data_34507 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR Structure of APP TMD ; _BMRB_accession_number 34507 _BMRB_flat_file_name bmr34507.str _Entry_type original _Submission_date 2020-03-30 _Accession_date 2020-03-30 _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 Silber M. . . 2 Muhle-Goll C. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 148 "13C chemical shifts" 98 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-12-04 original BMRB . stop_ _Original_release_date 2020-04-20 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Altered hinge conformations in APP transmembrane helix mutants may affect complex formation with gamma-secretase ; _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 Silber M. . . 2 Muhle-Goll C. . . 3 Hitzenberger M. . . 4 Zacharias M. . . stop_ _Journal_abbreviation 'To be published' _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 $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 3127.031 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; SNKGAIIGLMVGLVVIATVI VITLVMLKKK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 26 SER 2 27 ASN 3 28 LYS 4 29 GLY 5 30 ALA 6 31 ILE 7 32 ILE 8 33 GLY 9 34 LEU 10 35 MET 11 36 VAL 12 37 GLY 13 38 LEU 14 39 VAL 15 40 VAL 16 41 ILE 17 42 ALA 18 43 THR 19 44 VAL 20 45 ILE 21 46 VAL 22 47 ILE 23 48 THR 24 49 LEU 25 50 VAL 26 51 MET 27 52 LEU 28 53 LYS 29 54 LYS 30 55 LYS 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 $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 '500 uM APP G38L, 80% TFE-d2, 20% H2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 500 uM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger A. T. et.al.' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name ARIA _Version 2.3.2 loop_ _Vendor _Address _Electronic_address "Linge, O'Donoghue and Nilges" . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name 'CcpNmr Analysis' _Version 2.4.2 loop_ _Vendor _Address _Electronic_address 'Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED.' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'CP TCI' _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-1H-NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-1H-NOESY _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' 0 . 'Not defined' pH 7.0 . pH pressure 1 . Pa temperature 298 . 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_ _Experiment_label 1H-1H-NOESY 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 entity_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 26 1 SER HA H 4.400 . . 2 26 1 SER HB2 H 3.963 . . 3 26 1 SER HB3 H 3.834 . . 4 26 1 SER HG H 7.789 . . 5 26 1 SER CA C 58.000 . . 6 26 1 SER CB C 63.139 . . 7 27 2 ASN HA H 4.790 . . 8 27 2 ASN HB2 H 2.916 . . 9 27 2 ASN HB3 H 2.916 . . 10 27 2 ASN CB C 37.156 . . 11 28 3 LYS H H 8.044 . . 12 28 3 LYS HA H 4.116 . . 13 28 3 LYS CA C 58.153 . . 14 29 4 GLY H H 8.241 . . 15 29 4 GLY HA2 H 3.852 . . 16 29 4 GLY HA3 H 3.852 . . 17 29 4 GLY CA C 45.819 . . 18 30 5 ALA H H 7.652 . . 19 30 5 ALA HA H 4.228 . . 20 30 5 ALA HB H 1.498 . . 21 30 5 ALA CA C 53.678 . . 22 30 5 ALA CB C 17.258 . . 23 31 6 ILE H H 7.500 . . 24 31 6 ILE HA H 3.946 . . 25 31 6 ILE HB H 2.030 . . 26 31 6 ILE HG12 H 1.303 . . 