data_30596 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; S8 phosphorylated beta amyloid 40 fibrils ; _BMRB_accession_number 30596 _BMRB_flat_file_name bmr30596.str _Entry_type original _Submission_date 2019-03-22 _Accession_date 2019-03-22 _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 Qiang W. . . 2 Hu Z. W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 123 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-05-31 original BMRB . stop_ _Original_release_date 2019-05-20 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; The molecular structure of a "seeding-prone" N-terminal phosphorylated b-amyloid fibril. ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hu Z. W. . 2 Vugmeyster L. . . 3 Au D. F. . 4 Ostrovsky D. . . 5 Sun Y. . . 6 Qiang W. . . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Amyloid-beta precursor protein' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, 1' $entity_1 'entity_1, 2' $entity_1 'entity_1, 3' $entity_1 'entity_1, 4' $entity_1 'entity_1, 5' $entity_1 'entity_1, 6' $entity_1 'entity_1, 7' $entity_1 'entity_1, 8' $entity_1 'entity_1, 9' $entity_1 'entity_1, 10' $entity_1 'entity_2, 1' $entity_2PO 'entity_2, 2' $entity_2PO 'entity_2, 3' $entity_2PO 'entity_2, 4' $entity_2PO 'entity_2, 5' $entity_2PO 'entity_2, 6' $entity_2PO 'entity_2, 7' $entity_2PO 'entity_2, 8' $entity_2PO 'entity_2, 9' $entity_2PO 'entity_2, 10' $entity_2PO 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_ ############# # Ligands # ############# save_2PO _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "entity_2PO (PHOSPHONATE)" _BMRB_code 2PO _PDB_code 2PO _Molecular_mass 79.980 _Mol_charge -2 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? O1P O1P O . -1 . ? O2P O2P O . -1 . ? O3P O3P O . 0 . ? HP HP H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING P O1P ? ? SING P O2P ? ? DOUB P O3P ? ? SING P HP ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type 'fibrous protein' _Details ; 50 uM E3, G9, V18, F20, D23, S26, K28 beta amyloid peptide, 50 uM A2, F4, D7, Y10, V24, G25 beta amyloid peptide, 50 uM Q15, F19, A21, I31, L34, V36, G37 beta amyloid peptide, 50 uM V12, E22, G29, A30, M35 beta amyloid peptide, 50 uM E11, L17, N27, I32, G33, G38, V39 beta amyloid peptide, 50 uM F19, L34 beta amyloid peptide, 50 uM E3, F4, V24, G25, S26 beta amyloid peptide, 50 uM V12, F20, E22 beta amyloid peptide, 50 uM I31, G33, V39 beta amyloid peptide. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 50 uM 'E3, G9, V18, F20, D23, S26, K28' $entity_1 50 uM 'A2, F4, D7, Y10, V24, G25' $entity_1 50 uM 'Q15, F19, A21, I31, L34, V36, G37' $entity_1 50 uM 'V12, E22, G29, A30, M35' $entity_1 50 uM 'E11, L17, N27, I32, G33, G38, V39' $entity_1 50 uM 'F19, L34' $entity_1 50 uM 'E3, F4, V24, G25, S26' $entity_1 50 uM 'V12, F20, E22' $entity_1 50 uM 'I31, G33, V39' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type 'fibrous protein' _Details ; 50 uM L17, 2H-CD3 beta amyloid peptide, 50 uM F19, 2H-ring-D5 beta amyloid peptide, 50 uM L34, 2H-CD3 beta amyloid peptide, 50 uM M35, 2H-CD3 beta amyloid peptide, 50 uM V36, 2H-CD3 beta amyloid peptide. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 50 uM 'L17, 2H-CD3' $entity_1 50 uM 'F19, 2H-ring-D5' $entity_1 50 uM 'L34, 2H-CD3' $entity_1 50 uM 'M35, 2H-CD3' $entity_1 50 uM 'V36, 2H-CD3' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type 'fibrous protein' _Details ; 50 uM A2-CH3, V12-CO beta amyloid peptide, 50 uM V18-CO, A21-CH3 beta amyloid peptide, 50 uM V24-CO, A30-CH3 beta amyloid peptide, 50 uM G33-CO, V39-Ca beta amyloid peptide, 50 uM V36-Ca, G38-CO beta amyloid peptide, 50 uM G9-CO beta amyloid peptide. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 50 uM 'A2-CH3, V12-CO' $entity_1 50 uM 'V18-CO, A21-CH3' $entity_1 50 uM 'V24-CO, A30-CH3' $entity_1 50 uM 'G33-CO, V39-Ca' $entity_1 50 uM 'V36-Ca, G38-CO' $entity_1 50 uM G9-CO stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_spin_diffusion_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D spin diffusion' _Sample_label $sample_1 save_ save_1D_PITHIRDs-CT_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1D PITHIRDs-CT' _Sample_label $sample_3 save_ save_1D_13C-31P_REDOR_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 13C-31P REDOR' _Sample_label $sample_3 save_ save_2H_relaxation_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2H relaxation' _Sample_label $sample_2 save_ save_2H_static_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2H static' _Sample_label $sample_2 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 280 . 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 alanine C 13 'carbonyl carbon' ppm 177.95 external direct . . . 1.0 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 spin diffusion' '1D PITHIRDs-CT' '1D 13C-31P REDOR' '2H relaxation' '2H static' stop_ loop_ _Sample_label $sample_1 $sample_3 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 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 176.2 1.00 . 2 2 2 ALA CA C 53.0 1.00 . 3 2 2 ALA CB C 19.9 1.00 . 4 3 3 GLU C C 174.6 1.00 . 5 3 3 GLU CA C 54.8 1.00 . 6 3 3 GLU CB C 28.0 1.00 . 7 3 3 GLU CG C 36.6 1.00 . 8 3 3 GLU CD C 180.2 1.00 . 9 4 4 PHE C C 175.2 1.00 . 10 4 4 PHE CA C 55.7 1.00 . 11 4 4 PHE CB C 39.9 1.00 . 12 7 7 ASP C C 173.9 1.00 . 13 7 7 ASP CA C 54.9 1.00 . 14 7 7 ASP CB C 38.5 1.00 . 15 7 7 ASP CG C 177.9 1.00 . 16 9 9 GLY C C 171.9 1.00 . 17 9 9 GLY CA C 42.5 1.00 . 18 10 10 TYR C C 175.9 1.00 . 19 10 10 TYR CA C 57.3 1.00 . 20 10 10 TYR CB C 40.2 1.00 . 21 11 11 GLU C C 173.5 1.00 . 22 11 11 GLU CA C 54.0 1.00 . 23 11 11 GLU CB C 31.6 1.00 . 24 11 11 GLU CG C 34.7 1.00 . 25 11 11 GLU CD C 181.9 1.00 . 26 12 12 VAL C C 174.1 1.00 . 27 12 12 VAL CA C 60.4 1.00 . 28 12 12 VAL CB C 33.7 1.00 . 