data_34454 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; A New Structural Model of Abeta(1-40) Fibrils ; _BMRB_accession_number 34454 _BMRB_flat_file_name bmr34454.str _Entry_type original _Submission_date 2019-11-21 _Accession_date 2019-11-21 _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 Bertini I. . . 2 Gonnelli L. . . 3 Luchinat C. . . 4 Mao J. . . 5 Nesi A. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 159 "15N chemical shifts" 38 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-08-16 update BMRB 'update entry citation' 2020-07-18 original author 'original release' stop_ _Original_release_date 2020-07-14 save_ ############################# # Citation for this entry # ############################# save_citation_2 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Mixing Abeta(1-40) and Abeta(1-42) peptides generates unique amyloid fibrils ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 32749391 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Cerofolini L. . . 2 Ravera E. . . 3 Bologna S. . . 4 Wiglenda T. . . 5 Boddrich A. . . 6 Bettina P. . . 7 Benilova I. . . 8 Korsak M. . . 9 Gallo G. . . 10 Rizzo D. . . 11 Gonnelli L. . . 12 Fragai M. . . 13 'De Strooper' B. . . 14 Wanker E. E. . 15 Luchinat C. . . stop_ _Journal_abbreviation 'Chem. Commun. (Camb.)' _Journal_name_full 'Chemical communications (Cambridge, England)' _Journal_volume 56 _Journal_issue 62 _Journal_ISSN 1364-548X _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 8830 _Page_last 8833 _Year 2020 _Details . save_ ####################################### # Cited references within the entry # ####################################### save_citation_1 _Saveframe_category citation _Citation_full . _Citation_title ; A new structural model of Abeta40 fibrils. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21882806 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bertini I. . . 2 Gonnelli L. . . 3 Luchinat C. . . 4 Mao J. . . 5 Nesi A. . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full . _Journal_volume 133 _Journal_issue 40 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 16013 _Page_last 16022 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Amyloid beta A4 protein' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label unit_1 $entity_1 unit_2 $entity_1 unit_3 $entity_1 unit_4 $entity_1 unit_5 $entity_1 unit_6 $entity_1 unit_7 $entity_1 unit_8 $entity_1 unit_9 $entity_1 unit_10 $entity_1 unit_11 $entity_1 unit_12 $entity_1 unit_13 $entity_1 unit_14 $entity_1 unit_15 $entity_1 unit_16 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass 4335.852 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 40 _Mol_residue_sequence ; DAEFRHDSGYEVHHQKLVFF AEDVGSNKGAIIGLMVGGVV ; 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 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 _Gene_mnemonic $entity_1 Human 9606 Eukaryota Metazoa Homo sapiens 'APP, A4, AD1' 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 $entity_1 'recombinant technology' . Escherichia coli . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type fiber _Details '100 uM [U-100% 13C; U-100% 15N] Amyloid beta peptide 1-40, 50 mM ammonium acetate, H2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 100 uM '[U-100% 13C; U-100% 15N]' 'ammonium acetate' 50 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name TopSpin _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CARA _Version . loop_ _Vendor _Address _Electronic_address 'Keller and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name Sparky _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name HADDOCK _Version . loop_ _Vendor _Address _Electronic_address Bonvin . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE II' _Field_strength 700 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE III' _Field_strength 850 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_15N-13C_NCA_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C NCA' _Sample_label $sample_1 save_ save_2D_15N-13C_NCO_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C NCO' _Sample_label $sample_1 save_ save_3D_NCACX_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D NCACX' _Sample_label $sample_1 save_ save_3D_NCOCX_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D NCOCX' _Sample_label $sample_1 save_ save_3D_CANCO_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CANCO' _Sample_label $sample_1 save_ save_2D_13C-13C_DARR_(<100_ms)_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR (<100 ms)' _Sample_label $sample_1 save_ save_2D_15N-13C_PAIN_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C PAIN' _Sample_label $sample_1 save_ save_2D_13C-13C_DARR/PDSD_(>100_ms)_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR/PDSD (>100 ms)' _Sample_label $sample_1 save_ save_2D_13C-13C_PAR_(10-15_ms)_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C PAR (10-15 ms)' _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 pH 8.5 . pH pressure 1 . atm temperature 283 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 TSP C 13 'methyl carbons' ppm 0.000 external direct . . . 1 'liquid anhydrous ammonia' N 15 nitrogen ppm 0.000 external direct . . . 1 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 15N-13C NCA' '2D 15N-13C NCO' '3D NCACX' '3D NCOCX' '3D CANCO' '2D 13C-13C DARR (<100 ms)' '2D 15N-13C PAIN' '2D 13C-13C DARR/PDSD (>100 ms)' '2D 13C-13C PAR (10-15 ms)' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name unit_1 _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 173.900 0.3 1 2 2 2 ALA CA C 50.000 0.3 1 3 2 2 ALA CB C 22.100 0.3 1 4 3 3 GLU C C 172.600 0.3 1 5 3 3 GLU CA C 53.400 0.3 1 6 3 3 GLU CB C 32.400 0.3 1 7 3 3 GLU N N 118.100 0.3 1 8 4 4 PHE C C 173.300 0.3 1 9 4 4 PHE CA C 55.400 0.3 1 10 4 4 PHE CB C 40.200 0.3 1 11 4 4 PHE CG C 136.700 0.3 1 12 4 