data_17394 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of human amylin in SDS micelles at pH 7.3 ; _BMRB_accession_number 17394 _BMRB_flat_file_name bmr17394.str _Entry_type original _Submission_date 2011-01-04 _Accession_date 2011-01-04 _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 Nanga 'Ravi Prakash Reddy' . . 2 Brender Jeffrey R. . 3 Vivekanandan Subramanian . . 4 Ramamoorthy Ayyalusamy . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 188 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-06-19 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure and membrane orientation of IAPP in its natively amidated form at physiological pH in a membrane environment.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21723249 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nanga 'Ravi Prakash Reddy' . . 2 Brender Jeffrey R. . 3 Vivekanandan Subramanian . . 4 Ramamoorthy Ayyalusamy . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_name_full 'Biochimica et biophysica acta' _Journal_volume 1808 _Journal_issue 10 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2337 _Page_last 2342 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'amidated IAPP' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'amidated IAPP' $entity 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 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 3909.330 _Mol_thiol_state . _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 2015-06-13 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 4.86e-16 BMRB 16105 alpha-helix 100.00 37 100.00 100.00 4.86e-16 BMRB 18795 Amylin 100.00 37 100.00 100.00 4.86e-16 BMRB 20045 IAPP 51.35 19 100.00 100.00 1.92e-03 PDB 2G48 "Crystal Structure Of Human Insulin-Degrading Enzyme In Complex With Amylin" 100.00 37 100.00 100.00 4.86e-16 PDB 2KB8 "The Dynamic Alpha-Helix Structure Of Micelle-Bound Human Amylin" 97.30 37 100.00 100.00 6.11e-15 PDB 2L86 "Solution Nmr Structure Of Human Amylin In Sds Micelles At Ph 7.3" 100.00 38 100.00 100.00 4.93e-16 PDB 3G7V "Islet Amyloid Polypeptide (iapp Or Amylin) Fused To Maltose Binding Protein" 100.00 408 100.00 100.00 4.45e-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 4.63e-06 PDB 3HGZ "Crystal Structure Of Human Insulin-Degrading Enzyme In Complex With Amylin" 100.00 37 100.00 100.00 4.86e-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 1.77e-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 3.18e-15 REF XP_003265632 "PREDICTED: islet amyloid polypeptide [Nomascus leucogenys]" 100.00 89 97.30 97.30 3.18e-15 REF XP_003265633 "PREDICTED: islet amyloid polypeptide [Nomascus leucogenys]" 100.00 89 97.30 97.30 3.18e-15 REF XP_003828947 "PREDICTED: islet amyloid polypeptide [Pan paniscus]" 100.00 89 97.30 97.30 3.18e-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 $entity 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 'obtained from a vendor' . . . . . 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 $entity 2.5 mM 'natural abundance' 'sodium phosphate' 20 mM 'natural abundance' 'sodium chloride' 120 mM 'natural abundance' D2O 10 % '[U-99% 2H]' H2O 90 % 'natural abundance' SDS 200 mM '[U-99% 2H]' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' refinement stop_ _Details . save_ save_Molmol _Saveframe_category software _Name Molmol _Version . loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task 'structure solution' 'data analysis' stop_ _Details . save_ save_ProcheckNMR _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Bruker_Avance_900_MHz _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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 . