data_34506 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR Structure of APP TMD ; _BMRB_accession_number 34506 _BMRB_flat_file_name bmr34506.str _Entry_type original _Submission_date 2020-03-29 _Accession_date 2020-03-29 _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" 179 "13C chemical shifts" 110 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-12-04 original BMRB . stop_ _Original_release_date 2020-07-14 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 unit_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 3070.925 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; SNKGAIIGLMVGGVVIATVI 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 GLY 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 WT, 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 1.21 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 . mM pH 7.0 0.1 pH pressure 1 . atm 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 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 26 1 SER HA H 4.418 . . 2 26 1 SER HB2 H 3.834 . . 3 26 1 SER HB3 H 3.971 . . 4 26 1 SER HG H 7.795 . . 5 26 1 SER CA C 57.940 . . 6 26 1 SER CB C 63.202 . . 7 27 2 ASN H H 8.198 . . 8 27 2 ASN HA H 4.798 . . 9 27 2 ASN HB2 H 2.921 . . 10 27 2 ASN HB3 H 2.921 . . 11 27 2 ASN HD21 H 7.186 . . 12 27 2 ASN HD22 H 7.185 . . 13 27 2 ASN CA C 52.552 . . 14 27 2 ASN CB C 37.258 . . 15 28 3 LYS H H 8.081 . . 16 28 3 LYS HA H 4.107 . . 17 28 3 LYS HB2 H 1.887 . . 18 28 3 LYS HB3 H 1.887 . . 19 28 3 LYS HG2 H 1.557 . . 20 28 3 LYS HG3 H 1.489 . . 21 28 3 LYS HD2 H 1.726 . . 22 28 3 LYS HD3 H 1.726 . . 23 28 3 LYS HE2 H 3.006 . . 24 28 3 LYS HE3 H 3.006 . . 25 28 3 LYS CA C 58.253 . . 26 28 3 LYS CB C 31.525 . . 27 28 3 LYS CG C 24.191 . . 28 28 3 LYS CD C 28.174 . . 29 28 3 LYS CE C 41.598 . . 30 29 4 GLY H H 8.254 . . 31 29 4 GLY HA2 H 3.848 . . 32 29 4 GLY HA3 H 3.848 . . 33 29 4 GLY CA C 45.884 . . 34 30 5 ALA H H 7.664 . . 35 30 5 ALA HA H 4.221 . . 36 30 5 ALA HB H 1.498 . . 37 30 5 ALA CA C 53.764 . . 38 30 5 ALA CB C 17.222 . . 39 31 6 ILE H H 7.514 . . 40 31 6 ILE HA H 3.908 . . 41 31 6 ILE HB H 2.033 . . 42 31 6 ILE HG12 H 1.298 . . 43 31 6 ILE HG13 H 1.647 . . 44 31 6 ILE HG2 H 0.993 . . 45 31 6 ILE HD1 H 0.894 . . 46 31 6 ILE CA C 63.221 . . 47 31 6 ILE CB C 37.280 . . 48 31 6 ILE CG1 C 27.646 . . 49 31 6 ILE CG2 C 16.185 . . 