data_36009 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of Humanin containing a D-isomerized serine residue ; _BMRB_accession_number 36009 _BMRB_flat_file_name bmr36009.str _Entry_type original _Submission_date 2016-06-25 _Accession_date 2016-08-18 _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 Sugiki T. . . 2 Furuita K. . . 3 Alsanousi N. . . 4 Fujiwara T. . . 5 Kojima C. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 126 "15N chemical shifts" 22 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-02-21 update BMRB 'update entry citation' 2016-09-08 original author 'original release' stop_ _Original_release_date 2016-09-08 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution NMR structure and inhibitory effect against amyloid-beta fibrillation of Humanin containing a d-isomerized serine residue ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27349871 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Alsanousi N. . . 2 Sugiki T. . . 3 Furuita K. . . 4 So M. . . 5 Lee Y. H. . 6 Fujiwara T. . . 7 Kojima C. . . stop_ _Journal_abbreviation 'Biochem. Biophys. Res. Commun.' _Journal_volume 477 _Journal_issue 4 _Journal_ASTM BBRCA9 _Journal_ISSN 1090-2104 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 647 _Page_last 653 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Humanin _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 2691.264 _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 24 _Mol_residue_sequence ; MAPRGFSCLLLLTXEIDLPV KRRA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 MET 2 2 ALA 3 3 PRO 4 4 ARG 5 5 GLY 6 6 PHE 7 7 SER 8 8 CYS 9 9 LEU 10 10 LEU 11 11 LEU 12 12 LEU 13 13 THR 14 14 DSN 15 15 GLU 16 16 ILE 17 17 ASP 18 18 LEU 19 19 PRO 20 20 VAL 21 21 LYS 22 22 ARG 23 23 ARG 24 24 ALA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DSN _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-SERINE _BMRB_code DSN _PDB_code DSN _Standard_residue_derivative . _Molecular_mass 105.093 _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 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? OG OG O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG HG 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 CA ? ? SING N H ? ? SING N H2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB OG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING OG HG ? ? stop_ 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 '2.0 mM D-Ser-containing humanin, trifluoroethanol/water' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2.0 mM 'natural abundance' trifluoroethanol 30 % 'U-99% D' H2O 70 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version 3.97 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . 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 SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AvanceIII HD' _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _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 . 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 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_2 $software_3 stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 1H-15N HSQC' 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 1 1 MET HA H 4.116 0.01 1 2 1 1 MET HB2 H 2.164 0.002 2 3 1 1 MET HB3 H 2.164 0.002 2 4 1 1 MET HG2 H 2.633 0.01 2 5 1 1 MET HG3 H 2.633 0.01 2 6 2 2 ALA H H 8.495 0.003 1 7 2 2 ALA HA H 4.646 0.01 1 8 2 2 ALA HB H 1.375 0.01 1 9 2 2 ALA N N 127.124 0.1 1 10 3 3 PRO HA H 4.445 0.001 1 11 3 3 PRO HB3 H 2.308 0.01 1 12 3 3 PRO HG2 H 1.957 0.01 2 13 3 3 PRO HG3 H 1.957 0.01 2 14 3 3 PRO HD2 H 3.563 0.01 1 15 3 3 PRO HD3 H 3.783 0.01 1 16 4 4 ARG H H 8.303 0.002 1 17 4 4 ARG HA H 4.298 0.003 1 18 4 4 ARG HB2 H 1.843 0.01 2 19 4 4 ARG HB3 H 1.843 0.01 2 20 4 4 ARG HG2 H 1.729 0.01 1 21 4 4 ARG HG3 H 1.674 0.01 1 22 4 4 ARG HD2 H 3.224 0.01 2 23 4 4 ARG HD3 H 3.224 0.01 2 24 4 4 ARG HE H 7.174 0.01 1 25 4 4 