data_34019 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Zinc bound dimer of the fragment of human amyloid-beta peptide with Alzheimer's disease pathogenic Taiwanese mutation D7H ; _BMRB_accession_number 34019 _BMRB_flat_file_name bmr34019.str _Entry_type original _Submission_date 2016-07-05 _Accession_date 2016-07-05 _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 Polshakov V. I. . 2 Mantsyzov A. B. . 3 Kozin S. A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 58 "13C chemical shifts" 35 "15N chemical shifts" 8 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-10-18 update BMRB 'update entry citation' 2017-08-18 original author 'original release' stop_ _Original_release_date 2016-11-11 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; A Binuclear Zinc Interaction Fold Discovered in the Homodimer of Alzheimer's Amyloid-beta Fragment with Taiwanese Mutation D7H ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28570778 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Polshakov Vladimir I. . 2 Mantsyzov Alexey B. . 3 Kozin Sergey A. . 4 Adzhubei Alexei A. . 5 Zhokhov Sergey S. . 6 'van Beek' Wouter . . 7 Kulikova Alexandra A. . 8 Indeykina Maria I. . 9 Mitkevich Vladimir A. . 10 Makarov Alexander A. . stop_ _Journal_abbreviation 'Angew. Chem. Int. Ed. Engl.' _Journal_name_full 'Angewandte Chemie (International ed. in English)' _Journal_volume 56 _Journal_issue 39 _Journal_ISSN 1521-3773 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11734 _Page_last 11739 _Year 2017 _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 'entity_1, 1' $entity_1 'entity_1, 2' $entity_1 'ZINC ION, 1' $entity_ZN 'ZINC ION, 2' $entity_ZN 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 1219.267 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence ; DAEFRHHSGYX ; loop_ _Residue_seq_code _Residue_label 1 ASP 2 ALA 3 GLU 4 PHE 5 ARG 6 HIS 7 HIS 8 SER 9 GLY 10 TYR 11 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 N HN1 ? ? SING N HN2 ? ? stop_ save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "entity_ZN (ZINC ION)" _BMRB_code ZN _PDB_code ZN _Molecular_mass 65.409 _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 ZN ZN ZN . 2 . ? 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 solution _Details '1.4 mM D7H_Abeta(1-10), 2.8 mM ZnCl2, 10 mM [U-99% 2D] bis-Tris-d19, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.4 mM 'natural abundance' ZnCl2 2.8 mM 'natural abundance' bis-Tris-d19 10 mM '[U-99% 2D]' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '1.4 mM D7H_Abeta(1-10), 2.8 mM ZnCl2, 10 mM [U-99% 2D] bis-Tris-d19, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.4 mM 'natural abundance' ZnCl2 2.8 mM 'natural abundance' bis-Tris-d19 10 mM '[U-99% 2D]' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _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_ save_software_3 _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_5 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_2 save_ save_2D_1H-1H_ROESY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_DOSY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DOSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_11 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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' 3 . mM pH 7.0 0.02 pH pressure 1 . atm temperature 278 . 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 DSS C 13 'methyl protons' ppm 0.000 internal indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.000 internal indirect . . . 