50 31 6 ILE CD1 C 11.149 . . 51 32 7 ILE H H 7.896 . . 52 32 7 ILE HA H 3.845 . . 53 32 7 ILE HB H 1.935 . . 54 32 7 ILE HG12 H 1.266 . . 55 32 7 ILE HG13 H 1.702 . . 56 32 7 ILE HG2 H 0.949 . . 57 32 7 ILE HD1 H 0.881 . . 58 32 7 ILE CA C 64.092 . . 59 32 7 ILE CB C 36.962 . . 60 32 7 ILE CG1 C 27.974 . . 61 32 7 ILE CG2 C 15.891 . . 62 32 7 ILE CD1 C 11.055 . . 63 33 8 GLY H H 7.939 . . 64 33 8 GLY HA2 H 3.842 . . 65 33 8 GLY HA3 H 3.816 . . 66 33 8 GLY CA C 46.403 . . 67 34 9 LEU H H 7.875 . . 68 34 9 LEU HA H 4.245 . . 69 34 9 LEU HB2 H 2.011 . . 70 34 9 LEU HB3 H 2.011 . . 71 34 9 LEU HG H 1.839 . . 72 34 9 LEU HD1 H 0.932 . . 73 34 9 LEU HD2 H 0.905 . . 74 34 9 LEU CA C 57.008 . . 75 34 9 LEU CB C 41.400 . . 76 34 9 LEU CG C 26.098 . . 77 34 9 LEU CD1 C 23.493 . . 78 34 9 LEU CD2 C 21.911 . . 79 35 10 MET H H 8.236 . . 80 35 10 MET HA H 4.263 . . 81 35 10 MET HB2 H 2.361 . . 82 35 10 MET HB3 H 2.178 . . 83 35 10 MET HG2 H 2.775 . . 84 35 10 MET HG3 H 2.574 . . 85 35 10 MET HE H 2.063 . . 86 35 10 MET CA C 57.961 . . 87 35 10 MET CB C 31.901 . . 88 35 10 MET CG C 31.457 . . 89 35 10 MET CE C 15.467 . . 90 36 11 VAL H H 8.626 . . 91 36 11 VAL HA H 3.811 . . 92 36 11 VAL HB H 2.171 . . 93 36 11 VAL HG1 H 1.077 . . 94 36 11 VAL HG2 H 0.965 . . 95 36 11 VAL CA C 65.338 . . 96 36 11 VAL CB C 31.308 . . 97 36 11 VAL CG1 C 21.024 . . 98 36 11 VAL CG2 C 19.734 . . 99 37 12 GLY H H 8.151 . . 100 37 12 GLY HA2 H 3.901 . . 101 37 12 GLY HA3 H 3.901 . . 102 37 12 GLY CA C 46.355 . . 103 38 13 GLY H H 7.897 . . 104 38 13 GLY HA2 H 3.938 . . 105 38 13 GLY HA3 H 3.926 . . 106 38 13 GLY CA C 46.298 . . 107 39 14 VAL H H 7.743 . . 108 39 14 VAL HA H 3.849 . . 109 39 14 VAL HB H 2.364 . . 110 39 14 VAL HG1 H 0.991 . . 111 39 14 VAL HG2 H 1.114 . . 112 39 14 VAL CA C 65.385 . . 113 39 14 VAL CB C 31.043 . . 114 39 14 VAL CG1 C 19.842 . . 115 39 14 VAL CG2 C 21.049 . . 116 40 15 VAL H H 8.204 . . 117 40 15 VAL HA H 3.601 . . 118 40 15 VAL HB H 2.326 . . 119 40 15 VAL HG1 H 0.952 . . 120 40 15 VAL HG2 H 1.080 . . 121 40 15 VAL CA C 66.866 . . 122 40 15 VAL CB C 30.875 . . 123 40 15 VAL CG1 C 19.493 . . 124 40 15 VAL CG2 C 21.353 . . 125 41 16 ILE H H 8.152 . . 126 41 16 ILE HA H 3.751 . . 127 41 16 ILE HB H 1.925 . . 128 41 16 ILE HG12 H 1.263 . . 129 41 16 ILE HG13 H 1.733 . . 130 41 16 ILE HG2 H 0.970 . . 131 41 16 ILE HD1 H 0.857 . . 