data_19009 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 40-residue beta-amyloid fibril derived from Alzheimer's disease brain ; _BMRB_accession_number 19009 _BMRB_flat_file_name bmr19009.str _Entry_type original _Submission_date 2013-02-05 _Accession_date 2013-02-05 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details '20 structural models developed from solid state NMR data, supplemented by electron microscopy' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lu Jun-Xia . . 2 Qiang Wei . . 3 Meredith Stephen C. . 4 Yau Wai-Ming . . 5 Schweiters Charles D. . 6 Tycko Robert . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 175 "15N chemical shifts" 41 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-09-23 original BMRB . stop_ _Original_release_date 2013-02-19 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Molecular Structure of beta-Amyloid Fibrils in Alzheimer's Disease Brain Tissue ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24034249 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lu Jun-Xia . . 2 Qiang Wei . . 3 Yau Wai-Ming . . 4 Schweiters Charles D. . 5 Meredith Stephen C. . 6 Tycko Robert . . stop_ _Journal_abbreviation Cell _Journal_volume 154 _Journal_issue 6 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1257 _Page_last 1268 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name '40-residue beta-amyloid fibril' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label beta-amyloid_peptide_1 $beta-amyloid_peptide beta-amyloid_peptide_2 $beta-amyloid_peptide beta-amyloid_peptide_3 $beta-amyloid_peptide beta-amyloid_peptide_4 $beta-amyloid_peptide beta-amyloid_peptide_5 $beta-amyloid_peptide beta-amyloid_peptide_6 $beta-amyloid_peptide beta-amyloid_peptide_7 $beta-amyloid_peptide beta-amyloid_peptide_8 $beta-amyloid_peptide beta-amyloid_peptide_9 $beta-amyloid_peptide stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_beta-amyloid_peptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common beta-amyloid_peptide _Molecular_mass 4335.893 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 40 _Mol_residue_sequence ; DAEFRHDSGYEVHHQKLVFF AEDVGSNKGAIIGLMVGGVV ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ASP 2 2 ALA 3 3 GLU 4 4 PHE 5 5 ARG 6 6 HIS 7 7 ASP 8 8 SER 9 9 GLY 10 10 TYR 11 11 GLU 12 12 VAL 13 13 HIS 14 14 HIS 15 15 GLN 16 16 LYS 17 17 LEU 18 18 VAL 19 19 PHE 20 20 PHE 21 21 ALA 22 22 GLU 23 23 ASP 24 24 VAL 25 25 GLY 26 26 SER 27 27 ASN 28 28 LYS 29 29 GLY 30 30 ALA 31 31 ILE 32 32 ILE 33 33 GLY 34 34 LEU 35 35 MET 36 36 VAL 37 37 GLY 38 38 GLY 39 39 VAL 40 40 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value UNP P86906.1 'beta-amyloid protein 40' . . . . . stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $beta-amyloid_peptide 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_type _Vector_name $beta-amyloid_peptide 'chemical synthesis' . . . . . . $beta-amyloid_peptide 'recombinant technology' . . . . plasmid . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type fiber _Details ; 40-residue beta-amyloid peptide seeded with amyloid extracted from brain tissue. Lyophilized, then rehydrated after packing in MAS rotor. