data_27980 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 13C-chemical-shifts-for_SPA_amyloid-beta42_oligomer ; _BMRB_accession_number 27980 _BMRB_flat_file_name bmr27980.str _Entry_type original _Submission_date 2019-07-22 _Accession_date 2019-07-22 _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 Ishii Yoshitaka . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 74 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-02-05 update BMRB 'update entry citation' 2019-11-21 original author 'original release' stop_ _Original_release_date 2019-07-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR-based site-resolved profiling of beta-amyloid misfolding: structural transition from pathologically relevant spherical oligomer to fibril ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 31771980 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Xiao Yiling . . 2 Matsuda Isamu . . 3 Inoue Masafumi . . 4 Sasahara Tomoya . . 5 Hoshi Minako . . 6 Ishii Yoshitaka . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 295 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 458 _Page_last 467 _Year 2020 _Details . loop_ _Keyword ASPD Abeta42 amyloid oligomer 'solid-state NMR' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name SPA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label '42-residue amyloid-beta' $SPA-amyloid_beta_oligomer stop_ _System_molecular_weight . _System_physical_state na _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_SPA-amyloid_beta_oligomer _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common SPA-amyloid_beta_oligomer _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 42 _Mol_residue_sequence ; DAEFRHDSGYEVHHQKLVFF AEDVGSNKGAIIGLMVGGVV IA ; loop_ _Residue_seq_code _Residue_label 1 ASP 2 ALA 3 GLU 4 PHE 5 ARG 6 HIS 7 ASP 8 SER 9 GLY 10 TYR 11 GLU 12 VAL 13 HIS 14 HIS 15 GLN 16 LYS 17 LEU 18 VAL 19 PHE 20 PHE 21 ALA 22 GLU 23 ASP 24 VAL 25 GLY 26 SER 27 ASN 28 LYS 29 GLY 30 ALA 31 ILE 32 ILE 33 GLY 34 LEU 35 MET 36 VAL 37 GLY 38 GLY 39 VAL 40 VAL 41 ILE 42 ALA 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 _Details $SPA-amyloid_beta_oligomer Human 9606 Eukaryota Metazoa Homo sapiens 'Chemically synthesized' 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 $SPA-amyloid_beta_oligomer 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solid _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SPA-amyloid_beta_oligomer 20 '% w/w' '[U-98% 13C; U-98% 15N]' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 400 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_13C-13C_correlation_MAS_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C correlation MAS' _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 pressure 1 . atm temperature 293 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'DSS reference' 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 C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 13C-13C correlation MAS' 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 '42-residue amyloid-beta' _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 2 2 ALA C C 175.91 0.2 . 2 2 2 ALA CA C 52.81 0.2 . 3 2 2 ALA CB C 19.81 0.2 . 4 4 4 PHE CA C 58.21 0.2 . 5 4 4 PHE CB C 41.61 0.2 . 6 9 9 GLY C C 173.11 0.2 . 7 9 9 GLY CA C 45.81 0.2 . 8 12 12 VAL C C 175.91 0.2 . 9 12 12 VAL CA C 62.71 0.2 . 10 12 12 VAL CB C 33.01 0.2 . 11 13 13 HIS C C 173.61 0.2 . 12 13 13 HIS CA C 54.51 0.2 . 13 13 13 HIS CB C 32.41 0.2 . 14 14 14 HIS C C 174.71 0.2 . 15 14 14 HIS CA C 54.91 0.2 . 16 14 14 HIS CB C 32.81 0.2 . 17 17 17 LEU C C 173.21 0.2 . 18 17 17 LEU CA C 54.11 0.2 . 19 17 17 LEU CB C 45.31 0.2 . 20 18 18 VAL C C 174.11 0.2 . 21 18 18 VAL CA C 60.71 0.2 . 22 18 18 VAL CB C 35.71 0.2 . 23 19 19 PHE C C 173.41 0.2 . 24 19 19 PHE CA C 56.11 0.2 . 25 19 19 PHE CB C 43.31 0.2 . 26 20 20 PHE C C 173.51 0.2 . 27 20 20 PHE CA C 56.71 0.2 . 28 20 20 PHE CB C 44.71 0.2 . 29 21 21 ALA C C 175.21 0.2 . 30 21 21 ALA CA C 50.71 0.2 . 31 21 21 ALA CB C 23.41 0.2 . 32 23 23 ASP C C 176.51 0.2 . 33 23 23 ASP CA C 53.11 0.2 . 34 23 23 ASP CB C 42.31 0.2 . 35 24 24 VAL C C 176.01 0.2 . 36 24 24 VAL CA C 64.41 0.2 . 37 24 24 VAL CB C 32.31 0.2 . 38 25 25 GLY C C 173.01 0.2 . 39 25 25 GLY CA C 45.91 0.2 . 40 26 26 SER C C 174.61 0.2 . 41 26 26 SER CA C 57.41 0.2 . 42 26 26 SER CB C 63.91 0.2 . 43 29 29 GLY C C 173.21 0.2 . 44 29 29 GLY CA C 45.41 0.2 . 45 30 30 ALA C C 175.11 0.2 . 46 30 30 ALA CA C 51.11 0.2 . 47 30 30 ALA CB C 23.01 0.2 . 48 31 31 ILE C C 174.51 0.2 . 49 31 31 ILE CA C 60.41 0.2 . 50 31 31 ILE CB C 41.61 0.2 . 51 32 32 ILE C C 174.21 0.2 . 52 32 32 ILE CA C 59.91 0.2 . 53 32 32 ILE CB C 41.91 0.2 . 54 33 33 GLY C C 171.11 0.2 . 55 33 33 GLY CA C 44.61 0.2 . 56 34 34 LEU C C 174.41 0.2 . 57 34 34 LEU CA C 53.71 0.2 . 58 34 34 LEU CB C 46.31 0.2 . 59 36 36 VAL C C 174.31 0.2 . 60 36 36 VAL CA C 60.11 0.2 . 61 36 36 VAL CB C 35.81 0.2 . 62 37 37 GLY C C 171.51 0.2 . 63 37 37 GLY CA C 45.41 0.2 . 64 38 38 GLY C C 171.31 0.2 . 65 38 38 GLY CA C 46.01 0.2 . 66 39 39 VAL C C 174.01 0.2 . 67 39 39 VAL CA C 59.81 0.2 . 68 39 39 VAL CB C 36.51 0.2 . 69 40 40 VAL C C 174.41 0.2 . 70 40 40 VAL CA C 61.01 0.2 . 71 40 40 VAL CB C 35.31 0.2 . 72 41 41 ILE C C 174.21 0.2 . 73 41 41 ILE CA C 61.21 0.2 . 74 41 41 ILE CB C 40.81 0.2 . stop_ save_