data_27072 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; TDP-43 NTD ; _BMRB_accession_number 27072 _BMRB_flat_file_name bmr27072.str _Entry_type original _Submission_date 2017-04-13 _Accession_date 2017-04-13 _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 Afroz Tariq . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 71 "15N chemical shifts" 69 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-08-11 update BMRB 'update entry citation' 2017-05-15 original author 'original release' stop_ _Original_release_date 2017-04-13 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28663553 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Afroz Tariq . . 2 Hock Eva-Maria M. . 3 Ernst Patrick . . 4 Foglieni Chiara . . 5 Jambeau Melanie . . 6 Gilhespy Larissa . . 7 Laferriere Florent . . 8 Maniecka Zuzanna . . 9 Pluckthun Andreas . . 10 Mittl Peer . . 11 Paganetti Paolo . . 12 Allain Frederic . . 13 Polymenidou Magdalini . . stop_ _Journal_abbreviation 'Nat. Commun.' _Journal_name_full 'Nature communications' _Journal_volume 8 _Journal_issue 1 _Journal_ISSN 2041-1723 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 45 _Page_last 45 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'TDP-43 NTD' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'TDP-43 NTD' $TDP-43_NTD 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_TDP-43_NTD _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common TDP-43_NTD _Molecular_mass . _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 102 _Mol_residue_sequence ; MGSSHHHHHHSSGLVPRGSH MASSEYIRVTEDENDEPIEI PSEDDGTVLLSTVTAQFPGA CGLRYRNPVSQCMRGVRLVE GILHAPDAGWGNLVYVVNYP KD ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -21 MET 2 -20 GLY 3 -19 SER 4 -18 SER 5 -17 HIS 6 -16 HIS 7 -15 HIS 8 -14 HIS 9 -13 HIS 10 -12 HIS 11 -11 SER 12 -10 SER 13 -9 GLY 14 -8 LEU 15 -7 VAL 16 -6 PRO 17 -5 ARG 18 -4 GLY 19 -3 SER 20 -2 HIS 21 -1 MET 22 0 ALA 23 1 SER 24 2 SER 25 3 GLU 26 4 TYR 27 5 ILE 28 6 ARG 29 7 VAL 30 8 THR 31 9 GLU 32 10 ASP 33 11 GLU 34 12 ASN 35 13 ASP 36 14 GLU 37 15 PRO 38 16 ILE 39 17 GLU 40 18 ILE 41 19 PRO 42 20 SER 43 21 GLU 44 22 ASP 45 23 ASP 46 24 GLY 47 25 THR 48 26 VAL 49 27 LEU 50 28 LEU 51 29 SER 52 30 THR 53 31 VAL 54 32 THR 55 33 ALA 56 34 GLN 57 35 PHE 58 36 PRO 59 37 GLY 60 38 ALA 61 39 CYS 62 40 GLY 63 41 LEU 64 42 ARG 65 43 TYR 66 44 ARG 67 45 ASN 68 46 PRO 69 47 VAL 70 48 SER 71 49 GLN 72 50 CYS 73 51 MET 74 52 ARG 75 53 GLY 76 54 VAL 77 55 ARG 78 56 LEU 79 57 VAL 80 58 GLU 81 59 GLY 82 60 ILE 83 61 LEU 84 62 HIS 85 63 ALA 86 64 PRO 87 65 ASP 88 66 ALA 89 67 GLY 90 68 TRP 91 69 GLY 92 70 ASN 93 71 LEU 94 72 VAL 95 73 TYR 96 74 VAL 97 75 VAL 98 76 ASN 99 77 TYR 100 78 PRO 101 79 LYS 102 80 ASP 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 $TDP-43_NTD 'E. coli' 562 Bacteria . Escherichia coli 