data_50263 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR backbone assignment of the transmembrane helix of TREM2, an Alzheimer linked disease protein ; _BMRB_accession_number 50263 _BMRB_flat_file_name bmr50263.str _Entry_type original _Submission_date 2020-05-08 _Accession_date 2020-05-08 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'TREM2 trasnmembran helix in DPC micelles' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Steiner Andrea . . 2 Hagn Franz X. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 32 "13C chemical shifts" 103 "15N chemical shifts" 32 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-10-16 update BMRB 'update entry citation' 2020-06-08 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 50264 'TREM2 transmembrane helix K186A variant' 50265 'TREM2 transmembrane helix in complex with the partner protein DAP12' stop_ _Original_release_date 2020-05-08 save_ ############################# # Citation for this entry # ############################# save_citations_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; gamma-Secretase cleavage of the Alzheimer risk factor TREM2 is determined by its intrinsic structural dynamics ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 32830336 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Steiner Andrea . . 2 Schlepckow Kai . . 3 Brunner Bettina . . 4 Steiner Harald . . 5 Haass Christian . . 6 Hagn Franz X. . stop_ _Journal_abbreviation 'EMBO J.' _Journal_volume 39 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first e104247 _Page_last e104247 _Year 2020 _Details . loop_ _Keyword NMR TREM2 dynamics 'intramembrane protease' structure stop_ save_ ################################## # Molecular system description # ################################## save_assembly_1 _Saveframe_category molecular_system _Mol_system_name TREM2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label TREM2 $entity_1 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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass . _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 49 _Mol_residue_sequence ; GSGRSLLEGEIPFPPTSILL LLACIFLIKILAASALWAAA WHGQKPGTH ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -2 GLY 2 -1 SER 3 0 GLY 4 1 ARG 5 2 SER 6 3 LEU 7 4 LEU 8 5 GLU 9 6 GLY 10 7 GLU 11 8 ILE 12 9 PRO 13 10 PHE 14 11 PRO 15 12 PRO 16 13 THR 17 14 SER 18 15 ILE 19 16 LEU 20 17 LEU 21 18 LEU 22 19 LEU 23 20 ALA 24 21 CYS 25 22 ILE 26 23 PHE 27 24 LEU 28 25 ILE 29 26 LYS 30 27 ILE 31 28 LEU 32 29 ALA 33 30 ALA 34 31 SER 35 32 ALA 36 33 LEU 37 34 TRP 38 35 ALA 39 36 ALA 40 37 ALA 41 38 TRP 42 39 HIS 43 40 GLY 44 41 GLN 45 42 LYS 46 43 PRO 47 44 GLY 48 45 THR 49 46 HIS 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 Q9NZC2 TREM2 . . . . . stop_ save_ #################### # Natural source # #################### save_natural_source_1 _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_1 _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $entity_1 'recombinant technology' . Escherichia coli 'BL21 (DE3)' plasmid pET15b stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 500 uM TREM2-TMH in 200mM DPC 20 mM NaPi pH7.0 50 mM NaCl 0.5 mM EDTA 5 mM DTT ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 500 uM '[U-13C; U-15N; U-2H]' DPC 200 mM 