2026-04-22 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY atom_site citation citation_author em_admin entity entity_poly entity_poly_seq entity_src_gen pdbx_modification_feature pdbx_poly_seq_scheme pdbx_struct_mod_residue pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues struct_conf struct_conn struct_mon_prot_cis struct_ref_seq struct_ref_seq_dif struct_sheet_range _atom_site.label_seq_id _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update _entity.formula_weight _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_src_gen.pdbx_end_seq_num _pdbx_modification_feature.label_seq_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _struct_conf.beg_label_seq_id _struct_conf.end_label_seq_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_label_seq_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_label_seq_id STRUCTURE_SUMMARY citation citation_author em_admin entity entity_poly entity_src_gen struct_ref_seq struct_ref_seq_dif _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update _entity.formula_weight _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_src_gen.pdbx_end_seq_num _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end RCSB RCSB 2026-01-28 2026-04-08 2026-04-08 2026-04-22 National Science Foundation (NSF, United States) IOS 2152548 United States CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP Beamer LJ Samarakoon V Buckley DP Owuocha LF Durie CL Mitchum MG enzyme, missense variant, TRANSFERASE Samarakoon V Buckley DP Owuocha LF Durie CL Mitchum MG Beamer LJ Oligomeric defects in soybean serine hydroxymethyltransferase 8: tetramer destabilization by A149T and other variants associated with soybean cyst nematode resistance. Febs J. UK 2026 41914311 doi:10.1111/febs.70528 1742-464X 10nm FULLOVERLAP EMDB EMD-75307 associated EM volume
CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
 A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP 0 1 Glycine max SHMT Cytoplasm 0.1036 Serine hydroxymethyltransferase Glycine max 0.054951082 2 Escherichia coli LEVO MGMHHHHHHSSGVDLGTENLYFQSNMDPVSVWGNTPLATVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSAL TNKYSEGMPGNRYYGGNEYIDQIENLCRSRALQAFHLDAQSWGVNVQPYSGSPANFAAYTAVLNPHDRIMGLDLPSGGHL THGYYTSGGKKISTTSIYFESLPYKVNSTTGYIDYDRLEEKALDFRPKLIICGGSAYPRDWDYKRFREVADKCGALLLCD MAHTSGLVAAQEVNSPFEYCDIVTTTTH(LLP)SLRGPRAGMIFYRKGPKPPKKGQPENAVYDFEDKINFAVFPSLQGGP HNHQIGALAVALKQAASPGFKAYAKQVKANAVALGKYLMGKGYSLVTGGTENHLVLWDLRPLGLTGNKVEKLCDLCNITV NKNAVFGDSSALAPGGVRIGAPAMTSRGLVEKDFEQIGEFLHRAVTLTLEIQKEHGKLLKDFNKGLVNNKAIEDLKADVE KFSALFDMPGFLVSEMKYKD K4FZF8 2.1.2.1 singleParticle particle 0.25 7.5
50mM HEPES, 150mM NaCl, 0.5mM TCEP
 Quantifoil R2/2 COPPER 300 CARBON HOLEY GLOW DISCHARGE
15mA of current used
 ETHANE 100 277.15 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.6 2.3000000000000003 165000.0 98700.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum SerialEM FEI FALCON I (4k x 4k) 1 14550 0.951 80.0 1 5739678
Particles selected after 2 rounds of 2D template selections
 cryoSPARC v4.7.1 PHASE FLIPPING AND AMPLITUDE CORRECTION 9YBZ
Chains A and B only
 1 C2 FOURIER SPACE 2.92 FSC 0.143 CUT-OFF cryoSPARC v4.7.1 71315 MAXIMUM LIKELIHOOD cryoSPARC v4.7.1 MAXIMUM LIKELIHOOD cryoSPARC v4.7.1 emd_75307.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 0 0 0 224 224 224 226.7776 226.7776 226.7776 90.0 90.0 90.0 X Y Z -0.29977936 0.51120085 0.00034820847 0.012881589 1.0124 1.0124 1.0124 0.05 AUTHOR Sharpened map 9YBZ A 1-471 PDB experimental model 9YBZ B 1-471 PDB experimental model RIGID BODY FIT UCSF ChimeraX 1.11.1 Correlation coefficient REAL 81.409999999999997 emd_75307_msk_1.map emd_75307_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 0 0 0 224 224 224 226.7776 226.7776 226.7776 90.0 90.0 90.0 X Y Z -0.101902686 0.21752083 0.00034820873 0.006405731 1.0124 1.0124 1.0124 AUTHOR Gaussian filtered map at SD 1 emd_75307_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 0 0 0 224 224 224 226.7776 226.7776 226.7776 90.0 90.0 90.0 X Y Z -0.10083633 0.23538734 0.00030455083 0.008736619 1.0124 1.0124 1.0124 AUTHOR Half map B emd_75307_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 0 0 0 224 224 224 226.7776 226.7776 226.7776 90.0 90.0 90.0 X Y Z -0.09322897 0.220458 0.00029994157 0.008669786 1.0124 1.0124 1.0124 AUTHOR Half map A