data_27878 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; K1-K9 fragments of beta2-microglobulin ; _BMRB_accession_number 27878 _BMRB_flat_file_name bmr27878.str _Entry_type original _Submission_date 2019-04-16 _Accession_date 2019-04-16 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Muta Hiroya . . 2 So Masatomo . . 3 Sakurai Kazumasa . . 4 Goto Yuji . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 7 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 50 "13C chemical shifts" 60 "15N chemical shifts" 50 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-12-23 update BMRB 'update entry citation' 2019-11-22 original author 'original release' stop_ _Original_release_date 2019-04-16 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Amyloid formation under complicated conditions in which beta2-microglobulin coexists with its proteolytic fragments ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 31724398 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Muta Hiroya . . 2 So Masatomo . . 3 Sakurai Kazumasa . . 4 Kardos Jozsef . . 5 Naiki Hironobu . . 6 Goto Yuji . . stop_ _Journal_abbreviation Biochemistry _Journal_volume 58 _Journal_issue 49 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4925 _Page_last 4934 _Year 2019 _Details . loop_ _Keyword Amyloid stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'K1-K9 fragments' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label K1 $K1 K2 $K2 K4 $K4 K5 $K5 K7 $K7 K8 $K8 K9 $K9 stop_ _System_molecular_weight . _System_physical_state unfolded _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details 'proteolytic fragments of beta2-microglobulin' save_ ######################## # Monomeric polymers # ######################## save_K1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common K1 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence ; MIQRTPK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 0 MET 2 1 ILE 3 2 GLN 4 3 ARG 5 4 THR 6 5 PRO 7 6 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_K2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common K2 _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 13 _Mol_residue_sequence ; IQVYSRHPAENGK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 7 ILE 2 8 GLN 3 9 VAL 4 10 TYR 5 11 SER 6 12 ARG 7 13 HIS 8 14 PRO 9 15 ALA 10 16 GLU 11 17 ASN 12 18 GLY 13 19 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_K4 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common K4 _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 7 _Mol_residue_sequence ; NGERIEK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 42 ASN 2 43 GLY 3 44 GLU 4 45 ARG 5 46 ILE 6 47 GLU 7 48 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_K5 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common K5 _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 10 _Mol_residue_sequence ; VEHSDLSFSK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 49 VAL 2 50 GLU 3 51 HIS 4 52 SER 5 53 ASP 6 54 LEU 7 55 SER 8 56 PHE 9 57 SER 10 58 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_K7 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common K7 _Molecular_mass . _Mol_thiol_state 'all free' _Details . _Residue_count 16 _Mol_residue_sequence ; DEYACRVNHVTLSQPK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 76 ASP 2 77 GLU 3 78 TYR 4 79 ALA 5 80 CYS 6 81 ARG 7 82 VAL 8 83 ASN 9 84 HIS 10 85 VAL 11 86 THR 12 87 LEU 13 88 SER 14 89 GLN 15 90 PRO 16 91 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_K8 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common K8 _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 3 _Mol_residue_sequence ; IVK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 92 ILE 2 93 VAL 3 94 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_K9 