data_7Z07 # _entry.id 7Z07 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.364 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 7Z07 pdb_00007z07 10.2210/pdb7z07/pdb WWPDB D_1292121283 ? ? BMRB 34711 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'Solution NMR structure of N-acetylglucosaminyltransferase V (GnTV) G26P mutant TMD' _pdbx_database_related.db_id 34711 _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 7Z07 _pdbx_database_status.recvd_initial_deposition_date 2022-02-22 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs REL _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Silber, M.' 1 ? 'Muhle-Goll, C.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Sci Rep' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2045-2322 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 12 _citation.language ? _citation.page_first 20987 _citation.page_last 20987 _citation.title 'Helical stability of the GnTV transmembrane domain impacts on SPPL3 dependent cleavage.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41598-022-24772-8 _citation.pdbx_database_id_PubMed 36470941 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Papadopoulou, A.A.' 1 ? primary 'Stelzer, W.' 2 ? primary 'Silber, M.' 3 ? primary 'Schlosser, C.' 4 ? primary 'Spitz, C.' 5 ? primary 'Haug-Kroper, M.' 6 ? primary 'Straub, T.' 7 ? primary 'Muller, S.A.' 8 ? primary 'Lichtenthaler, S.F.' 9 ? primary 'Muhle-Goll, C.' 10 ? primary 'Langosch, D.' 11 ? primary 'Fluhrer, R.' 12 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A' _entity.formula_weight 3591.487 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec 2.4.1.155 _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name ;Alpha-mannoside beta-1,6-N-acetylglucosaminyltransferase V,GlcNAc-T V,GNT-V,Mannoside acetylglucosaminyltransferase 5,N-acetylglucosaminyl-transferase V ; # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code KKKLGFFLVTFGFIWPMMLLHFTIQQRKK _entity_poly.pdbx_seq_one_letter_code_can KKKLGFFLVTFGFIWPMMLLHFTIQQRKK _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 LYS n 1 2 LYS n 1 3 LYS n 1 4 LEU n 1 5 GLY n 1 6 PHE n 1 7 PHE n 1 8 LEU n 1 9 VAL n 1 10 THR n 1 11 PHE n 1 12 GLY n 1 13 PHE n 1 14 ILE n 1 15 TRP n 1 16 PRO n 1 17 MET n 1 18 MET n 1 19 LEU n 1 20 LEU n 1 21 HIS n 1 22 PHE n 1 23 THR n 1 24 ILE n 1 25 GLN n 1 26 GLN n 1 27 ARG n 1 28 LYS n 1 29 LYS n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 29 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name human _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code MGT5A_HUMAN _struct_ref.pdbx_db_accession Q09328 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code KLGFFLVTFGFIWGMMLLHFTIQQR _struct_ref.pdbx_align_begin 13 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7Z07 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 3 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 27 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q09328 _struct_ref_seq.db_align_beg 13 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 37 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 13 _struct_ref_seq.pdbx_auth_seq_align_end 37 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 7Z07 LYS A 1 ? UNP Q09328 ? ? 'expression tag' 11 1 1 7Z07 LYS A 2 ? UNP Q09328 ? ? 'expression tag' 12 2 1 7Z07 PRO A 16 ? UNP Q09328 GLY 26 'engineered mutation' 26 3 1 7Z07 LYS A 28 ? UNP Q09328 ? ? 'expression tag' 38 4 1 7Z07 LYS A 29 ? UNP Q09328 ? ? 