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 $TDP-43_NTD 'recombinant technology' . Escherichia coli . pET28A(1) stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $TDP-43_NTD 600 uM '[U-100% 15N]' $TDP-43_NTD 600 uM '[U-100% 13C; U-100% 15N]' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _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_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_3D_CBCA(CO)NH_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _Sample_label $sample_1 save_ save_3D_HNCA_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label $sample_1 save_ save_3D_HN(CO)CA_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HN(CO)CA' _Sample_label $sample_1 save_ save_3D_1H-15N_NOESY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_1 save_ save_3D_1H-13C_NOESY_aliphatic_8 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY aliphatic' _Sample_label $sample_1 save_ save_3D_1H-13C_NOESY_aromatic_9 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY aromatic' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_d20_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC d20' _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 pH 7.4 . pH pressure 1 . atm temperature 273 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_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 water H 1 protons ppm 4.7 internal indirect . . . 1.000000000 water N 15 protons ppm 4.7 internal indirect . . . 0.101329118 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-13C HSQC' '3D HNCA' '3D HN(CO)CA' '3D 1H-15N NOESY' '3D 1H-13C NOESY aliphatic' '3D 1H-13C NOESY aromatic' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'TDP-43 NTD' _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 0 22 ALA H H 8.288 . . 2 0 22 ALA N N 125.197 . . 3 1 23 SER H H 8.254 . . 4 1 23 SER N N 114.995 . . 5 2 24 SER H H 8.338 . . 6 2 24 SER N N 117.674 . . 7 3 25 GLU H H 8.433 . . 8 3 25 GLU N N 122.592 . . 9 4 26 TYR H H 8.133 . . 10 4 26 TYR N N 119.099 . . 11 5 27 ILE H H 8.925 . . 12 5 27 ILE N N 116.275 . . 13 6 28 ARG H H 8.744 . . 14 6 28 ARG N N 123.877 . . 15 7 29 VAL H H 9.019 . . 16 7 29 VAL N N 122.858 . . 17 8 30 THR H H 8.773 . . 18 8 30 THR N N 118.505 . . 19 9 31 GLU H H 8.700 . . 20 9 31 GLU N N 121.644 . . 21 10 32 ASP H H 8.007 . . 22 10 32 ASP N N 119.444 . . 23 11 33 GLU H H 9.193 . . 24 11 33 GLU N N 126.040 . . 25 12 34 ASN H H 9.081 . . 26 12 34 ASN HD21 H 7.940 . . 27 12 34 ASN HD22 H 6.941 . . 28 12 34 ASN N N 116.945 . . 29 12 34 ASN ND2 N 114.998 . . 30 13 35 ASP H H 8.097 . . 31 13 35 ASP N N 121.428 . . 32 14 36 GLU H H 8.598 . . 33 14 36 GLU N N 123.037 . . 34 16 38 ILE H H 9.239 . . 35 16 38 ILE N N 119.116 . . 36 18 40 ILE H H 9.494 . . 37 18 40 ILE N N 126.297 . . 38 20 42 SER H H 7.910 . . 39 20 42 SER N N 114.758 . . 40 21 43 GLU H H 9.327 . . 41 21 43 GLU N N 118.095 . . 