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7.3 . pH pressure 1 . atm 'ionic strength' 20 . mM 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label water H 1 protons ppm 4.7 internal indirect . . . 1 $entry_citation $entry_citation 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-1H TOCSY' '2D 1H-1H NOESY' 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 'amidated IAPP' _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 4.070 0.02 1 2 1 1 LYS HB2 H 1.902 0.02 1 3 1 1 LYS HB3 H 1.902 0.02 1 4 1 1 LYS HG2 H 1.451 0.02 1 5 1 1 LYS HG3 H 1.451 0.02 1 6 1 1 LYS HD2 H 1.698 0.02 2 7 1 1 LYS HD3 H 1.698 0.02 2 8 1 1 LYS HE2 H 3.000 0.02 2 9 1 1 LYS HE3 H 3.000 0.02 2 10 2 2 CYS H H 8.741 0.02 1 11 2 2 CYS HB2 H 3.207 0.02 2 12 2 2 CYS HB3 H 3.171 0.02 2 13 3 3 ASN H H 8.672 0.02 1 14 3 3 ASN HB2 H 2.941 0.02 2 15 3 3 ASN HB3 H 2.814 0.02 2 16 3 3 ASN HD21 H 6.763 0.02 2 17 3 3 ASN HD22 H 7.457 0.02 2 18 4 4 THR H H 7.404 0.02 1 19 4 4 THR HG2 H 1.240 0.02 1 20 5 5 ALA H H 8.694 0.02 1 21 5 5 ALA HA H 4.117 0.02 1 22 5 5 ALA HB H 1.492 0.02 1 23 6 6 THR H H 7.979 0.02 1 24 6 6 THR HA H 4.120 0.02 1 25 6 6 THR HB H 4.169 0.02 1 26 6 6 THR HG2 H 1.201 0.02 1 27 7 7 CYS H H 7.844 0.02 1 28 7 7 CYS HA H 4.455 0.02 1 29 7 7 CYS HB2 H 3.403 0.02 1 30 7 7 CYS HB3 H 3.403 0.02 1 31 8 8 ALA H H 8.127 0.02 1 32 8 8 ALA HA H 4.012 0.02 1 33 8 8 ALA HB H 1.468 0.02 1 34 9 9 THR H H 8.373 0.02 1 35 9 9 THR HA H 3.833 0.02 1 36 9 9 THR HB H 4.222 0.02 1 37 9 9 THR HG2 H 1.286 0.02 1 38 10 10 GLN H H 7.667 0.02 1 39 10 10 GLN HA H 4.082 0.02 1 40 10 10 GLN HB2 H 2.217 0.02 2 41 10 10 GLN HB3 H 2.142 0.02 2 42 10 10 GLN HG2 H 2.505 0.02 2 43 10 10 GLN HG3 H 2.389 0.02 2 44 10 10 GLN HE21 H 6.761 0.02 2 45 10 10 GLN HE22 H 7.401 0.02 2 46 11 11 ARG H H 7.917 0.02 1 47 11 11 ARG HA H 4.132 0.02 1 48 11 11 ARG HB2 H 1.950 0.02 2 49 11 11 ARG HB3 H 1.848 0.02 2 50 11 11 ARG HG2 H 1.699 0.02 1 51 11 11 ARG HG3 H 1.699 0.02 1 52 11 11 ARG HD2 H 3.215 0.02 1 53 11 11 ARG HD3 H 3.163 0.02 1 54 11 11 ARG HE H 7.086 0.02 1 55 12 12 LEU H H 8.167 0.02 1 56 12 12 LEU HA H 4.133 0.02 1 57 12 12 LEU HB2 H 1.854 0.02 2 58 12 12 LEU HB3 H 1.710 0.02 2 59 12 12 LEU HG H 1.453 0.02 1 60 12 12 LEU HD1 H 0.894 0.02 2 61 12 12 LEU HD2 H 0.956 0.02 2 62 13 13 ALA H H 8.435 0.02 1 63 13 13 ALA HA H 3.963 0.02 1 64 13 13 ALA HB H 1.513 0.02 1 65 14 14 ASN H H 8.120 0.02 1 66 14 14 ASN HA H 4.392 0.02 1 67 14 14 ASN HB2 H 2.943 0.02 2 68 14 14 ASN HB3 H 2.845 0.02 2 69 14 14 ASN HD21 H 6.928 0.02 2 70 14 14 ASN HD22 H 7.651 0.02 2 71 15 15 PHE H H 8.088 0.02 1 72 15 15 PHE HA H 4.393 0.02 1 73 15 15 PHE HB2 H 3.359 0.02 2 74 15 15 PHE HB3 H 3.300 0.02 2 75 15 15 PHE HD1 H 7.207 0.02 1 76 15 15 PHE HD2 H 7.207 0.02 1 77 15 15 PHE HE1 H 7.254 0.02 1 78 15 15 PHE HE2 H 7.254 0.02 1 79 16 16 LEU H H 8.393 0.02 1 80 16 16 LEU HA H 3.888 0.02 1 81 16 16 LEU HB2 H 2.014 0.02 2 82 16 16 LEU HB3 H 1.935 0.02 2 83 16 16 LEU HD1 H 0.900 0.02 2 84 16 16 LEU HD2 H 0.961 0.02 2 85 17 17 VAL H H 8.077 0.02 1 86 