'natural abundance' NaPi 20 mM 'natural abundance' NaCl 50 mM 'natural abundance' EDTA 0.5 mM 'natural abundance' DTT 5 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name TOPSPIN _Version 3.5 loop_ _Task collection stop_ _Details . save_ save_software_2 _Saveframe_category software _Name NMRFAM-SPARKY _Version . loop_ _Task 'chemical shift assignment' 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_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_3D_HNCO_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $sample_1 save_ save_3D_HNCA_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label $sample_1 save_ save_3D_HNCACB_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_3D_HN(CO)CA_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HN(CO)CA' _Sample_label $sample_1 save_ save_3D_1H-15N_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N 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' 0.1 . M pH 7.0 . pH pressure 1 . atm temperature 310 . 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 external indirect . . . . DSS H 1 'methyl protons' ppm 0 external direct . . . 1 DSS N 15 'methyl protons' ppm 0 external indirect . . . . 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_1 $software_2 stop_ loop_ _Experiment_label '2D 1H-15N HSQC' '3D HNCO' '3D HNCA' '3D HNCACB' '3D HN(CO)CA' '3D 1H-15N 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 TREM2 _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 5 SER C C 175.66 0.05 1 2 2 5 SER CA C 58.43 0.05 1 3 2 5 SER CB C 64.43 0.05 1 4 3 6 LEU H H 8.64 0.02 1 5 3 6 LEU C C 177.64 0.05 1 6 3 6 LEU CA C 56.95 0.05 1 7 3 6 LEU CB C 42.79 0.05 1 8 3 6 LEU N N 125.83 0.05 1 9 4 7 LEU H H 8.64 0.02 1 10 4 7 LEU C C 177.64 0.05 1 11 4 7 LEU CA C 56.95 0.05 1 12 4 7 LEU CB C 42.79 0.05 1 13 4 7 LEU N N 125.83 0.05 1 14 5 8 GLU H H 7.75 0.02 1 15 5 8 GLU C C 176.84 0.05 1 16 5 8 GLU CA C 56.33 0.05 1 17 5 8 GLU CB C 30.79 0.05 1 18 5 8 GLU N N 119.18 0.05 1 19 6 9 GLY H H 7.96 0.02 1 20 6 9 GLY C C 173.44 0.05 1 21 6 9 GLY CA C 44.94 0.05 1 22 6 9 GLY N N 109.58 0.05 1 23 7 10 GLU H H 8.11 0.02 1 24 7 10 GLU C C 176.14 0.05 1 25 7 10 GLU CA C 55.95 0.05 1 26 7 10 GLU CB C 30.51 0.05 1 27 7 10 GLU N N 121.08 0.05 1 28 8 11 ILE H H 8.16 0.02 1 29 8 11 ILE C C 174.84 0.05 1 30 8 11 ILE CA C 57.96 0.05 1 31 8 11 ILE CB C 39.15 0.05 1 32 8 11 ILE N N 123.78 0.05 1 33 9 12 PRO CA C 62.66 0.05 1 34 9 12 PRO CB C 31.58 0.05 1 35 10 13 PHE H H 7.68 0.02 1 36 10 13 PHE C C 173.84 0.05 1 37 10 13 PHE CA C 62.62 0.05 1 38 10 13 PHE N N 119.88 0.05 1 39 13 16 THR C C 176.04 0.05 1 40 13 16 THR CA C 66.26 0.05 1 41 13 16 THR CB C 68.91 0.05 1 42 14 17 SER H H 8.25 0.02 1 43 14 17 SER C C 175.44 0.05 1 44 14 17 SER CA C 61.84 0.05 1 45 14 17 SER N N 116.78 0.05 1 46 15 18 ILE H H 7.25 0.02 1 47 15 18 ILE C C 177.34 0.05 1 48 15 18 ILE CA C 63.19 0.05 1 49 15 18 ILE CB C 37.24 0.05 1 50 15 18 ILE N N 121.28 0.05 1 51 16 19 LEU H H 7.77 0.02 1 52 16 19 LEU C C 178.34 0.05 1 53 16 19 LEU CA C 58.05 0.05 1 54 16 19 LEU CB C 41.72 0.05 1 55 16 19 LEU N N 120.48 0.05 1 56 17 20 LEU H H 8.03 0.02 1 57 17 20 LEU C C 178.44 0.05 1 58 17 20 LEU CA C 57.86 0.05 1 59 17 20 LEU CB C 41.81 0.05 1 60 17 20 LEU N N 118.38 0.05 1 61 18 21 LEU H H 7.75 0.02 1 62 18 21 LEU C C 178.54 