data_18795 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR assignments of Amylin in DMSO ; _BMRB_accession_number 18795 _BMRB_flat_file_name bmr18795.str _Entry_type original _Submission_date 2012-10-20 _Accession_date 2012-10-20 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'NMR assignments of Amylin in 95% DMSO / 5% Dichloroacetic acid for quenched hydrogen exchange studies of amylin fibrils.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Alexandrescu Andrei . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 112 "15N chemical shifts" 35 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-04-02 original author . stop_ _Original_release_date 2013-04-02 save_ ############################# # Citation for this entry # ############################# save_NMR_assignments_of_amylin_in_DMSO _Saveframe_category entry_citation _Citation_full . _Citation_title 'Amide proton solvent protection in amylin fibrils probed by quenched hydrogen exchange NMR' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23457571 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Alexandrescu Andrei T. . stop_ _Journal_abbreviation 'PLOS One' _Journal_volume 8 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first e56467 _Page_last e56467 _Year 2013 _Details . loop_ _Keyword 'amyloidogenic proteins' IAPP 'islet amyloid polypeptide' 'protein dynamics' 'type 2 diabetes' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Amylin monomer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Amylin $Amylin stop_ _System_molecular_weight . _System_physical_state denatured _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Amylin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Amylin _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 37 _Mol_residue_sequence ; KCNTATCATQRLANFLVHSS NNFGAILSSTNVGSNTY ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 CYS 3 ASN 4 THR 5 ALA 6 THR 7 CYS 8 ALA 9 THR 10 GLN 11 ARG 12 LEU 13 ALA 14 ASN 15 PHE 16 LEU 17 VAL 18 HIS 19 SER 20 SER 21 ASN 22 ASN 23 PHE 24 GLY 25 ALA 26 ILE 27 LEU 28 SER 29 SER 30 THR 31 ASN 32 VAL 33 GLY 34 SER 35 ASN 36 THR 37 TYR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-06-02 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 BMRB 16104 alpha-helix 100.00 37 100.00 100.00 4.84e-16 BMRB 16105 alpha-helix 100.00 37 100.00 100.00 4.84e-16 BMRB 17394 entity 100.00 37 100.00 100.00 4.84e-16 BMRB 20045 IAPP 51.35 19 100.00 100.00 1.91e-03 PDB 2G48 "Crystal Structure Of Human Insulin-Degrading Enzyme In Complex With Amylin" 100.00 37 100.00 100.00 4.84e-16 PDB 2KB8 "The Dynamic Alpha-Helix Structure Of Micelle-Bound Human Amylin" 97.30 37 100.00 100.00 6.09e-15 PDB 2L86 "Solution Nmr Structure Of Human Amylin In Sds Micelles At Ph 7.3" 100.00 38 100.00 100.00 4.91e-16 PDB 3G7V "Islet Amyloid Polypeptide (iapp Or Amylin) Fused To Maltose Binding Protein" 100.00 408 100.00 100.00 4.43e-16 PDB 3G7W "Islet Amyloid Polypeptide (Iapp Or Amylin) Residues 1 To 22 Fused To Maltose Binding Protein" 59.46 393 100.00 100.00 4.62e-06 PDB 3HGZ "Crystal Structure Of Human Insulin-Degrading Enzyme In Complex With Amylin" 100.00 37 100.00 100.00 4.84e-16 DBJ BAG73319 "islet amyloid polypeptide [synthetic construct]" 100.00 89 100.00 100.00 1.75e-16 EMBL CAA33032 "unnamed protein product [Homo sapiens]" 100.00 89 100.00 100.00 1.75e-16 EMBL CAA37002 "islet amyloid polypeptide [Homo sapiens]" 100.00 89 100.00 100.00 1.75e-16 EMBL CAA39504 "IAPP [Homo sapiens]" 100.00 89 97.30 97.30 1.76e-15 EMBL CAA48724 "islet amyloid polypeptide (IAAP) [Homo sapiens]" 100.00 89 100.00 100.00 1.75e-16 EMBL CAB57803 "prepro-IAPP [Homo sapiens]" 100.00 62 100.00 100.00 2.29e-16 GB AAA35524 "amylin, partial [Homo sapiens]" 100.00 62 100.00 100.00 2.29e-16 GB AAA35983 "islet amyloid polypeptide (hIAPP), partial [Homo sapiens]" 100.00 89 100.00 100.00 1.75e-16 GB AAA51728 "amyloid protein, partial [Homo sapiens]" 100.00 62 100.00 100.00 2.29e-16 GB AAA52281 "islet amyloid polypeptide [Homo sapiens]" 100.00 89 100.00 100.00 1.75e-16 GB AAI11850 "IAPP protein, partial [synthetic construct]" 100.00 89 100.00 100.00 1.75e-16 REF NP_000406 "islet amyloid polypeptide precursor [Homo sapiens]" 100.00 89 100.00 100.00 1.75e-16 REF XP_001144800 "PREDICTED: islet amyloid polypeptide [Pan troglodytes]" 100.00 89 97.30 97.30 3.17e-15 REF XP_003265632 "PREDICTED: islet amyloid polypeptide [Nomascus leucogenys]" 100.00 89 97.30 97.30 3.17e-15 REF XP_003265633 "PREDICTED: islet amyloid polypeptide [Nomascus leucogenys]" 100.00 89 97.30 97.30 3.17e-15 REF XP_003828947 "PREDICTED: islet amyloid polypeptide [Pan paniscus]" 100.00 89 97.30 97.30 3.17e-15 SP P10997 "RecName: Full=Islet amyloid polypeptide; AltName: Full=Amylin; AltName: Full=Diabetes-associated peptide; Short=DAP; AltName: F" 100.00 89 100.00 100.00 1.75e-16 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Amylin 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 $Amylin 'recombinant technology' . Escherichia coli . 'Purchased from rPeptide - proprietary vector' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '95% DMSO, 5% DCA, apparent pH 3.5' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Amylin 0.5 mM '[U-99% 15N]' DMSO-d6 95 % [U-2H] DCA-d2 5 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version . loop_ _Vendor _Address _Electronic_address 'Varian-Agilent Technologies' . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details 'With Cryogenic Probe' 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_1H-15N_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_1 save_ save_3D_1H-15N_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N TOCSY' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'no added salts' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 . mM pH* 3.5 . 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na 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' '3D 1H-15N NOESY' '3D 1H-15N TOCSY' 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 Amylin _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 LYS HA H 3.86 0.08 1 2 1 1 LYS HB2 H 1.83 0.08 2 3 2 2 CYS H H 9.034 0.001 1 4 2 2 CYS HA H 4.80 0.08 1 5 2 2 CYS HB2 H 3.08 0.08 2 6 2 2 CYS HB3 H 3.24 0.08 2 7 2 2 CYS N N 119.38 0.14 1 8 3 3 ASN H H 8.801 0.001 1 9 3 3 ASN HA H 4.64 0.08 1 10 3 3 ASN HB2 H 2.92 0.08 2 11 3 3 ASN N N 118.81 0.14 1 12 4 4 THR H H 7.698 0.001 1 13 4 4 THR HA H 4.49 0.08 1 14 4 4 THR N N 111.18 0.14 1 15 5 5 ALA H H 8.752 0.001 1 16 5 5 ALA HA H 4.17 0.08 1 17 5 5 ALA HB H 1.36 0.08 1 18 5 5 ALA N N 120.96 0.14 1 19 7 7 CYS H H 7.910 0.001 1 20 7 7 CYS HB2 H 2.92 0.08 2 21 7 7 CYS N N 119.69 0.14 1 22 8 8 ALA H H 7.586 0.001 1 23 8 8 ALA HA H 4.32 0.08 1 24 8 8 ALA HB H 1.29 0.08 1 25 8 8 ALA N N 120.76 0.14 1 26 9 9 THR H H 8.194 0.001 1 27 9 9 THR HA H 4.33 0.08 1 28 9 9 THR HG2 H 1.32 0.08 1 29 9 9 THR N N 111.60 0.14 1 30 10 10 GLN H H 8.009 0.001 1 31 10 10 GLN HA H 4.33 0.08 1 32 10 10 GLN HB2 H 1.99 0.08 2 33 10 10 GLN HG3 H 2.30 0.08 2 34 10 10 GLN N N 118.79 0.14 1 35 11 11 