27 31 6 ILE HG13 H 1.646 . . 28 31 6 ILE HG2 H 0.995 . . 29 31 6 ILE HD1 H 0.901 . . 30 31 6 ILE CA C 63.024 . . 31 31 6 ILE CB C 37.358 . . 32 31 6 ILE CG1 C 27.631 . . 33 31 6 ILE CG2 C 16.198 . . 34 31 6 ILE CD1 C 11.224 . . 35 32 7 ILE H H 7.844 . . 36 32 7 ILE HA H 3.841 . . 37 32 7 ILE HB H 1.930 . . 38 32 7 ILE HG12 H 1.264 . . 39 32 7 ILE HG13 H 1.690 . . 40 32 7 ILE HG2 H 0.945 . . 41 32 7 ILE HD1 H 0.884 . . 42 32 7 ILE CA C 63.981 . . 43 32 7 ILE CB C 37.016 . . 44 32 7 ILE CG1 C 27.926 . . 45 32 7 ILE CG2 C 15.861 . . 46 32 7 ILE CD1 C 11.178 . . 47 33 8 GLY H H 7.897 . . 48 33 8 GLY HA2 H 3.823 . . 49 33 8 GLY HA3 H 3.823 . . 50 33 8 GLY CA C 46.295 . . 51 34 9 LEU H H 7.773 . . 52 34 9 LEU HA H 4.266 . . 53 34 9 LEU HB2 H 1.887 . . 54 34 9 LEU HB3 H 1.812 . . 55 34 9 LEU HG H 1.786 . . 56 34 9 LEU HD1 H 0.952 . . 57 34 9 LEU HD2 H 0.924 . . 58 34 9 LEU CA C 57.116 . . 59 34 9 LEU CB C 41.367 . . 60 34 9 LEU CG C 26.221 . . 61 34 9 LEU CD1 C 23.036 . . 62 34 9 LEU CD2 C 22.605 . . 63 35 10 MET H H 8.121 . . 64 35 10 MET HA H 4.246 . . 65 35 10 MET HB2 H 2.331 . . 66 35 10 MET HB3 H 2.172 . . 67 35 10 MET HG2 H 2.767 . . 68 35 10 MET HG3 H 2.605 . . 69 35 10 MET CA C 58.022 . . 70 35 10 MET CB C 31.576 . . 71 35 10 MET CG C 31.538 . . 72 36 11 VAL H H 8.454 . . 73 36 11 VAL HA H 3.715 . . 74 36 11 VAL HB H 2.144 . . 75 36 11 VAL HG1 H 1.082 . . 76 36 11 VAL HG2 H 0.957 . . 77 36 11 VAL CA C 65.828 . . 78 36 11 VAL CB C 31.111 . . 79 36 11 VAL CG1 C 20.967 . . 80 36 11 VAL CG2 C 19.763 . . 81 37 12 GLY H H 7.864 . . 82 37 12 GLY HA2 H 3.892 . . 83 37 12 GLY HA3 H 3.808 . . 84 37 12 GLY CA C 46.528 . . 85 38 13 LEU H H 7.941 . . 86 38 13 LEU HA H 4.217 . . 87 38 13 LEU HB2 H 2.016 . . 88 38 13 LEU HB3 H 1.636 . . 89 38 13 LEU HG H 1.929 . . 90 38 13 LEU HD1 H 0.906 . . 91 38 13 LEU HD2 H 0.952 . . 92 38 13 LEU CA C 57.417 . . 93 38 13 LEU CB C 41.085 . . 94 38 13 LEU CG C 26.005 . . 95 38 13 LEU CD1 C 21.695 . . 96 38 13 LEU CD2 C 23.657 . . 97 39 14 VAL H H 7.865 . . 98 39 14 VAL HA H 3.747 . . 99 39 14 VAL HB H 2.378 . . 100 39 14 VAL HG1 H 1.113 . . 101 39 14 VAL HG2 H 0.981 . . 102 39 14 VAL CA C 65.798 . . 103 39 14 VAL CB C 30.912 . . 104 39 14 VAL CG1 C 21.352 . . 105 39 14 VAL CG2 C 19.885 . . 106 40 15 VAL H H 8.390 . . 107 40 15 VAL HA H 3.605 . . 108 40 15 VAL HB H 2.342 . . 109 40 15 VAL HG1 H 0.947 . . 110 40 15 VAL HG2 H 1.090 . . 111 40 15 VAL CA C 67.085 . . 112 40 15 VAL CB C 30.862 . . 113 40 15 VAL CG1 C 19.565 . . 114 40 15 VAL CG2 C 21.337 . . 115 41 16 ILE H H 8.208 . . 116 41 16 ILE HA H 3.739 . . 117 41 16 ILE HB H 1.978 . . 118 41 16 ILE HG12 H 1.236 . . 119 41 16 ILE HG13 H 1.789 . . 120 41 16 ILE HG2 H 0.980 . . 121 41 16 ILE HD1 H 0.871 . . 122 41 16 ILE CA C 64.510 . . 123 41 16 ILE CB C 37.054 . . 124 41 16 ILE CG1 C 28.263 . . 125 41 16 ILE CG2 C 16.072 . . 126 41 16 ILE CD1 C 11.153 . . 127 42 17 ALA H H 8.241 . . 128 42 17 ALA HA H 4.046 . . 129 42 17 ALA HB H 1.547 . . 130 42 17 ALA CA C 54.938 . . 131 42 17 ALA CB C 16.948 . . 132 43 18 THR H H 7.996 . . 133 43 18 THR HA H 3.896 . . 134 43 18 THR HB H 4.584 . . 135 43 18 THR HG1 H 5.644 . . 136 43 18 THR HG2 H 1.281 . . 137 43 18 THR CA C 66.765 . . 138 43 18 THR CB C 68.303 . . 