0.05 1 63 18 21 LEU CA C 58.14 0.05 1 64 18 21 LEU CB C 41.75 0.05 1 65 18 21 LEU N N 120.75 0.05 1 66 19 22 LEU H H 8.25 0.02 1 67 19 22 LEU C C 178.34 0.05 1 68 19 22 LEU CA C 57.89 0.05 1 69 19 22 LEU CB C 41.72 0.05 1 70 19 22 LEU N N 118.63 0.05 1 71 20 23 ALA H H 8.3 0.02 1 72 20 23 ALA C C 179.04 0.05 1 73 20 23 ALA CA C 55.39 0.05 1 74 20 23 ALA CB C 18.04 0.05 1 75 20 23 ALA N N 121.05 0.05 1 76 21 24 CYS H H 8.11 0.02 1 77 21 24 CYS C C 176.54 0.05 1 78 21 24 CYS CA C 64.35 0.05 1 79 21 24 CYS CB C 27.37 0.05 1 80 21 24 CYS N N 116.05 0.05 1 81 22 25 ILE H H 8.13 0.02 1 82 22 25 ILE C C 177.34 0.05 1 83 22 25 ILE CA C 65.35 0.05 1 84 22 25 ILE CB C 37.58 0.05 1 85 22 25 ILE N N 119.76 0.05 1 86 23 26 PHE H H 8.34 0.02 1 87 23 26 PHE C C 177.24 0.05 1 88 23 26 PHE CA C 61.15 0.05 1 89 23 26 PHE N N 119.73 0.05 1 90 24 27 LEU H H 8.4 0.02 1 91 24 27 LEU C C 178.64 0.05 1 92 24 27 LEU CA C 58.02 0.05 1 93 24 27 LEU CB C 41.92 0.05 1 94 24 27 LEU N N 119.37 0.05 1 95 25 28 ILE H H 8.24 0.02 1 96 25 28 ILE C C 177.44 0.05 1 97 25 28 ILE CA C 65.19 0.05 1 98 25 28 ILE CB C 37.27 0.05 1 99 25 28 ILE N N 119.34 0.05 1 100 26 29 LYS H H 8.11 0.02 1 101 26 29 LYS C C 178.94 0.05 1 102 26 29 LYS CA C 59.33 0.05 1 103 26 29 LYS N N 120.22 0.05 1 104 27 30 ILE H H 8.13 0.02 1 105 27 30 ILE C C 178.84 0.05 1 106 27 30 ILE CA C 64.22 0.05 1 107 27 30 ILE CB C 37.66 0.05 1 108 27 30 ILE N N 119.04 0.05 1 109 28 31 LEU H H 8.5 0.02 1 110 28 31 LEU C C 179.14 0.05 1 111 28 31 LEU CA C 57.64 0.05 1 112 28 31 LEU CB C 41.92 0.05 1 113 28 31 LEU N N 122.63 0.05 1 114 29 32 ALA H H 8.62 0.02 1 115 29 32 ALA C C 178.44 0.05 1 116 29 32 ALA CA C 54.38 0.05 1 117 29 32 ALA CB C 18.46 0.05 1 118 29 32 ALA N N 121.85 0.05 1 119 30 33 ALA C C 178.94 0.05 1 120 30 33 ALA CA C 53.38 0.05 1 121 30 33 ALA CB C 18.16 0.05 1 122 31 34 SER H H 8.04 0.02 1 123 31 34 SER CA C 60.71 0.05 1 124 31 34 SER N N 115.3 0.05 1 125 32 35 ALA C C 179.44 0.05 1 126 32 35 ALA CA C 54.26 0.05 1 127 32 35 ALA CB C 18.71 0.05 1 128 33 36 LEU H H 8.11 0.02 1 129 33 36 LEU C C 178.74 0.05 1 130 33 36 LEU CA C 57.36 0.05 1 131 33 36 LEU CB C 42.14 0.05 1 132 33 36 LEU N N 119.1 0.05 1 133 34 37 TRP H H 7.78 0.02 1 134 34 37 TRP C C 177.44 0.05 1 135 34 37 TRP CA C 59.18 0.05 1 136 34 37 TRP CB C 29.87 0.05 1 137 34 37 TRP N N 120.11 0.05 1 138 35 38 ALA H H 7.98 0.02 1 139 35 38 ALA C C 179.14 0.05 1 140 35 38 ALA CA C 54.26 0.05 1 141 35 38 ALA CB C 18.71 0.05 1 142 35 38 ALA N N 121.59 0.05 1 143 36 39 ALA H H 7.93 0.02 1 144 36 39 ALA C C 178.94 0.05 1 145 36 39 ALA CA C 54.22 0.05 1 146 36 39 ALA CB C 18.88 0.05 1 147 36 39 ALA N N 120.32 0.05 1 148 37 40 ALA H H 7.84 0.02 1 149 37 40 ALA C C 178.24 0.05 1 150 37 40 ALA CA C 53.44 0.05 1 151 37 40 ALA CB C 18.94 0.05 1 152 37 40 ALA N N 120.89 0.05 1 153 38 41 TRP H H 7.82 0.02 1 154 38 41 TRP C C 176.74 0.05 1 155 38 41 TRP CA C 53.41 0.05 1 156 38 41 TRP N N 118.39 0.05 1 157 39 42 HIS H H 7.9 0.02 1 158 39 42 HIS C C 176.74 0.05 1 159 39 42 HIS CA C 56.98 0.05 1 160 39 42 HIS N N 119.0 0.05 1 161 45 48 THR C C 173.74 0.05 1 162 45 48 THR CA C 61.68 0.05 1 163 45 48 THR CB C 70.57 0.05 1 164 46 49 HIS H H 7.87 0.02 1 165 46 49 HIS C C 179.84 0.05 1 166 46 49 HIS CA C 57.55 0.05 1 167 46 49 HIS N N 127.65 0.05 1 stop_ save_