29 12 12 VAL CG1 C 20.7 1.00 . 30 15 15 GLN C C 172.6 1.00 . 31 15 15 GLN CA C 53.7 1.00 . 32 15 15 GLN CB C 27.1 1.00 . 33 15 15 GLN CG C 33.1 1.00 . 34 15 15 GLN CD C 181.6 1.00 . 35 17 17 LEU C C 173.4 1.00 . 36 17 17 LEU CA C 53.1 1.00 . 37 17 17 LEU CB C 44.3 1.00 . 38 17 17 LEU CG C 26.3 1.00 . 39 17 17 LEU CD1 C 24.3 1.00 . 40 17 17 LEU CD2 C 24.3 1.00 . 41 18 18 VAL C C 173.0 1.00 . 42 18 18 VAL CA C 60.6 1.00 . 43 18 18 VAL CB C 35.3 1.00 . 44 18 18 VAL CG1 C 20.9 1.00 . 45 19 19 PHE C C 172.2 1.00 . 46 19 19 PHE CA C 54.7 1.00 . 47 19 19 PHE CB C 40.3 1.00 . 48 20 20 PHE C C 173.0 1.00 . 49 20 20 PHE CA C 54.7 1.00 . 50 20 20 PHE CB C 43.1 1.00 . 51 21 21 ALA C C 173.5 1.00 . 52 21 21 ALA CA C 49.1 1.00 . 53 21 21 ALA CB C 21.8 1.00 . 54 22 22 GLU C C 172.8 1.00 . 55 22 22 GLU CA C 53.4 1.00 . 56 22 22 GLU CB C 32.4 1.00 . 57 22 22 GLU CG C 35.5 1.00 . 58 22 22 GLU CD C 179.4 1.00 . 59 23 23 ASP C C 175.2 1.00 . 60 23 23 ASP CA C 52.4 1.00 . 61 23 23 ASP CB C 38.6 1.00 . 62 23 23 ASP CG C 176.5 1.00 . 63 24 24 VAL C C 176.8 1.00 . 64 24 24 VAL CA C 60.2 1.00 . 65 24 24 VAL CB C 33.3 1.00 . 66 24 24 VAL CG1 C 21.8 1.00 . 67 25 25 GLY C C 171.0 1.00 . 68 25 25 GLY CA C 47.6 1.00 . 69 26 26 SER C C 172.6 1.00 . 70 26 26 SER CA C 55.7 1.00 . 71 26 26 SER CB C 65.6 1.00 . 72 27 27 ASN C C 172.1 1.00 . 73 27 27 ASN CA C 51.8 1.00 . 74 27 27 ASN CB C 39.3 1.00 . 75 27 27 ASN CG C 175.0 1.00 . 76 28 28 LYS C C 174.6 1.00 . 77 28 28 LYS CA C 55.8 1.00 . 78 28 28 LYS CB C 35.7 1.00 . 79 28 28 LYS CG C 25.8 1.00 . 80 28 28 LYS CD C 29.6 1.00 . 81 28 28 LYS CE C 42.6 1.00 . 82 29 29 GLY C C 171.2 1.00 . 83 29 29 GLY CA C 47.9 1.00 . 84 30 30 ALA C C 174.1 1.00 . 85 30 30 ALA CA C 49.1 1.00 . 86 30 30 ALA CB C 20.7 1.00 . 87 31 31 ILE C C 173.4 1.00 . 88 31 31 ILE CA C 59.9 1.00 . 89 31 31 ILE CB C 39.1 1.00 . 90 31 31 ILE CG1 C 27.3 1.00 . 91 31 31 ILE CG2 C 19.0 1.00 . 92 31 31 ILE CD1 C 12.8 1.00 . 93 32 32 ILE C C 174.9 1.00 . 94 32 32 ILE CA C 56.9 1.00 . 95 32 32 ILE CB C 41.3 1.00 . 96 32 32 ILE CG1 C 25.6 1.00 . 97 32 32 ILE CG2 C 15.9 1.00 . 98 32 32 ILE CD1 C 12.9 1.00 . 99 33 33 GLY C C 171.0 1.00 . 100 33 33 GLY CA C 42.9 1.00 . 101 34 34 LEU C C 173.1 1.00 . 102 34 34 LEU CA C 52.8 1.00 . 103 34 34 LEU CB C 45.3 1.00 . 104 34 34 LEU CG C 26.5 1.00 . 105 34 34 LEU CD1 C 25.1 1.00 . 106 34 34 LEU CD2 C 25.1 1.00 . 107 35 35 MET C C 172.8 1.00 . 108 35 35 MET CA C 53.5 1.00 . 109 35 35 MET CB C 35.4 1.00 . 110 35 35 MET CG C 31.3 1.00 . 111 35 35 MET CE C 16.9 1.00 . 112 36 36 VAL C C 174.4 1.00 . 113 36 36 VAL CA C 59.5 1.00 . 114 36 36 VAL CB C 34.5 1.00 . 115 36 36 VAL CG1 C 20.3 1.00 . 116 37 37 GLY C C 170.4 1.00 . 117 37 37 GLY CA C 42.4 1.00 . 118 38 38 GLY C C 170.1 1.00 . 119 38 38 GLY CA C 42.4 1.00 . 120 39 39 VAL C C 173.4 1.00 . 121 39 39 VAL CA C 59.5 1.00 . 122 39 39 VAL CB C 33.5 1.00 . 123 39 39 VAL CG1 C 20.6 1.00 . stop_ save_