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $beta-amyloid_peptide . mg 1 2 'selectively and uniformly labeled samples' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculations' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model InfinityPlus _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Infinity _Field_strength 750 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model InfinityPlus _Field_strength 400 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_13C-13C_with_fpRFDR_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C with fpRFDR' _Sample_label $sample_1 save_ save_2D_and_3D_NCACX_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D and 3D NCACX' _Sample_label $sample_1 save_ save_2D_NCOCX_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NCOCX' _Sample_label $sample_1 save_ save_3D_NCOCX_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D NCOCX' _Sample_label $sample_1 save_ save_2D_NCACX_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NCACX' _Sample_label $sample_1 save_ save_2D_13C-13C_with_spin_diffusion_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C with spin diffusion' _Sample_label $sample_1 save_ save_2D_13C-13C_with_RAD_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C with RAD' _Sample_label $sample_1 save_ save_2D_13C-13C_with_PAR_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C with PAR' _Sample_label $sample_1 save_ save_2D_15N-13C_TEDOR_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C TEDOR' _Sample_label $sample_1 save_ save_2D_15N-13C_TEDOR_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C TEDOR' _Sample_label $sample_1 save_ save_15N-_and_13C-BARE_11 _Saveframe_category NMR_applied_experiment _Experiment_name '15N- and 13C-BARE' _Sample_label $sample_1 save_ save_13C_PITHIRDS-CT_12 _Saveframe_category NMR_applied_experiment _Experiment_name '13C PITHIRDS-CT' _Sample_label $sample_1 save_ save_2D_13C-13C_with_fpRFDR_13 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C with fpRFDR' _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' 10 . mM pH 7.4 . pH pressure 1 . atm temperature 273 . 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 C 13 'methyl carbon' ppm 0 external direct . . . 1.0 'liquid anhydrous ammonia' N 15 nitrogen ppm 0 external indirect . . . 0.4029800 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 with fpRFDR' '2D and 3D NCACX' '2D NCOCX' '3D NCOCX' '2D 13C-13C with RAD' 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 beta-amyloid_peptide_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 1 1 ASP C C 172 0.15 1 2 1 1 ASP CA C 54.14 0.15 1 3 1 1 ASP CB C 41.37 0.15 1 4 1 1 ASP CG C 178.2 0.15 1 5 1 1 ASP N N 35.02 0.15 1 6 2 2 ALA C C 175.2 0.15 1 7 2 2 ALA CA C 50.1 0.15 1 8 2 2 ALA CB C 24.14 0.15 1 9 2 2 ALA N N 120.4 0.15 1 10 3 3 GLU C C 173.2 0.15 1 11 3 3 GLU CA C 54.42 0.15 1 12 3 3 GLU CB C 33.66 0.15 1 13 3 3 GLU CG C 35.72 0.15 1 14 3 3 GLU CD C 182 0.15 1 15 3 3 GLU N N 120.1 0.15 1 16 4 4 PHE C C 173.3 0.15 1 17 