ARG H H 8.226 0.001 1 36 11 11 ARG HA H 4.33 0.08 1 37 11 11 ARG HB2 H 1.67 0.08 4 38 11 11 ARG N N 118.59 0.14 1 39 12 12 LEU H H 8.040 0.001 1 40 12 12 LEU HA H 4.33 0.08 1 41 12 12 LEU HB2 H 1.67 0.08 2 42 12 12 LEU N N 119.12 0.14 1 43 13 13 ALA H H 8.091 0.001 1 44 13 13 ALA HA H 4.33 0.08 1 45 13 13 ALA HB H 1.20 0.08 1 46 13 13 ALA N N 120.10 0.14 1 47 14 14 ASN H H 8.149 0.001 1 48 14 14 ASN HA H 4.64 0.08 1 49 14 14 ASN HB2 H 2.61 0.08 2 50 14 14 ASN N N 115.62 0.14 1 51 15 15 PHE H H 8.094 0.001 1 52 15 15 PHE HA H 4.49 0.08 1 53 15 15 PHE HB2 H 3.24 0.08 2 54 15 15 PHE HB3 H 2.92 0.08 2 55 15 15 PHE N N 116.34 0.14 1 56 16 16 LEU H H 8.215 0.001 1 57 16 16 LEU HA H 4.33 0.08 1 58 16 16 LEU HB2 H 1.67 0.08 2 59 16 16 LEU HD1 H 0.88 0.08 2 60 16 16 LEU N N 117.86 0.14 1 61 17 17 VAL H H 7.78 0.001 1 62 17 17 VAL HA H 4.17 0.08 1 63 17 17 VAL HB H 2.14 0.08 1 64 17 17 VAL HG1 H 0.89 0.08 2 65 17 17 VAL N N 114.77 0.14 1 66 18 18 HIS H H 8.326 0.001 1 67 18 18 HIS HA H 4.80 0.08 1 68 18 18 HIS HB2 H 3.08 0.08 2 69 18 18 HIS HB3 H 3.24 0.08 2 70 18 18 HIS N N 118.74 0.14 1 71 19 19 SER H H 8.191 0.001 1 72 19 19 SER HA H 4.49 0.08 1 73 19 19 SER HB2 H 3.70 0.08 2 74 19 19 SER N N 114.83 0.14 1 75 20 20 SER H H 8.111 0.001 1 76 20 20 SER HA H 4.49 0.08 1 77 20 20 SER HB2 H 3.71 0.08 2 78 20 20 SER N N 114.83 0.14 1 79 21 21 ASN H H 8.264 0.001 1 80 21 21 ASN HA H 4.64 0.08 1 81 21 21 ASN HB2 H 2.61 0.08 2 82 21 21 ASN N N 117.98 0.14 1 83 22 22 ASN H H 8.205 0.001 1 84 22 22 ASN HA H 4.64 0.08 1 85 22 22 ASN HB2 H 2.61 0.08 2 86 22 22 ASN N N 116.73 0.14 1 87 23 23 PHE H H 8.241 0.001 1 88 23 23 PHE HA H 4.49 0.08 1 89 23 23 PHE HB2 H 3.08 0.08 2 90 23 23 PHE N N 116.68 0.14 1 91 24 24 GLY H H 8.292 0.001 1 92 24 24 GLY HA2 H 3.82 0.08 2 93 24 24 GLY N N 105.43 0.14 1 94 25 25 ALA H H 7.961 0.001 1 95 25 25 ALA HA H 4.49 0.08 1 96 25 25 ALA HB H 1.36 0.08 1 97 25 25 ALA N N 119.83 0.14 1 98 26 26 ILE H H 8.043 0.001 1 99 26 26 ILE HA H 4.17 0.08 1 100 26 26 ILE HB H 1.83 0.08 1 101 26 26 ILE HG2 H 0.90 0.08 1 102 26 26 ILE N N 115.87 0.14 1 103 27 27 LEU H H 8.052 0.001 1 104 27 27 LEU HA H 4.49 0.08 1 105 27 27 LEU HB2 H 1.52 0.08 2 106 27 27 LEU N N 121.48 0.14 1 107 28 28 SER H H 8.005 0.001 1 108 28 28 SER HA H 4.49 0.08 1 109 28 28 SER HB2 H 3.71 0.08 2 110 28 28 SER N N 112.92 0.14 1 111 29 29 SER H H 8.249 0.001 1 112 29 29 SER HA H 4.49 0.08 1 113 29 29 SER HB2 H 3.71 0.08 2 114 29 29 SER N N 115.10 0.14 1 115 30 30 THR H H 7.872 0.001 1 116 30 30 THR HA H 4.33 0.08 1 117 30 30 THR HG2 H 1.20 0.08 1 118 30 30 THR N N 111.13 0.14 1 119 31 31 ASN H H 8.185 0.001 1 120 31 31 ASN HA H 4.64 0.08 1 121 31 31 ASN HB2 H 2.61 0.08 2 122 31 31 ASN N N 118.81 0.14 1 123 32 32 VAL H H 7.869 0.001 1 124 32 32 VAL HA H 4.18 0.08 1 125 32 32 VAL HB H 2.14 0.08 1 126 32 32 VAL HG1 H 0.89 0.08 2 127 32 32 VAL HG2 H 1.05 0.08 2 128 32 32 VAL N N 114.34 0.14 1 129 33 33 GLY H H 8.304 0.001 1 130 33 33 GLY HA2 H 3.86 0.08 2 131 33 33 GLY N N 107.85 0.14 1 132 34 34 SER H H 8.042 0.001 1 133 34 34 SER HA H 4.49 0.08 1 134 34 34 SER HB2 H 3.71 0.08 2 135 34 34 SER N N 112.49 0.14 1 136 35 35 ASN H H 8.416 0.001 1 137 35 35 ASN HA H 4.64 0.08 1 138 35 35 ASN HB2 H 2.61 0.08 2 139 35 35 ASN N N 119.41 0.14 1 140 36 36 THR H H 7.715 0.001 1 141 36 36 THR HA H 4.33 0.08 1 142 36 36 THR HG2 H 1.20 0.08 1 143 36 36 THR N N 109.73 0.14 1 144 37 37 TYR H H 8.089 0.001 1 145 37 37 TYR HA H 4.49 0.08 1 146 37 37 TYR HB2 H 2.92 0.08 2 147 37 37 TYR N N 118.08 0.14 1 stop_ save_