4 PHE N N 122.700 0.3 1 13 5 5 ARG C C 172.400 0.3 1 14 5 5 ARG CA C 53.700 0.3 1 15 5 5 ARG CB C 32.400 0.3 1 16 5 5 ARG CG C 26.300 0.3 1 17 5 5 ARG CD C 42.700 0.3 1 18 5 5 ARG N N 124.400 0.3 1 19 6 6 HIS C C 173.600 0.3 1 20 6 6 HIS CA C 53.800 0.3 1 21 6 6 HIS CB C 34.000 0.3 1 22 6 6 HIS N N 125.000 0.3 1 23 7 7 ASP C C 174.998 0.3 1 24 7 7 ASP CA C 52.400 0.3 1 25 7 7 ASP CB C 42.700 0.3 1 26 7 7 ASP CG C 179.700 0.3 1 27 7 7 ASP N N 125.700 0.3 1 28 8 8 SER C C 172.493 0.3 1 29 8 8 SER CA C 55.997 0.3 1 30 8 8 SER CB C 65.696 0.3 1 31 8 8 SER N N 118.007 0.3 1 32 9 9 GLY C C 170.500 0.3 1 33 9 9 GLY CA C 43.688 0.3 1 34 9 9 GLY N N 111.798 0.3 1 35 10 10 TYR C C 174.188 0.3 1 36 10 10 TYR CA C 56.541 0.3 1 37 10 10 TYR CB C 41.300 0.3 1 38 10 10 TYR CG C 127.000 0.3 1 39 10 10 TYR N N 120.082 0.3 1 40 11 11 GLU C C 173.000 0.3 1 41 11 11 GLU CA C 54.200 0.3 1 42 11 11 GLU CB C 31.300 0.3 1 43 11 11 GLU CG C 37.400 0.3 1 44 11 11 GLU CD C 181.500 0.3 1 45 11 11 GLU N N 127.816 0.3 1 46 12 12 VAL C C 173.500 0.3 1 47 12 12 VAL CA C 59.500 0.3 1 48 12 12 VAL CB C 33.600 0.3 1 49 12 12 VAL CG1 C 19.600 0.3 1 50 12 12 VAL CG2 C 19.400 0.3 1 51 12 12 VAL N N 126.300 0.3 1 52 13 13 HIS C C 173.300 0.3 1 53 13 13 HIS CA C 53.500 0.3 1 54 13 13 HIS CB C 33.800 0.3 1 55 13 13 HIS CD2 C 115.200 0.3 1 56 13 13 HIS N N 124.400 0.3 1 57 14 14 HIS C C 173.200 0.3 1 58 14 14 HIS CA C 53.500 0.3 1 59 14 14 HIS CB C 36.000 0.3 1 60 14 14 HIS N N 125.100 0.3 1 61 15 15 GLN C C 172.700 0.3 1 62 15 15 GLN CA C 53.900 0.3 1 63 15 15 GLN CB C 31.300 0.3 1 64 15 15 GLN CG C 33.200 0.3 1 65 15 15 GLN CD C 176.500 0.3 1 66 15 15 GLN N N 126.300 0.3 1 67 16 16 LYS C C 172.700 0.3 1 68 16 16 LYS CA C 53.900 0.3 1 69 16 16 LYS CB C 33.800 0.3 1 70 16 16 LYS CG C 26.500 0.3 1 71 16 16 LYS CD C 28.600 0.3 1 72 16 16 LYS CE C 41.200 0.3 1 73 16 16 LYS N N 128.900 0.3 1 74 17 17 LEU C C 173.900 0.3 1 75 17 17 LEU CA C 52.100 0.3 1 76 17 17 LEU CB C 43.300 0.3 1 77 17 17 LEU CG C 26.700 0.3 1 78 17 17 LEU CD1 C 24.700 0.3 1 79 17 17 LEU CD2 C 19.000 0.3 1 80 17 17 LEU N N 124.900 0.3 1 81 18 18 VAL C C 171.800 0.3 1 82 18 18 VAL CA C 60.198 0.3 1 83 18 18 VAL CB C 33.700 0.3 1 84 18 18 VAL CG1 C 21.100 0.3 1 85 18 18 VAL CG2 C 20.500 0.3 1 86 18 18 VAL N N 124.353 0.3 1 87 19 19 PHE C C 171.900 0.3 1 88 19 19 PHE CA C 50.596 0.3 1 89 19 19 PHE CB C 39.400 0.3 1 90 19 19 PHE CG C 137.000 0.3 1 91 19 19 PHE CD1 C 129.100 0.3 1 92 19 19 PHE N N 128.680 0.3 1 93 20 20 PHE C C 172.700 0.3 1 94 20 20 PHE CA C 52.500 0.3 1 95 20 20 PHE CB C 41.600 0.3 1 96 20 20 PHE N N 129.000 0.3 1 97 21 21 ALA C C 172.690 0.3 1 98 21 21 ALA CA C 49.200 0.3 1 99 21 21 ALA CB C 19.900 0.3 1 100 21 21 ALA N N 125.600 0.3 1 101 22 22 GLU C C 172.500 0.3 1 102 22 22 GLU CA C 52.500 0.3 1 103 22 22 GLU CB C 32.400 0.3 1 104 22 22 GLU CG C 35.100 0.3 1 105 22 22 GLU CD C 181.600 0.3 1 106 22 22 GLU N N 117.793 0.3 1 107 23 23 ASP