'expression tag' 39 5 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 '2D 1H-1H NOESY' 1 isotropic 2 1 1 '2D 1H-1H TOCSY' 1 isotropic 3 1 1 '2D 1H-13C HSQC' 1 isotropic 4 1 1 '2D 1H-15N HSQC' 1 isotropic # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 300 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength 1 _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units 'Not defined' _pdbx_nmr_exptl_sample_conditions.label GNTV_G26P _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '0.5 mM GNTV_G26P, trifluoroethanol/water' _pdbx_nmr_sample_details.solvent_system trifluoroethanol/water _pdbx_nmr_sample_details.label GNTV_G26P _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details '80% TFE, 20% H2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model 'AVANCE III' _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.details 'cry probe' # _pdbx_nmr_refine.entry_id 7Z07 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 7Z07 _pdbx_nmr_ensemble.conformers_calculated_total_number 400 _pdbx_nmr_ensemble.conformers_submitted_total_number 50 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.representative_conformer ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 7Z07 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 refinement CNS ? 'Brunger A. T. et.al.' 2 'structure calculation' ARIA ? ;Linge, O'Donoghue and Nilges ; 3 'chemical shift assignment' 'CcpNmr Analysis' ? 'Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED' 4 'peak picking' 'CcpNmr Analysis' ? 'Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED' # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7Z07 _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7Z07 _struct.title 'Solution NMR structure of N-acetylglucosaminyltransferase V (GnTV) G26P mutant TMD' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7Z07 _struct_keywords.text 'GnTV, TMD, Golgi, Glycosyltransferase, intramembrane, SPPL3, MEMBRANE PROTEIN' _struct_keywords.pdbx_keywords 'MEMBRANE PROTEIN' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id AA1 _struct_conf.beg_label_comp_id LYS _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 1 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id LYS _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 29 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id LYS _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 11 _struct_conf.end_auth_comp_id LYS _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 39 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 29 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 7Z07 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C H N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 LYS 1 11 11 LYS LYS A . n A 1 2 LYS 2 12 12 LYS LYS A . n A 1 3 LYS 3 13 13 LYS LYS A . n A 1 4 LEU 4 14 14 LEU LEU A . n A 1 5 GLY 5 15 15 GLY GLY A . n A 1 6 PHE 6 16 16 PHE PHE A . n A 1 7 PHE 7 17 17 PHE PHE A . n A 1 8 LEU 8 18 18 LEU LEU A . n A 1 9 VAL 9 19 19 VAL VAL A . n A 1 10 THR 10 20 20 THR THR A . n A 1 11 PHE 11 21 21 PHE PHE A . n A 1 12 GLY 12 22 22 GLY GLY A . n A 1 13 PHE 13 23 23 PHE PHE A . n A 1 14 ILE 14 24 24 ILE ILE A . n A 1 15 TRP 15 25 25 TRP TRP A . n A 1 16 PRO 16 26 26 PRO PRO A . n A 1 17 MET 17 27 27 MET MET A . n A 1 18 MET 18 28 28 MET MET A . n A 1 19 LEU 19 29 29 LEU LEU A . n A 1 20 LEU 20 30 30 LEU LEU A . n A 1 21 HIS 21 31 31 HIS HIS A . n A 1 22 PHE 22 32 32 PHE PHE A . n A 1 23 THR 23 33 33 THR THR A . n A 1 24 ILE 24 34 34 ILE ILE A . n A 1 25 GLN 25 35 35 GLN GLN A . n A 1 26 GLN 26 36 36 GLN GLN A . n A 1 27 ARG 27 37 37 ARG ARG A . n A 1 28 LYS 28 38 38 LYS LYS A . n A 1 29 LYS 29 39 39 LYS LYS A . n # _pdbx_contact_author.id 3 _pdbx_contact_author.email claudia.muhle-goll@kit.edu _pdbx_contact_author.name_first Claudia _pdbx_contact_author.name_last Muhle-Goll _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-9474-9041 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2022-12-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_nmr_exptl_sample.solution_id 1 _pdbx_nmr_exptl_sample.component GNTV_G26P _pdbx_nmr_exptl_sample.concentration 0.5 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mM _pdbx_nmr_exptl_sample.isotopic_labeling none # _pdbx_audit_support.funding_organization 'German Research Foundation (DFG)' _pdbx_audit_support.country Germany _pdbx_audit_support.grant_number FOR2290 _pdbx_audit_support.ordinal 1 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'NMR Distance Restraints' _pdbx_struct_assembly_auth_evidence.details ? #