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common K9 _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 5 _Mol_residue_sequence ; WDRDM ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 95 TRP 2 96 ASP 3 97 ARG 4 98 ASP 5 99 MET stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $K1 Human 9606 Eukaryota Metazoa Homo sapiens $K2 Human 9606 Eukaryota Metazoa Homo sapiens $K4 Human 9606 Eukaryota Metazoa Homo sapiens $K5 Human 9606 Eukaryota Metazoa Homo sapiens $K7 Human 9606 Eukaryota Metazoa Homo sapiens $K8 Human 9606 Eukaryota Metazoa Homo sapiens $K9 Human 9606 Eukaryota Metazoa Homo sapiens stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $K1 'recombinant technology' . Escherichia coli . pColdB2M $K2 'recombinant technology' . Escherichia coli . pColdB2M $K4 'recombinant technology' . Escherichia coli . pColdB2M $K5 'recombinant technology' . Escherichia coli . pColdB2M $K7 'recombinant technology' . Escherichia coli . pColdB2M $K8 'recombinant technology' . Escherichia coli . pColdB2M $K9 'recombinant technology' . Escherichia coli . pColdB2M stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $K1 50 uM '[U-99% 13C; U-99% 15N]' $K2 50 uM '[U-99% 13C; U-99% 15N]' $K4 50 uM '[U-99% 13C; U-99% 15N]' $K5 50 uM '[U-99% 13C; U-99% 15N]' $K7 50 uM '[U-99% 13C; U-99% 15N]' $K8 50 uM '[U-99% 13C; U-99% 15N]' $K9 50 uM '[U-99% 13C; U-99% 15N]' HCl 10 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' D2O 10 % '[U-99% 2H]' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 950 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_HNCA_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label $sample_1 save_ save_3D_HNCO_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.1 . M pH 1.5 . pH pressure 1 . atm temperature 310 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '3D HNCA' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name K1 _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 0 1 MET CA C 54.918 . . 2 1 2 ILE H H 8.516 . . 3 1 2 ILE CA C 61.166 . . 4 1 2 ILE N N 124.368 . . 5 2 3 GLN H H 8.504 . . 6 2 3 GLN CA C 55.461 . . 7 2 3 GLN N N 125.674 . . 8 3 4 ARG H H 8.453 . . 9 3 4 ARG CA C 55.9 . . 10 3 4 ARG N N 123.854 . . 11 4 5 THR H H 8.215 . . 12 4 5 THR CA C 59.808 . . 13 4 5 THR N N 118.502 . . 14 5 6 PRO CA C 63.081 . . 15 6 7 LYS H H 8.399 . . 16 6 7 LYS CA C 55.374 . . 17 6 7 LYS N N 122.193 . . stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '3D HNCA' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name K2 _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 7 1 ILE CA C 60.391 . . 2 8 2 GLN H H 8.547 . . 3 8 2 GLN CA C 55.454 . . 4 8 2 GLN N N 124.832 . . 5 9 3 VAL H H 8.223 . . 6 9 3 VAL CA C 62.094 . . 7 9 3 VAL N N 122.935 . . 8 10 4 TYR H H 8.32 . . 9 10 4 TYR CA C 57.691 . . 10 10 4 TYR N N 124.721 . . 11 11 5 SER H H 8.108 . . 12 11 5 SER CA C 57.744 . . 13 11 5 SER N N 118.022 . . 14 12 6 ARG H H 8.207 . . 15 12 6 ARG CA C 55.977 . . 16 12 6 ARG N N 122.8 . . 17 13 7 HIS H H 8.391 . . 18 13 7 HIS CA C 53.128 . . 19 13 7 HIS N N 119.886 . . 20 14 8 PRO CA C 63.165 . . 21 15 9 ALA H H 8.42 . . 22 15 9 ALA CA C 52.449 . . 23 15 9 ALA N N 124.521 . . 24 16 10 GLU H H 8.309 . . 25 16 10 GLU CA C 55.526 . . 26 16 10 GLU N N 119.635 . . 27 17 11 ASN H H 8.419 . . 28 17 11 ASN CA C 53.302 . . 29 17 11 ASN N N 119.605 . . 30 18 12 GLY H H 8.304 . . 31 18 12 GLY CA C 45.236 . . 32 18 12 GLY N N 109.032 . . 33 19 13 LYS H H 8.06 . . 34 19 13 LYS CA C 55.098 . . 35 19 13 LYS N N 120.969 . . stop_ save_ save_assigned_chem_shift_list_1_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '3D HNCA' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name K4 _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 42 1 ASN CA C 52.668 . . 