4 4 PHE CA C 56.59 0.15 1 18 4 4 PHE CB C 40.77 0.15 1 19 4 4 PHE N N 125.6 0.15 1 20 5 5 ARG C C 173.4 0.15 1 21 5 5 ARG CA C 54.19 0.15 1 22 5 5 ARG CB C 32.6 0.15 1 23 5 5 ARG CG C 26.94 0.15 1 24 5 5 ARG CD C 43.03 0.15 1 25 5 5 ARG CZ C 159.2 0.15 1 26 5 5 ARG N N 124.6 0.15 1 27 6 6 HIS C C 171.7 0.15 1 28 6 6 HIS CA C 50.57 0.15 1 29 6 6 HIS CB C 31.45 0.15 1 30 6 6 HIS CG C 136.8 0.15 1 31 6 6 HIS CD2 C 117 0.15 1 32 6 6 HIS CE1 C 130.8 0.15 1 33 6 6 HIS N N 124.7 0.15 1 34 7 7 ASP C C 173.6 0.15 1 35 7 7 ASP CA C 51.94 0.15 1 36 7 7 ASP CB C 42.34 0.15 1 37 7 7 ASP CG C 180 0.15 1 38 7 7 ASP N N 129.4 0.15 1 39 8 8 SER C C 175.1 0.15 1 40 8 8 SER CA C 54.66 0.15 1 41 8 8 SER CB C 65.82 0.15 1 42 8 8 SER N N 115.7 0.15 1 43 9 9 GLY C C 173 0.15 1 44 9 9 GLY CA C 47.1 0.15 1 45 9 9 GLY N N 112.6 0.15 1 46 10 10 TYR C C 173 0.15 1 47 10 10 TYR CA C 56.42 0.15 1 48 10 10 TYR CB C 41.03 0.15 1 49 10 10 TYR CG C 129.1 0.15 1 50 10 10 TYR CD1 C 132.7 0.15 1 51 10 10 TYR CD2 C 132.7 0.15 1 52 10 10 TYR CE1 C 117.7 0.15 1 53 10 10 TYR CE2 C 117.7 0.15 1 54 10 10 TYR CZ C 157.7 0.15 1 55 10 10 TYR N N 120.4 0.15 1 56 11 11 GLU C C 173.3 0.15 1 57 11 11 GLU CA C 53.92 0.15 1 58 11 11 GLU CB C 32.16 0.15 1 59 11 11 GLU CG C 37.57 0.15 1 60 11 11 GLU CD C 183.3 0.15 1 61 11 11 GLU N N 129.2 0.15 1 62 12 12 VAL C C 175.1 0.15 1 63 12 12 VAL CA C 60.22 0.15 1 64 12 12 VAL CB C 34.08 0.15 1 65 12 12 VAL CG1 C 20.79 0.15 2 66 12 12 VAL CG2 C 19.98 0.15 2 67 12 12 VAL N N 125.3 0.15 1 68 13 13 HIS C C 172.7 0.15 1 69 13 13 HIS CA C 50.87 0.15 1 70 13 13 HIS CB C 31.56 0.15 1 71 13 13 HIS CG C 139.4 0.15 1 72 13 13 HIS CD2 C 113.8 0.15 1 73 13 13 HIS CE1 C 132.5 0.15 1 74 13 13 HIS N N 125.7 0.15 1 75 15 15 GLN C C 173.8 0.15 1 76 15 15 GLN CA C 53.99 0.15 1 77 15 15 GLN CB C 32.98 0.15 1 78 15 15 GLN CG C 31.06 0.15 1 79 15 15 GLN CD C 176.3 0.15 1 80 15 15 GLN N N 123.2 0.15 1 81 15 15 GLN NE2 N 107.9 0.15 1 82 16 16 LYS C C 173.5 0.15 1 83 16 16 LYS CA C 54.18 0.15 1 84 16 16 LYS CB C 35.96 0.15 1 85 16 16 LYS CG C 24.99 0.15 1 86 16 16 LYS CD C 29.4 0.15 1 87 16 16 LYS CE C 42.01 0.15 1 88 16 16 LYS N N 120.2 0.15 1 89 17 17 LEU C C 174.2 0.15 1 90 17 17 LEU CA C 53.64 0.15 1 91 17 17 LEU CB C 43.69 0.15 1 92 17 17 LEU CG C 29.34 0.15 1 93 17 17 LEU CD1 C 24.17 0.15 2 94 17 17 LEU CD2 C 22.6 0.15 2 95 17 17 LEU N N 126.3 0.15 1 96 18 18 VAL C C 172 0.15 1 97 18 18 VAL CA C 61.24 0.15 1 98 18 18 VAL CB C 33.19 0.15 1 99 18 18 VAL CG1 C 21.41 0.15 2 100 18 18 VAL CG2 C 19.82 0.15 2 101 18 18 VAL N N 123.1 0.15 1 102 19 19 PHE C C 174.5 0.15 1 103 19 19 PHE CA C 54.55 0.15 1 104 19 19 PHE CB C 41.47 0.15 1 105 19 19 PHE CG C 142.2 0.15 1 106 19 19 PHE CD1 C 130.2 0.15 1 107 19 19 PHE CD2 C 130.2 0.15 1 108 19 19 PHE N N 128.2 0.15 1 109 20 20 PHE C C 176.8 0.15 1 110 20 20 PHE CA C 57.01 0.15 1 111 20 20 PHE CB C 34.15 0.15 1 112 20 20 PHE CG C 141.7 0.15 1 113 20 20 PHE CD1 C 127.2 0.15 1 114 20 20 PHE CD2 C 127.2 0.15 1 115 20 20 PHE N N 119 0.15 1 116 21 21 ALA C C 176.3 0.15 1 117 21 21 ALA CA C 56.99 0.15 1 118 21 21 ALA CB C 18.5 0.15 1 119 21 21 