17 17 VAL HA H 3.805 0.02 1 87 17 17 VAL HB H 2.044 0.02 1 88 17 17 VAL HG1 H 0.766 0.02 2 89 17 17 VAL HG2 H 0.961 0.02 2 90 18 18 HIS H H 7.751 0.02 1 91 18 18 HIS HA H 4.583 0.02 1 92 18 18 HIS HB2 H 3.357 0.02 2 93 18 18 HIS HB3 H 3.201 0.02 2 94 18 18 HIS HD2 H 7.339 0.02 1 95 18 18 HIS HE1 H 8.574 0.02 1 96 19 19 SER H H 7.840 0.02 1 97 19 19 SER HA H 4.303 0.02 1 98 19 19 SER HB2 H 3.683 0.02 2 99 19 19 SER HB3 H 3.641 0.02 2 100 20 20 SER H H 8.099 0.02 1 101 20 20 SER HA H 4.201 0.02 1 102 20 20 SER HB2 H 3.855 0.02 1 103 20 20 SER HB3 H 3.855 0.02 1 104 21 21 ASN H H 8.099 0.02 1 105 21 21 ASN HA H 4.580 0.02 1 106 21 21 ASN HB2 H 2.584 0.02 1 107 21 21 ASN HB3 H 2.584 0.02 1 108 21 21 ASN HD21 H 6.784 0.02 2 109 21 21 ASN HD22 H 7.370 0.02 2 110 22 22 ASN H H 8.180 0.02 1 111 22 22 ASN HB2 H 2.763 0.02 2 112 22 22 ASN HB3 H 2.593 0.02 2 113 22 22 ASN HD21 H 6.800 0.02 2 114 22 22 ASN HD22 H 7.397 0.02 2 115 23 23 PHE H H 8.175 0.02 1 116 23 23 PHE HA H 4.388 0.02 1 117 23 23 PHE HB2 H 3.109 0.02 1 118 23 23 PHE HB3 H 3.109 0.02 1 119 23 23 PHE HD1 H 7.206 0.02 1 120 23 23 PHE HD2 H 7.206 0.02 1 121 23 23 PHE HE1 H 7.233 0.02 1 122 23 23 PHE HE2 H 7.233 0.02 1 123 24 24 GLY H H 8.476 0.02 1 124 24 24 GLY HA2 H 3.996 0.02 2 125 24 24 GLY HA3 H 3.664 0.02 2 126 25 25 ALA H H 7.874 0.02 1 127 25 25 ALA HA H 4.197 0.02 1 128 25 25 ALA HB H 1.436 0.02 1 129 26 26 ILE H H 7.853 0.02 1 130 26 26 ILE HA H 3.846 0.02 1 131 26 26 ILE HB H 1.962 0.02 1 132 26 26 ILE HG12 H 1.663 0.02 1 133 26 26 ILE HG13 H 1.663 0.02 1 134 26 26 ILE HG2 H 1.200 0.02 1 135 26 26 ILE HD1 H 0.879 0.02 1 136 27 27 LEU H H 8.004 0.02 1 137 27 27 LEU HA H 4.084 0.02 1 138 27 27 LEU HB2 H 1.718 0.02 2 139 27 27 LEU HB3 H 1.663 0.02 2 140 27 27 LEU HG H 1.571 0.02 1 141 27 27 LEU HD1 H 0.832 0.02 2 142 28 28 SER H H 8.029 0.02 1 143 28 28 SER HA H 4.325 0.02 1 144 28 28 SER HB2 H 3.929 0.02 1 145 28 28 SER HB3 H 3.929 0.02 1 146 29 29 SER H H 7.788 0.02 1 147 29 29 SER HA H 4.527 0.02 1 148 29 29 SER HB2 H 4.007 0.02 2 149 29 29 SER HB3 H 3.967 0.02 2 150 30 30 THR H H 7.634 0.02 1 151 30 30 THR HA H 4.489 0.02 1 152 30 30 THR HB H 4.335 0.02 1 153 30 30 THR HG2 H 1.260 0.02 1 154 31 31 ASN H H 8.409 0.02 1 155 31 31 ASN HB2 H 2.905 0.02 2 156 31 31 ASN HB3 H 2.741 0.02 2 157 31 31 ASN HD21 H 6.837 0.02 2 158 31 31 ASN HD22 H 7.530 0.02 2 159 32 32 VAL H H 8.000 0.02 1 160 32 32 VAL HA H 3.994 0.02 1 161 32 32 VAL HB H 2.078 0.02 1 162 32 32 VAL HG1 H 0.938 0.02 2 163 32 32 VAL HG2 H 0.992 0.02 2 164 33 33 GLY H H 8.359 0.02 1 165 33 33 GLY HA2 H 4.050 0.02 2 166 33 33 GLY HA3 H 3.900 0.02 2 167 34 34 SER H H 8.003 0.02 1 168 34 34 SER HA H 4.377 0.02 1 169 34 34 SER HB2 H 3.894 0.02 1 170 34 34 SER HB3 H 3.894 0.02 1 171 35 35 ASN H H 8.175 0.02 1 172 35 35 ASN HA H 3.888 0.02 1 173 35 35 ASN HB2 H 2.744 0.02 1 174 35 35 ASN HB3 H 2.744 0.02 1 175 35 35 ASN HD21 H 6.832 0.02 2 176 35 35 ASN HD22 H 7.472 0.02 2 177 36 36 THR H H 7.934 0.02 1 178 36 36 THR HA H 4.173 0.02 1 179 36 36 THR HB H 4.007 0.02 1 180 36 36 THR HG2 H 0.995 0.02 1 181 37 37 TYR H H 8.026 0.02 1 182 37 37 TYR HA H 4.483 0.02 1 183 37 37 TYR HB2 H 2.834 0.02 2 184 37 37 TYR HB3 H 3.038 0.02 2 185 37 37 TYR HD1 H 7.097 0.02 1 186 37 37 TYR HD2 H 7.097 0.02 1 187 37 37 TYR HE1 H 6.766 0.02 1 188 37 37 TYR HE2 H 6.766 0.02 1 stop_ save_