132 41 16 ILE CA C 64.177 . . 133 41 16 ILE CB C 36.962 . . 134 41 16 ILE CG1 C 27.974 . . 135 41 16 ILE CG2 C 16.074 . . 136 41 16 ILE CD1 C 10.863 . . 137 42 17 ALA H H 7.889 . . 138 42 17 ALA HA H 4.052 . . 139 42 17 ALA HB H 1.539 . . 140 42 17 ALA CA C 54.956 . . 141 42 17 ALA CB C 16.990 . . 142 43 18 THR H H 7.938 . . 143 43 18 THR HA H 3.894 . . 144 43 18 THR HB H 4.566 . . 145 43 18 THR HG1 H 5.537 . . 146 43 18 THR HG2 H 1.281 . . 147 43 18 THR CA C 66.736 . . 148 43 18 THR CB C 68.334 . . 149 43 18 THR CG2 C 19.557 . . 150 44 19 VAL H H 8.267 . . 151 44 19 VAL HA H 3.635 . . 152 44 19 VAL HB H 2.350 . . 153 44 19 VAL HG1 H 0.940 . . 154 44 19 VAL HG2 H 1.094 . . 155 44 19 VAL CA C 67.376 . . 156 44 19 VAL CB C 31.043 . . 157 44 19 VAL CG1 C 21.049 . . 158 44 19 VAL CG2 C 19.839 . . 159 45 20 ILE H H 8.481 . . 160 45 20 ILE HA H 3.636 . . 161 45 20 ILE HB H 2.113 . . 162 45 20 ILE HG12 H 1.883 . . 163 45 20 ILE HG13 H 1.115 . . 164 45 20 ILE HG2 H 0.919 . . 165 45 20 ILE HD1 H 0.854 . . 166 45 20 ILE CA C 65.708 . . 167 45 20 ILE CB C 36.866 . . 168 45 20 ILE CG1 C 28.232 . . 169 45 20 ILE CG2 C 15.493 . . 170 45 20 ILE CD1 C 10.842 . . 171 46 21 VAL H H 8.221 . . 172 46 21 VAL HA H 3.637 . . 173 46 21 VAL HB H 2.275 . . 174 46 21 VAL HG1 H 1.134 . . 175 46 21 VAL HG2 H 0.981 . . 176 46 21 VAL CA C 66.473 . . 177 46 21 VAL CB C 30.875 . . 178 46 21 VAL CG1 C 21.848 . . 179 46 21 VAL CG2 C 19.842 . . 180 47 22 ILE H H 8.559 . . 181 47 22 ILE HA H 3.700 . . 182 47 22 ILE HB H 1.976 . . 183 47 22 ILE HG12 H 1.247 . . 184 47 22 ILE HG13 H 1.848 . . 185 47 22 ILE HG2 H 0.959 . . 186 47 22 ILE HD1 H 0.845 . . 187 47 22 ILE CA C 64.780 . . 188 47 22 ILE CB C 36.946 . . 189 47 22 ILE CG1 C 28.195 . . 190 47 22 ILE CG2 C 16.093 . . 191 47 22 ILE CD1 C 11.159 . . 192 48 23 THR H H 8.160 . . 193 48 23 THR HA H 3.844 . . 194 48 23 THR HB H 4.548 . . 195 48 23 THR HG1 H 5.672 . . 196 48 23 THR HG2 H 1.244 . . 197 48 23 THR CA C 67.287 . . 198 48 23 THR CB C 68.024 . . 199 48 23 THR CG2 C 19.362 . . 200 49 24 LEU H H 8.486 . . 201 49 24 LEU HA H 4.108 . . 202 49 24 LEU HB2 H 2.120 . . 203 49 24 LEU HB3 H 2.120 . . 204 49 24 LEU HG H 1.979 . . 205 49 24 LEU HD1 H 0.895 . . 206 49 24 LEU HD2 H 0.872 . . 207 49 24 LEU CA C 57.974 . . 208 49 24 LEU CB C 41.039 . . 209 49 24 LEU CG C 25.905 . . 210 49 24 LEU CD1 C 23.929 . . 