVO MVTDSEKVAEYLRRATLDLRAARQRIRELESEPIAIIGMACRLPGGVDSPEGLWELVDSGTDAIAGFPLDRGWDVEGMYD PDAEAPGKTYVKEAGFLYDAGEFDAGFFGISPREAVSMDPQQRLMLEASWEAFERAGLDPARQRGTATGVFVGATATGYV SPAAEVPEGAEGFAITGNMTAVTSGRISYTLGLQGPAVTIDTACSSSLVALHLACQSLRQGECTTALAGGVTVMPTPTAF TEFSRQRGLAPDGRCKSFAAAADGTNWAEGVAVLVVERLSDARRNGHRVLAVVRGTAINQDGASNGLSAPNDLAQERVIR SALDNAGLTASDVDAVEAHGTGTTLGDPIEAQALLAAYGHERPAHRPLRVGSLKSNIGHAGPAAGVAGVIKMVMAMRHGV LPRSLHIDEPTPQVDWSSGAVTLLTEPVDWPDSDRPRRAGVSAFGISGTNAHVILEQAPTQDPQQPAPPVPAAPWLLSAK TPAALRAQARRLHTHLARHPHPDPTDIAHALATTRTPHEHRAALVTDDHGTRGPALAALAEGAPDACLISGTALSKGRTV FVFPGQGSQWTGMGRELLHTSPEFAAYIAECETALNDFVDWSLTDVLRGTEGAPGYDRVDVVQPALFAVMVSLARLWQHH GIHPDAVIGHSQGEIAAAHIAGALSLQDAARIVALRSQALLPLAGLGGMTSLALPHDQALQLIQPWGQDLSIASVNGPHS TVVSGTTHALDELHTTCDTQGVRARRIPVDYASHSAQVESIRDTVLQAATGINPQPTTIPLYSTVTGQPIDGTQLDADYW YTNLRHTVRFEETTRALLGSGHRHFIETTAHPVLALALEETIEATGSDARVTGTLRRDHGDLTQLHTALATAWTHGIDVD WTAVLGDRRTPFELPTYAFQRQRYWLEPGAGVGVPVGGTSAEARFWDAVEDEDLEALVAAIGADGDDASWAGVLPALAGW RRRQREQSALDDLRYKVTWKPTAVADGASATGTWLVVVPESLAGGGWPVVVARAVDQAGGRPVVLSVDAADGADRSRLGL RIHEALGEGPVPDAVVSLLALDPSALPGLPDVPQALASTAALVQALLDLGLEARLWCVTSGAVSVSGADGPSAPEQAAVW GFGRVAGLEHPHLWAGLVDLPPEADERTAARLVGVLAGAGGEDQVALRSSGVFVRRLVRAPASEVPAVRSWKPGGTVLVT GGTGGLGRQVARWLARGGADHLLLVSRRGVDAPGADELVDELTDLGARVTVAACDVADRDAVQRLLSEQVPSDAPLTAVI HTAAVLDDGVIDSLSPERMEQVLRVKVGGAVHLYELTRESDLSAFVLFSSFGSTFGLPGLGNYAPGNAALEALAEQWRAE GRPATAVGWGTWAGGGMADGGVGERGRTHGIHELEPALATAALEQALERDESSPVIIDIDWERFAVAFHAKRPTRGFELV PEAQAALEAADGGPGPDGGAGDPSELLDRLAALPDAERDRALLEVVRGNAASVMSHGAMRTATLEAVEPTRAFRDLGFDS LMAVELRNRIGAATGLRLAPTLVFDHPTPEAVVRHLRAELGLEGDGAPDPVFDELDGLERALSSYTPDTDTRVKITKRLE SLLWEWTRSEADAPDPVDAADLAAVSDDEMFELIDRELGSALEHHHHHH Q03132 B6ZK67 2.3.1.94 Fab 1B2 heavy chain Homo sapiens 0.026447611 2 Escherichia coli BL21(DE3) LEVO MAEVQLVQSGGGLVQPGRSLRLSCTASGFTFGDYAMSWVRQAPGKGLEWVGFIRSKAYGGTTEYAASVKGRFTISRDDSK SIAYLQMNSLKTEDTAVYYCTRGGTLFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS WNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAALVPRGSAHHHHHHAA DYKDDDDKA Fab 1B2 light chain Homo sapiens 0.025715831999999997 2 Escherichia coli BL21(DE3) LEVO LFAIPLVVPFYSHSALDVVMTQSPLSLPVTPGEPASISCRSSQSLLHSNGYNYLDWYLQKPGQSPQLLIYLGSNRASGVP DRFSGSGSGTDFTLKISRVEAEDVGVYYCMQSLQTPRLTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNN FYPRGAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE 0.000507181 1 ATR 4'-PHOSPHOPANTETHEINE 0.000358348 1 PNS singleParticle particle 4.2 7.2 100.0 sodium chloride 100.0 citrate 10.0 HEPES 1.0 2-Acetaminoethyl-thio-3-oxobutanoate 0.4 methylmalonyl-CoA 0.8 NADP 0.8 TCEP Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY 120.0 GLOW DISCHARGE AIR 0.039 ETHANE 100 277 FEI VITROBOT MARK IV
Blot for 5 seconds before plunging in liquid ethane..
Size exclusion chromatography purified monodisperse holo-Lsd14-DD* + 1B2 complex was first incubated with KS substrate analog (2-Acetaminoethyl-thio-3-oxobutanoate) and TCEP at 30C for 20 minutes, followed by addition of NADP and methylmalonyl-CoA. The sample was further incubated at 30C for 15 minutes before applying to cryoEM grids.
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 1.0 2.7 79000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1 1278 2.2 53.0
Images were collected as 50 frame movies.
 1 397539 cryoSPARC 3.2.0 Patch CTF estimation (multi) RELION 3.1 PHASE FLIPPING AND AMPLITUDE CORRECTION Used Ab-initio Reconstruction job in cryoSPARC to generate starting map. C1 3.1 FSC 0.143 CUT-OFF RELION 3.1
Composite map was generated by combining the unsharpened focused maps for KS-KS'-ACP domains (EMD-24863), LDAT domains (EMD-24864), LD'AT' domains (EMD-24865), KR domain (EMD-24866), Fab + DD* (EMD-24867), and the unsharpened consensus map (EMD-24862) using Combine Focused Maps in Phenix.
397539 MAXIMUM LIKELIHOOD cryoSPARC 3.2.0 MAXIMUM LIKELIHOOD RELION 3.1 emd_24868.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 364 364 364 0 0 0 364 364 364 379.652 379.652 379.652 90.0 90.0 90.0 Z Y X -21.715669999999999 47.708660000000002 -0.0023788104 1.126138 1.043 1.043 1.043 7.0 AUTHOR Composite map 7S6B PDB experimental model 6C9U H PDB experimental model 6C9U L PDB experimental model OTHER
Model was manually rebuilt in Coot and phenix.real_space_refine was used for refinement.
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