2 43 2 GLY H H 8.63 . . 3 43 2 GLY CA C 45.161 . . 4 43 2 GLY N N 109.597 . . 5 44 3 GLU H H 8.238 . . 6 44 3 GLU CA C 55.675 . . 7 44 3 GLU N N 120.052 . . 8 45 4 ARG H H 8.363 . . 9 45 4 ARG CA C 56.069 . . 10 45 4 ARG N N 122.884 . . 11 46 5 ILE H H 8.19 . . 12 46 5 ILE CA C 60.874 . . 13 46 5 ILE N N 123.254 . . 14 47 6 GLU H H 8.382 . . 15 47 6 GLU CA C 55.319 . . 16 47 6 GLU N N 125.321 . . 17 48 7 LYS H H 8.42 . . 18 48 7 LYS CA C 55.355 . . 19 48 7 LYS N N 123.981 . . stop_ save_ save_assigned_chem_shift_list_1_4 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '3D HNCA' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name K5 _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 49 1 VAL CA C 61.082 . . 2 50 2 GLU H H 8.623 . . 3 50 2 GLU CA C 55.662 . . 4 50 2 GLU N N 124.447 . . 5 51 3 HIS H H 8.674 . . 6 51 3 HIS CA C 55.207 . . 7 51 3 HIS N N 120.695 . . 8 52 4 SER H H 8.373 . . 9 52 4 SER CA C 58.132 . . 10 52 4 SER N N 117.244 . . 11 53 5 ASP H H 8.57 . . 12 53 5 ASP CA C 52.862 . . 13 53 5 ASP N N 121.284 . . 14 54 6 LEU H H 8.11 . . 15 54 6 LEU CA C 55.244 . . 16 54 6 LEU N N 122.453 . . 17 55 7 SER H H 8.04 . . 18 55 7 SER CA C 58.156 . . 19 55 7 SER N N 115.92 . . 20 56 8 PHE H H 8.075 . . 21 56 8 PHE CA C 57.575 . . 22 56 8 PHE N N 121.939 . . 23 57 9 SER H H 8.093 . . 24 57 9 SER CA C 58.138 . . 25 57 9 SER N N 117.385 . . 26 58 10 LYS H H 8.221 . . 27 58 10 LYS CA C 55.298 . . 28 58 10 LYS N N 123.429 . . stop_ save_ save_assigned_chem_shift_list_1_5 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '3D HNCA' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name K7 _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 76 1 ASP CA C 52.236 . . 2 77 2 GLU H H 8.659 . . 3 77 2 GLU CA C 56.071 . . 4 77 2 GLU N N 121.274 . . 5 78 3 TYR H H 8.132 . . 6 78 3 TYR CA C 57.721 . . 7 78 3 TYR N N 121.257 . . 8 79 4 ALA H H 8.079 . . 9 79 4 ALA CA C 52.402 . . 10 79 4 ALA N N 125.394 . . 11 80 5 CYS H H 8.14 . . 12 80 5 CYS CA C 58.406 . . 13 80 5 CYS N N 118.426 . . 14 81 6 ARG H H 8.329 . . 15 81 6 ARG CA C 56.17 . . 16 81 6 ARG N N 123.825 . . 17 82 7 VAL H H 8.039 . . 18 82 7 VAL CA C 62.124 . . 19 82 7 VAL N N 121.218 . . 20 83 8 ASN H H 8.408 . . 21 83 8 ASN CA C 52.968 . . 22 83 8 ASN N N 122.732 . . 23 84 9 HIS H H 8.414 . . 24 84 9 HIS CA C 55.257 . . 25 84 9 HIS N N 119.556 . . 26 85 10 VAL H H 8.17 . . 27 85 10 VAL CA C 62.396 . . 28 85 10 VAL N N 122.111 . . 29 86 11 THR H H 8.286 . . 30 86 11 THR CA C 61.849 . . 31 86 11 THR N N 119.683 . . 32 87 12 LEU H H 8.309 . . 33 87 12 LEU CA C 54.994 . . 34 87 12 LEU N N 125.852 . . 35 88 13 SER H H 8.229 . . 36 88 13 SER CA C 58.084 . . 37 88 13 SER N N 117.054 . . 38 90 15 PRO CA C 63.081 . . 39 91 16 LYS H H 8.439 . . 40 91 16 LYS CA C 55.305 . . 41 91 16 LYS N N 122.09 . . stop_ save_ save_assigned_chem_shift_list_1_6 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '3D HNCA' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name K8 _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 92 1 ILE CA C 60.248 . . 2 93 2 VAL H H 8.369 . . 3 93 2 VAL CA C 62.267 . . 4 93 2 VAL N N 125.141 . . 5 94 3 LYS H H 8.332 . . 6 94 3 LYS CA C 56.278 . . 7 94 3 LYS N N 126.104 . . stop_ save_ save_assigned_chem_shift_list_1_7 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '3D HNCA' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name K9 _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 95 1 TRP CA C 56.199 . . 2 96 2 ASP H H 8.543 . . 3 96 2 ASP CA C 52.611 . . 4 96 2 ASP N N 122.084 . . 5 97 3 ARG H H 8.115 . . 6 97 3 ARG CA C 56.352 . . 7 97 3 ARG N N 121.94 . . 8 98 4 ASP H H 8.248 . . 9 98 4 ASP CA C 52.894 . . 10 98 4 ASP N N 119.217 . . 11 99 5 MET H H 8.153 . . 12 99 5 MET CA C 54.431 . . 13 99 5 MET N N 121.082 . . stop_ save_