211 49 24 LEU CD2 C 21.505 . . 212 50 25 VAL H H 8.624 . . 213 50 25 VAL HA H 3.609 . . 214 50 25 VAL HB H 2.334 . . 215 50 25 VAL HG1 H 0.953 . . 216 50 25 VAL HG2 H 1.100 . . 217 50 25 VAL CA C 66.582 . . 218 50 25 VAL CB C 30.875 . . 219 50 25 VAL CG1 C 20.023 . . 220 50 25 VAL CG2 C 21.353 . . 221 51 26 MET H H 8.553 . . 222 51 26 MET HA H 4.201 . . 223 51 26 MET HB2 H 2.427 . . 224 51 26 MET HB3 H 2.106 . . 225 51 26 MET HG2 H 2.803 . . 226 51 26 MET HG3 H 2.669 . . 227 51 26 MET HE H 2.053 . . 228 51 26 MET CA C 58.029 . . 229 51 26 MET CB C 31.052 . . 230 51 26 MET CG C 31.937 . . 231 51 26 MET CE C 15.414 . . 232 52 27 LEU H H 8.528 . . 233 52 27 LEU HA H 4.141 . . 234 52 27 LEU HB2 H 2.011 . . 235 52 27 LEU HB3 H 2.011 . . 236 52 27 LEU HG H 1.933 . . 237 52 27 LEU HD1 H 0.905 . . 238 52 27 LEU HD2 H 0.885 . . 239 52 27 LEU CA C 57.134 . . 240 52 27 LEU CB C 41.400 . . 241 52 27 LEU CG C 26.001 . . 242 52 27 LEU CD1 C 23.867 . . 243 52 27 LEU CD2 C 21.583 . . 244 53 28 LYS H H 8.195 . . 245 53 28 LYS HA H 4.127 . . 246 53 28 LYS HB2 H 2.067 . . 247 53 28 LYS HB3 H 1.997 . . 248 53 28 LYS HG2 H 1.621 . . 249 53 28 LYS HG3 H 1.541 . . 250 53 28 LYS HD2 H 1.721 . . 251 53 28 LYS HD3 H 1.721 . . 252 53 28 LYS HE2 H 3.006 . . 253 53 28 LYS HE3 H 3.006 . . 254 53 28 LYS CA C 57.665 . . 255 53 28 LYS CB C 31.376 . . 256 53 28 LYS CG C 24.187 . . 257 53 28 LYS CD C 28.174 . . 258 53 28 LYS CE C 41.598 . . 259 54 29 LYS H H 8.241 . . 260 54 29 LYS HA H 4.193 . . 261 54 29 LYS HB2 H 1.995 . . 262 54 29 LYS HB3 H 1.952 . . 263 54 29 LYS HG2 H 1.515 . . 264 54 29 LYS HG3 H 1.638 . . 265 54 29 LYS HD2 H 1.717 . . 266 54 29 LYS HD3 H 1.716 . . 267 54 29 LYS HE2 H 3.006 . . 268 54 29 LYS HE3 H 3.006 . . 269 54 29 LYS CA C 57.214 . . 270 54 29 LYS CB C 31.728 . . 271 54 29 LYS CG C 24.195 . . 272 54 29 LYS CD C 28.174 . . 273 54 29 LYS CE C 41.598 . . 274 55 30 LYS H H 8.021 . . 275 55 30 LYS HA H 4.237 . . 276 55 30 LYS HB2 H 1.948 . . 277 55 30 LYS HB3 H 1.948 . . 278 55 30 LYS HG2 H 1.577 . . 279 55 30 LYS HG3 H 1.529 . . 280 55 30 LYS HD2 H 1.723 . . 281 55 30 LYS HD3 H 1.723 . . 282 55 30 LYS HE2 H 3.006 . . 283 55 30 LYS HE3 H 3.006 . . 284 55 30 LYS HZ H 7.272 . . 285 55 30 LYS CA C 56.120 . . 286 55 30 LYS CB C 32.029 . . 287 55 30 LYS CG C 24.040 . . 288 55 30 LYS CD C 28.174 . . 289 55 30 LYS CE C 41.598 . . stop_ save_