ALA N N 117 0.15 1 120 22 22 GLU CA C 54.98 0.15 1 121 22 22 GLU CB C 33.8 0.15 1 122 22 22 GLU CG C 35.7 0.15 1 123 22 22 GLU CD C 181.9 0.15 1 124 22 22 GLU N N 113.8 0.15 1 125 23 23 ASP C C 174.6 0.15 1 126 23 23 ASP CA C 52.28 0.15 1 127 23 23 ASP CB C 42.78 0.15 1 128 23 23 ASP CG C 178 0.15 1 129 23 23 ASP N N 130.9 0.15 1 130 24 24 VAL C C 178.3 0.15 1 131 24 24 VAL CA C 59.69 0.15 1 132 24 24 VAL CB C 34.59 0.15 1 133 24 24 VAL CG1 C 20.65 0.15 2 134 24 24 VAL CG2 C 20.65 0.15 2 135 24 24 VAL N N 122.8 0.15 1 136 25 25 GLY C C 172.6 0.15 1 137 25 25 GLY CA C 46.75 0.15 1 138 25 25 GLY N N 110.1 0.15 1 139 26 26 SER C C 173.5 0.15 1 140 26 26 SER CA C 56.88 0.15 1 141 26 26 SER CB C 64.76 0.15 1 142 26 26 SER N N 111.2 0.15 1 143 27 27 ASN C C 175.7 0.15 1 144 27 27 ASN CA C 52.45 0.15 1 145 27 27 ASN CB C 42.88 0.15 1 146 27 27 ASN CG C 182.1 0.15 1 147 27 27 ASN N N 113.4 0.15 1 148 27 27 ASN ND2 N 120.7 0.15 1 149 28 28 LYS C C 175.1 0.15 1 150 28 28 LYS CA C 53.8 0.15 1 151 28 28 LYS CB C 36.93 0.15 1 152 28 28 LYS CG C 26.32 0.15 1 153 28 28 LYS CD C 29.71 0.15 1 154 28 28 LYS CE C 41.95 0.15 1 155 28 28 LYS N N 123.6 0.15 1 156 29 29 GLY C C 171.9 0.15 1 157 29 29 GLY CA C 48.57 0.15 1 158 29 29 GLY N N 113.8 0.15 1 159 30 30 ALA C C 175.1 0.15 1 160 30 30 ALA CA C 50.27 0.15 1 161 30 30 ALA CB C 23.49 0.15 1 162 30 30 ALA N N 119.6 0.15 1 163 31 31 ILE C C 172.8 0.15 1 164 31 31 ILE CA C 56.33 0.15 1 165 31 31 ILE CB C 38.43 0.15 1 166 31 31 ILE CG1 C 27.75 0.15 1 167 31 31 ILE CG2 C 14.45 0.15 1 168 31 31 ILE CD1 C 15.19 0.15 1 169 31 31 ILE N N 117.1 0.15 1 170 32 32 ILE C C 175.9 0.15 1 171 32 32 ILE CA C 58.5 0.15 1 172 32 32 ILE CB C 41.08 0.15 1 173 32 32 ILE CG1 C 27.1 0.15 1 174 32 32 ILE CG2 C 16.54 0.15 1 175 32 32 ILE CD1 C 14.69 0.15 1 176 32 32 ILE N N 124.7 0.15 1 177 33 33 GLY C C 171.6 0.15 1 178 33 33 GLY CA C 48.55 0.15 1 179 33 33 GLY N N 113.9 0.15 1 180 34 34 LEU C C 173.8 0.15 1 181 34 34 LEU CA C 54.16 0.15 1 182 34 34 LEU CB C 45.2 0.15 1 183 34 34 LEU CG C 27.72 0.15 1 184 34 34 LEU CD1 C 25.86 0.15 2 185 34 34 LEU CD2 C 23.99 0.15 2 186 34 34 LEU N N 123 0.15 1 187 35 35 MET C C 173.4 0.15 1 188 35 35 MET CA C 53.47 0.15 1 189 35 35 MET CB C 37.34 0.15 1 190 35 35 MET CG C 30.99 0.15 1 191 35 35 MET CE C 17.36 0.15 1 192 35 35 MET N N 125.1 0.15 1 193 36 36 VAL C C 175.8 0.15 1 194 36 36 VAL CA C 58.94 0.15 1 195 36 36 VAL CB C 35.04 0.15 1 196 36 36 VAL CG1 C 20.94 0.15 2 197 36 36 VAL CG2 C 19.61 0.15 2 198 36 36 VAL N N 125.2 0.15 1 199 37 37 GLY C C 173.4 0.15 1 200 37 37 GLY CA C 47.75 0.15 1 201 37 37 GLY N N 116.1 0.15 1 202 38 38 GLY C C 169.8 0.15 1 203 38 38 GLY CA C 44.87 0.15 1 204 38 38 GLY N N 106 0.15 1 205 39 39 VAL C C 172.7 0.15 1 206 39 39 VAL CA C 60.24 0.15 1 207 39 39 VAL CB C 36.09 0.15 1 208 39 39 VAL CG1 C 22.64 0.15 2 209 39 39 VAL CG2 C 22.64 0.15 2 210 39 39 VAL N N 117.9 0.15 1 211 40 40 VAL C C 178.9 0.15 1 212 40 40 VAL CA C 59.35 0.15 1 213 40 40 VAL CB C 33.23 0.15 1 214 40 40 VAL CG1 C 21.66 0.15 2 215 40 40 VAL CG2 C 21.66 0.15 2 216 40 40 VAL N N 127.5 0.15 1 stop_ save_