42 22 44 ASP H H 9.028 . . 43 22 44 ASP N N 122.267 . . 44 23 45 ASP H H 7.654 . . 45 23 45 ASP N N 115.655 . . 46 24 46 GLY H H 8.229 . . 47 24 46 GLY N N 107.744 . . 48 25 47 THR H H 7.924 . . 49 25 47 THR N N 113.319 . . 50 26 48 VAL H H 8.630 . . 51 26 48 VAL N N 117.597 . . 52 27 49 LEU H H 8.594 . . 53 27 49 LEU N N 125.964 . . 54 28 50 LEU H H 8.802 . . 55 28 50 LEU N N 125.660 . . 56 29 51 SER H H 8.840 . . 57 29 51 SER N N 112.772 . . 58 30 52 THR H H 7.519 . . 59 30 52 THR N N 121.080 . . 60 31 53 VAL H H 7.472 . . 61 31 53 VAL N N 121.392 . . 62 32 54 THR H H 9.480 . . 63 32 54 THR N N 112.880 . . 64 33 55 ALA H H 7.296 . . 65 33 55 ALA N N 122.486 . . 66 34 56 GLN H H 7.017 . . 67 34 56 GLN HE22 H 6.662 . . 68 34 56 GLN N N 111.351 . . 69 34 56 GLN NE2 N 114.217 . . 70 35 57 PHE H H 8.317 . . 71 35 57 PHE N N 117.549 . . 72 37 59 GLY H H 8.751 . . 73 37 59 GLY N N 111.187 . . 74 38 60 ALA H H 8.146 . . 75 38 60 ALA N N 122.656 . . 76 39 61 CYS H H 9.028 . . 77 39 61 CYS N N 112.966 . . 78 40 62 GLY H H 7.396 . . 79 40 62 GLY N N 105.604 . . 80 41 63 LEU H H 8.869 . . 81 41 63 LEU N N 117.877 . . 82 42 64 ARG H H 9.563 . . 83 42 64 ARG N N 120.301 . . 84 43 65 TYR H H 9.102 . . 85 43 65 TYR N N 116.395 . . 86 44 66 ARG H H 9.076 . . 87 44 66 ARG N N 122.013 . . 88 45 67 ASN H H 8.608 . . 89 45 67 ASN N N 127.800 . . 90 47 69 VAL H H 7.957 . . 91 47 69 VAL N N 116.646 . . 92 49 71 GLN H H 8.390 . . 93 49 71 GLN N N 114.939 . . 94 50 72 CYS H H 7.807 . . 95 50 72 CYS N N 117.922 . . 96 51 73 MET H H 9.002 . . 97 51 73 MET N N 122.228 . . 98 52 74 ARG H H 9.150 . . 99 52 74 ARG N N 123.316 . . 100 55 77 ARG H H 9.464 . . 101 55 77 ARG N N 132.091 . . 102 57 79 VAL H H 9.297 . . 103 57 79 VAL N N 127.482 . . 104 58 80 GLU H H 9.476 . . 105 58 80 GLU N N 127.524 . . 106 59 81 GLY H H 8.229 . . 107 59 81 GLY N N 102.627 . . 108 60 82 ILE H H 8.293 . . 109 60 82 ILE N N 123.978 . . 110 61 83 LEU H H 9.315 . . 111 61 83 LEU N N 128.497 . . 112 63 85 ALA H H 8.375 . . 113 63 85 ALA N N 125.399 . . 114 67 89 GLY H H 7.995 . . 115 67 89 GLY N N 107.905 . . 116 68 90 TRP H H 8.476 . . 117 68 90 TRP HE1 H 10.158 . . 118 68 90 TRP N N 119.801 . . 119 68 90 TRP NE1 N 127.992 . . 120 69 91 GLY H H 8.575 . . 121 69 91 GLY N N 103.157 . . 122 71 93 LEU H H 6.970 . . 123 71 93 LEU N N 118.399 . . 124 72 94 VAL H H 7.806 . . 125 72 94 VAL N N 118.324 . . 126 73 95 TYR H H 8.942 . . 127 73 95 TYR N N 127.294 . . 128 74 96 VAL H H 9.549 . . 129 74 96 VAL N N 122.762 . . 130 75 97 VAL H H 7.874 . . 131 75 97 VAL N N 121.588 . . 132 76 98 ASN H H 7.784 . . 133 76 98 ASN HD21 H 7.189 . . 134 76 98 ASN HD22 H 6.327 . . 135 76 98 ASN N N 121.063 . . 136 76 98 ASN ND2 N 110.572 . . 137 79 101 LYS H H 8.419 . . 138 79 101 LYS N N 121.657 . . 139 80 102 ASP H H 7.913 . . 140 80 102 ASP N N 126.685 . . stop_ save_