C C 173.000 0.3 1 108 23 23 ASP CA C 53.600 0.3 1 109 23 23 ASP CB C 35.190 0.3 1 110 23 23 ASP CG C 181.000 0.3 1 111 23 23 ASP N N 124.400 0.3 1 112 24 24 VAL C C 173.000 0.3 1 113 24 24 VAL CA C 59.094 0.3 1 114 24 24 VAL CB C 33.540 0.3 1 115 24 24 VAL CG1 C 19.900 0.3 1 116 24 24 VAL CG2 C 19.900 0.3 1 117 24 24 VAL N N 123.100 0.3 1 118 25 25 GLY C C 171.300 0.3 1 119 25 25 GLY CA C 45.630 0.3 1 120 25 25 GLY N N 110.400 0.3 1 121 26 26 SER C C 172.900 0.3 1 122 26 26 SER CA C 55.210 0.3 1 123 26 26 SER CB C 66.370 0.3 1 124 26 26 SER N N 110.500 0.3 1 125 27 27 ASN C C 172.800 0.3 1 126 27 27 ASN CA C 52.275 0.3 1 127 27 27 ASN CB C 34.410 0.3 1 128 27 27 ASN CG C 175.300 0.3 1 129 27 27 ASN N N 116.399 0.3 1 130 28 28 LYS C C 173.137 0.3 1 131 28 28 LYS CA C 53.400 0.3 1 132 28 28 LYS CB C 33.660 0.3 1 133 28 28 LYS CG C 26.100 0.3 1 134 28 28 LYS CD C 29.000 0.3 1 135 28 28 LYS CE C 41.200 0.3 1 136 28 28 LYS N N 128.200 0.3 1 137 29 29 GLY C C 169.900 0.3 1 138 29 29 GLY CA C 39.684 0.3 1 139 29 29 GLY N N 105.953 0.3 1 140 30 30 ALA C C 173.900 0.3 1 141 30 30 ALA CA C 51.331 0.3 1 142 30 30 ALA CB C 16.480 0.3 1 143 30 30 ALA N N 122.477 0.3 1 144 31 31 ILE C C 172.767 0.3 1 145 31 31 ILE CA C 59.760 0.3 1 146 31 31 ILE CB C 38.762 0.3 1 147 31 31 ILE CG1 C 27.184 0.3 1 148 31 31 ILE CG2 C 16.356 0.3 1 149 31 31 ILE CD1 C 13.019 0.3 1 150 31 31 ILE N N 120.739 0.3 1 151 32 32 ILE C C 174.264 0.3 1 152 32 32 ILE CA C 58.131 0.3 1 153 32 32 ILE CB C 38.694 0.3 1 154 32 32 ILE CG1 C 25.550 0.3 1 155 32 32 ILE CG2 C 16.220 0.3 1 156 32 32 ILE CD1 C 13.263 0.3 1 157 32 32 ILE N N 124.938 0.3 1 158 33 33 GLY C C 168.462 0.3 1 159 33 33 GLY CA C 44.196 0.3 1 160 33 33 GLY N N 115.699 0.3 1 161 34 34 LEU C C 172.810 0.3 1 162 34 34 LEU CA C 52.505 0.3 1 163 34 34 LEU CB C 43.400 0.3 1 164 34 34 LEU CG C 27.700 0.3 1 165 34 34 LEU CD1 C 26.100 0.3 1 166 34 34 LEU CD2 C 21.500 0.3 1 167 34 34 LEU N N 127.930 0.3 1 168 35 35 MET C C 173.200 0.3 1 169 35 35 MET CA C 52.200 0.3 1 170 35 35 MET CB C 35.100 0.3 1 171 35 35 MET CG C 32.300 0.3 1 172 35 35 MET CE C 17.500 0.3 1 173 35 35 MET N N 125.000 0.3 1 174 36 36 VAL C C 175.235 0.3 1 175 36 36 VAL CA C 59.543 0.3 1 176 36 36 VAL CB C 32.301 0.3 1 177 36 36 VAL CG1 C 19.523 0.3 1 178 36 36 VAL CG2 C 18.700 0.3 1 179 36 36 VAL N N 125.700 0.3 1 180 37 37 GLY C C 170.842 0.3 1 181 37 37 GLY CA C 44.965 0.3 1 182 37 37 GLY N N 109.880 0.3 1 183 38 38 GLY C C 169.283 0.3 1 184 38 38 GLY CA C 42.952 0.3 1 185 38 38 GLY N N 104.736 0.3 1 186 39 39 VAL C C 171.907 0.3 1 187 39 39 VAL CA C 59.634 0.3 1 188 39 39 VAL CB C 34.100 0.3 1 189 39 39 VAL CG1 C 19.300 0.3 1 190 39 39 VAL CG2 C 18.300 0.3 1 191 39 39 VAL N N 122.281 0.3 1 192 40 40 VAL C C 171.900 0.3 1 193 40 40 VAL CA C 60.200 0.3 1 194 40 40 VAL CB C 33.800 0.3 1 195 40 40 VAL CG1 C 19.800 0.3 1 196 40 40 VAL CG2 C 19.800 0.3 1 197 40 40 VAL N N 128.826 0.3 1 stop_ save_