ARG N N 120.653 0.1 1 26 4 4 ARG NE N 120.143 0.1 1 27 5 5 GLY H H 8.369 0.002 1 28 5 5 GLY HA2 H 4.024 0.01 1 29 5 5 GLY HA3 H 3.873 0.01 1 30 5 5 GLY N N 108.471 0.1 1 31 6 6 PHE H H 8.052 0.001 1 32 6 6 PHE HA H 4.418 0.001 1 33 6 6 PHE HB2 H 3.098 0.002 1 34 6 6 PHE HB3 H 3.164 0.006 1 35 6 6 PHE HD1 H 7.181 0.005 3 36 6 6 PHE HD2 H 7.181 0.005 3 37 6 6 PHE HE1 H 7.277 0.003 3 38 6 6 PHE HE2 H 7.277 0.003 3 39 6 6 PHE N N 120.691 0.1 1 40 7 7 SER H H 7.998 0.003 1 41 7 7 SER HA H 4.089 0.01 1 42 7 7 SER HB2 H 3.974 0.01 1 43 7 7 SER HB3 H 3.881 0.01 1 44 7 7 SER N N 114.093 0.1 1 45 8 8 CYS H H 7.889 0.004 1 46 8 8 CYS HA H 4.160 0.01 1 47 8 8 CYS HB2 H 2.983 0.01 2 48 8 8 CYS HB3 H 2.983 0.01 2 49 8 8 CYS N N 119.428 0.1 1 50 9 9 LEU H H 7.725 0.002 1 51 9 9 LEU HA H 4.079 0.01 1 52 9 9 LEU HB2 H 1.718 0.01 2 53 9 9 LEU HB3 H 1.718 0.01 2 54 9 9 LEU HG H 1.647 0.007 1 55 9 9 LEU HD1 H 0.911 0.01 2 56 9 9 LEU HD2 H 0.855 0.01 2 57 9 9 LEU N N 120.601 0.1 1 58 10 10 LEU H H 7.807 0.001 1 59 10 10 LEU HA H 3.855 0.01 1 60 10 10 LEU HB2 H 1.271 0.01 1 61 10 10 LEU HB3 H 1.843 0.01 1 62 10 10 LEU HG H 1.505 0.01 1 63 10 10 LEU HD1 H 0.713 0.01 2 64 10 10 LEU HD2 H 0.785 0.01 2 65 10 10 LEU N N 119.082 0.1 1 66 11 11 LEU H H 7.582 0.01 1 67 11 11 LEU HA H 4.081 0.01 1 68 11 11 LEU HB2 H 1.769 0.01 1 69 11 11 LEU HB3 H 1.835 0.01 1 70 11 11 LEU HD1 H 0.912 0.01 2 71 11 11 LEU HD2 H 0.912 0.01 2 72 11 11 LEU N N 118.684 0.1 1 73 12 12 LEU H H 8.447 0.002 1 74 12 12 LEU HA H 4.125 0.01 1 75 12 12 LEU HB2 H 1.624 0.01 2 76 12 12 LEU HB3 H 1.624 0.01 2 77 12 12 LEU HG H 1.872 0.01 1 78 12 12 LEU N N 119.824 0.1 1 79 13 13 THR H H 7.783 0.002 1 80 13 13 THR HA H 4.300 0.01 1 81 13 13 THR HB H 4.456 0.001 1 82 13 13 THR HG2 H 1.327 0.001 1 83 13 13 THR N N 105.122 0.1 1 84 14 14 DSN H H 7.702 0.001 1 85 14 14 DSN N N 116.415 0.1 1 86 14 14 DSN HA H 4.313 0.01 1 87 14 14 DSN HB2 H 4.106 0.01 1 88 14 14 DSN HB3 H 4.106 0.01 1 89 15 15 GLU H H 8.136 0.001 1 90 15 15 GLU HA H 4.340 0.001 1 91 15 15 GLU HB2 H 2.264 0.01 1 92 15 15 GLU HB3 H 1.910 0.002 1 93 15 15 GLU HG2 H 2.463 0.002 1 94 15 15 GLU HG3 H 2.437 0.003 1 95 15 15 GLU N N 120.450 0.1 1 96 16 16 ILE H H 7.452 0.001 1 97 16 16 ILE HA H 4.093 0.01 1 98 16 16 ILE HB H 1.732 0.004 1 99 16 16 ILE HG12 H 1.156 0.001 2 100 16 16 ILE HG13 H 1.156 0.001 2 101 16 16 ILE HG2 H 0.856 0.01 2 102 16 16 ILE HD1 H 1.366 0.01 1 103 16 16 ILE N N 116.271 0.1 1 104 17 17 ASP H H 7.947 0.001 1 105 17 17 ASP HA H 4.792 0.01 1 106 17 17 ASP HB2 H 2.925 0.01 1 107 17 17 ASP HB3 H 2.755 0.01 1 108 17 17 ASP N N 119.740 0.1 1 109 18 18 LEU H H 7.760 0.001 1 110 18 18 LEU HA H 4.532 0.01 1 111 18 18 LEU HB2 H 1.715 0.01 2 112 18 18 LEU HB3 H 1.715 0.01 2 113 18 18 LEU HG H 1.531 0.002 1 114 18 18 LEU HD1 H 0.948 0.01 2 115 18 18 LEU HD2 H 0.914 0.001 2 116 18 18 LEU N N 122.450 0.1 1 117 19 19 PRO HA H 4.458 0.001 1 118 19 19 PRO HB3 H 2.229 0.01 1 119 19 19 PRO HG2 H 2.026 0.01 2 120 19 19 PRO HG3 H 2.026 0.01 2 121 19 19 PRO HD2 H 3.628 0.01 1 122 19 19 PRO HD3 H 3.800 0.01 1 123 20 20 VAL H H 7.511 0.001 1 124 20 20 VAL HA H 4.060 0.01 1 125 20 20 VAL HB H 2.112 0.01 1 126 20 20 VAL HG1 H 0.941 0.01 2 127 20 20 VAL HG2 H 0.941 0.01 2 128 20 20 VAL N N 116.495 0.1 1 129 21 21 LYS H H 8.032 0.001 1 130 21 21 LYS HA H 4.304 0.001 1 131 21 21 LYS HB2 H 1.792 0.003 1 132 21 21 LYS HB3 H 1.864 0.005 1 133 21 21 LYS HG2 H 1.434 0.002 1 134 21 21 LYS HG3 H 1.491 0.002 1 135 21 21 LYS HD2 H 1.705 0.01 2 136 21 21 LYS HD3 H 1.705 0.01 2 137 21 21 LYS HE2 H 3.000 0.001 2 138 21 21 LYS HE3 H 3.000 0.001 2 139 21 21 LYS HZ H 7.610 0.01 1 140 21 21 LYS N N 122.468 0.1 1 141 22 22 ARG H H 8.080 0.01 1 142 22 22 ARG N N 120.730 0.1 1 143 23 23 ARG H H 8.095 0.01 1 144 23 23 ARG N N 121.356 0.1 1 145 24 24 ALA H H 8.095 0.01 1 146 24 24 ALA HA H 4.293 0.01 1 147 24 24 ALA HB H 1.414 0.001 1 148 24 24 ALA N N 126.854 0.1 1 stop_ save_