139 43 18 THR CG2 C 19.481 . . 140 44 19 VAL H H 8.337 . . 141 44 19 VAL HA H 3.637 . . 142 44 19 VAL HB H 2.362 . . 143 44 19 VAL HG1 H 1.094 . . 144 44 19 VAL HG2 H 0.937 . . 145 44 19 VAL CA C 67.378 . . 146 44 19 VAL CB C 30.862 . . 147 44 19 VAL CG1 C 21.337 . . 148 44 19 VAL CG2 C 19.835 . . 149 45 20 ILE H H 8.532 . . 150 45 20 ILE HA H 3.637 . . 151 45 20 ILE HB H 2.116 . . 152 45 20 ILE HG12 H 1.099 . . 153 45 20 ILE HG13 H 1.907 . . 154 45 20 ILE HG2 H 0.922 . . 155 45 20 ILE HD1 H 0.850 . . 156 45 20 ILE CA C 65.767 . . 157 45 20 ILE CB C 36.871 . . 158 45 20 ILE CG1 C 28.236 . . 159 45 20 ILE CG2 C 15.495 . . 160 45 20 ILE CD1 C 11.547 . . 161 46 21 VAL H H 8.220 . . 162 46 21 VAL HA H 3.640 . . 163 46 21 VAL HB H 2.284 . . 164 46 21 VAL HG1 H 1.139 . . 165 46 21 VAL HG2 H 0.978 . . 166 46 21 VAL CA C 66.486 . . 167 46 21 VAL CB C 30.838 . . 168 46 21 VAL CG1 C 21.858 . . 169 46 21 VAL CG2 C 19.885 . . 170 47 22 ILE H H 8.576 . . 171 47 22 ILE HA H 3.699 . . 172 47 22 ILE HB H 1.983 . . 173 47 22 ILE HG12 H 1.238 . . 174 47 22 ILE HG13 H 1.857 . . 175 47 22 ILE HG2 H 0.957 . . 176 47 22 ILE HD1 H 0.848 . . 177 47 22 ILE CA C 64.797 . . 178 47 22 ILE CB C 37.054 . . 179 47 22 ILE CG1 C 28.222 . . 180 47 22 ILE CG2 C 16.099 . . 181 47 22 ILE CD1 C 11.729 . . 182 48 23 THR H H 8.185 . . 183 48 23 THR HA H 3.845 . . 184 48 23 THR HB H 4.551 . . 185 48 23 THR HG1 H 5.674 . . 186 48 23 THR HG2 H 1.244 . . 187 48 23 THR CA C 67.273 . . 188 48 23 THR CB C 68.019 . . 189 48 23 THR CG2 C 19.364 . . 190 49 24 LEU H H 8.499 . . 191 49 24 LEU HA H 4.111 . . 192 49 24 LEU HB2 H 2.124 . . 193 49 24 LEU HB3 H 1.521 . . 194 49 24 LEU HG H 1.979 . . 195 49 24 LEU HD1 H 0.896 . . 196 49 24 LEU HD2 H 0.874 . . 197 49 24 LEU CA C 57.949 . . 198 49 24 LEU CB C 41.023 . . 199 49 24 LEU CG C 25.933 . . 200 49 24 LEU CD1 C 23.912 . . 201 49 24 LEU CD2 C 21.513 . . 202 50 25 VAL H H 8.629 . . 203 50 25 VAL HA H 3.610 . . 204 50 25 VAL HB H 2.341 . . 205 50 25 VAL HG1 H 1.107 . . 206 50 25 VAL HG2 H 0.947 . . 207 50 25 VAL CA C 66.563 . . 208 50 25 VAL CB C 30.862 . . 209 50 25 VAL CG1 C 21.635 . . 210 50 25 VAL CG2 C 20.007 . . 211 51 26 MET H H 8.561 . . 212 51 26 MET HA H 4.204 . . 213 51 26 MET HB2 H 2.434 . . 214 51 26 MET HB3 H 2.109 . . 215 51 26 MET HG2 H 2.805 . . 216 51 26 MET HG3 H 2.671 . . 217 51 26 MET HE H 2.071 . . 218 51 26 MET CA C 58.038 . . 219 51 26 MET CB C 31.000 . . 220 51 26 MET CG C 31.937 . . 221 51 26 MET CE C 15.459 . . 222 52 27 LEU H H 8.543 . . 223 52 27 LEU HA H 4.140 . . 224 52 27 LEU HB2 H 2.010 . . 225 52 27 LEU HB3 H 1.567 . . 226 52 27 LEU HG H 1.927 . . 227 52 27 LEU HD1 H 0.908 . . 228 52 27 LEU HD2 H 0.888 . . 229 52 27 LEU CA C 57.176 . . 230 52 27 LEU CB C 41.354 . . 231 52 27 LEU CG C 26.005 . . 232 52 27 LEU CD1 C 23.875 . . 233 52 27 LEU CD2 C 21.616 . . 234 53 28 LYS H H 8.202 . . 235 53 28 LYS HA H 4.125 . . 236 53 28 LYS CA C 57.654 . . 237 54 29 LYS H H 8.246 . . 238 54 29 LYS HA H 4.182 . . 239 54 29 LYS CA C 57.250 . . 240 55 30 LYS H H 8.006 . . 241 55 30 LYS HA H 4.223 . . 242 55 30 LYS HB2 H 1.948 . . 243 55 30 LYS HG2 H 1.716 . . 244 55 30 LYS CA C 56.195 . . 245 55 30 LYS CB C 32.024 . . 246 55 30 LYS CG C 28.232 . . stop_ save_