0.10132912 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_ _Software_label $software_4 stop_ loop_ _Experiment_label '2D DQF-COSY' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-15N HSQC' '2D 1H-13C HSQC aromatic' '2D 1H-13C HSQC aliphatic' stop_ loop_ _Sample_label $sample_1 $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 1 1 ASP HA H 4.013 0.002 1 2 1 1 ASP HB2 H 2.041 0.002 2 3 1 1 ASP HB3 H 1.535 0.002 2 4 1 1 ASP CA C 52.413 0.02 1 5 1 1 ASP CB C 42.195 0.02 1 6 2 2 ALA H H 8.707 0.002 1 7 2 2 ALA HA H 4.412 0.002 1 8 2 2 ALA HB H 1.413 0.002 1 9 2 2 ALA CA C 52.222 0.02 1 10 2 2 ALA CB C 19.822 0.02 1 11 2 2 ALA N N 122.029 0.02 1 12 3 3 GLU H H 9.108 0.002 1 13 3 3 GLU HA H 4.752 0.002 1 14 3 3 GLU HB2 H 2.405 0.002 2 15 3 3 GLU HB3 H 2.058 0.002 2 16 3 3 GLU HG2 H 2.691 0.002 2 17 3 3 GLU HG3 H 2.523 0.002 2 18 3 3 GLU CA C 59.361 0.02 1 19 3 3 GLU CB C 29.681 0.02 1 20 3 3 GLU CG C 34.737 0.02 1 21 3 3 GLU N N 122.329 0.02 1 22 4 4 PHE H H 8.472 0.002 1 23 4 4 PHE HA H 4.502 0.002 1 24 4 4 PHE HB2 H 3.292 0.002 2 25 4 4 PHE HB3 H 3.012 0.002 2 26 4 4 PHE HD1 H 7.227 0.002 3 27 4 4 PHE HD2 H 7.227 0.002 3 28 4 4 PHE HE1 H 7.326 0.002 3 29 4 4 PHE HE2 H 7.326 0.002 3 30 4 4 PHE HZ H 7.309 0.002 1 31 4 4 PHE CA C 59.918 0.02 1 32 4 4 PHE CB C 37.847 0.02 1 33 4 4 PHE CD1 C 132.141 0.02 3 34 4 4 PHE CD2 C 132.141 0.02 3 35 4 4 PHE CE1 C 131.791 0.02 3 36 4 4 PHE CE2 C 131.791 0.02 3 37 4 4 PHE CZ C 130.481 0.02 1 38 5 5 ARG H H 6.959 0.002 1 39 5 5 ARG HA H 3.949 0.002 1 40 5 5 ARG HB2 H 1.539 0.002 2 41 5 5 ARG HB3 H 1.474 0.002 2 42 5 5 ARG HG2 H 1.175 0.002 2 43 5 5 ARG HG3 H 1.078 0.002 2 44 5 5 ARG HD2 H 2.998 0.002 2 45 5 5 ARG HD3 H 2.998 0.002 2 46 5 5 ARG CA C 56.855 0.02 1 47 5 5 ARG CB C 29.439 0.02 1 48 5 5 ARG CG C 26.946 0.02 1 49 5 5 ARG CD C 42.532 0.02 1 50 5 5 ARG N N 118.123 0.02 1 51 6 6 HIS H H 7.432 0.002 1 52 6 6 HIS HA H 4.153 0.002 1 53 6 6 HIS HB2 H 2.593 0.002 2 54 6 6 HIS HB3 H 1.939 0.002 2 55 6 6 HIS HD2 H 6.404 0.002 1 56 6 6 HIS HE1 H 7.604 0.002 1 57 6 6 HIS CA C 58.046 0.02 1 58 6 6 HIS CB C 29.579 0.02 1 59 6 6 HIS CD2 C 129.208 0.02 1 60 6 6 HIS CE1 C 139.772 0.02 1 61 6 6 HIS N N 115.868 0.02 1 62 7 7 HIS H H 7.672 0.002 1 63 7 7 HIS HA H 4.783 0.002 1 64 7 7 HIS HB2 H 3.266 0.002 2 65 7 7 HIS HB3 H 2.931 0.002 2 66 7 7 HIS HD2 H 7.088 0.002 1 67 7 7 HIS HE1 H 8.072 0.002 1 68 7 7 HIS CA C 54.991 0.02 1 69 7 7 HIS CB C 29.037 0.02 1 70 7 7 HIS CD2 C 129.358 0.02 1 71 7 7 HIS CE1 C 139.17 0.02 1 72 7 7 HIS N N 115.399 0.02 1 73 8 8 SER H H 8.041 0.002 1 74 8 8 SER HA H 4.432 0.002 1 75 8 8 SER HB2 H 3.856 0.002 2 76 8 8 SER HB3 H 3.856 0.002 2 77 8 8 SER CA C 59.019 0.02 1 78 8 8 SER CB C 63.702 0.02 1 79 9 9 GLY H H 8.614 0.002 1 80 9 9 GLY HA2 H 3.952 0.002 2 81 9 9 GLY HA3 H 3.851 0.002 2 82 9 9 GLY CA C 45.364 0.02 1 83 9 9 GLY N N 110.852 0.02 1 84 10 10 TYR H H 8.151 0.002 1 85 10 10 TYR HA H 4.488 0.002 1 86 10 10 TYR HB2 H 3.095 0.002 2 87 10 10 TYR HB3 H 2.984 0.002 2 88 10 10 TYR HD1 H 7.138 0.002 3 89 10 10 TYR HD2 H 7.138 0.002 3 90 10 10 TYR HE1 H 6.824 0.002 3 91 10 10 TYR HE2 H 6.824 0.002 3 92 10 10 TYR CA C 58.087 0.02 1 93 10 10 TYR CB C 39.081 0.02 1 94 10 10 TYR CD1 C 133.294 0.02 3 95 10 10 TYR CD2 C 133.294 0.02 3 96 10 10 TYR CE1 C 118.26 0.02 3 97 10 10 TYR CE2 C 118.26 0.02 3 98 10 10 TYR N N 120.786 0.02 1 99 11 11 NH2 N N 109.476 0.02 1 100 11 11 NH2 HN1 H 7.677 0.02 2 101 11 11 NH2 HN2 H 7.203 0.02 2 stop_ save_