data_16314 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Three-Dimensional NMR Structure of Rat Islet Amyloid Polypeptide in DPC micelles. ; _BMRB_accession_number 16314 _BMRB_flat_file_name bmr16314.str _Entry_type original _Submission_date 2009-05-22 _Accession_date 2009-05-22 _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 P R' . . 2 Jeffrey Brender R. . 3 Xu Jiadi . . 4 Hartman Kevin . . 5 Subramanian Vivekanandan . . 6 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" 172 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-05-28 update BMRB 'edit entity/assembly name' 2009-06-11 update BMRB 'complete entry citation' 2009-05-29 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Three-Dimensional Structure and Orientation of Rat Islet Amyloid Polypeptide Protein in a Membrane Environment by Solution NMR Spectroscopy.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19456151 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nanga 'Ravi P. R.' . . 2 Jeffrey Brender R. . 3 Xu Jiadi . . 4 Hartman Kevin . . 5 Subramanian Vivekanandan . . 6 Ramamoorthy Ayyalusamy . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 131 _Journal_issue 23 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 8252 _Page_last 8261 _Year 2009 _Details . loop_ _Keyword Amylin IAPP 'Islet Amyloid Polypeptide' 'rat IAPP' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name IAPP _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label IAPP $entity stop_ _System_molecular_weight 3926.447 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function 'Associated with glucose metabolism' stop_ _Database_query_date . _Details Monomer save_ ######################## # Monomeric polymers # ######################## save_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common IAPP _Molecular_mass 3926.447 _Mol_thiol_state 'all disulfide bound' loop_ _Biological_function 'Associated with glucose metabolism' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 37 _Mol_residue_sequence ; KCNTATCATQRLANFLVRSS NNLGPVLPPTNVGSNTY ; 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 ARG 19 SER 20 SER 21 ASN 22 ASN 23 LEU 24 GLY 25 PRO 26 VAL 27 LEU 28 PRO 29 PRO 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 2015-02-05 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 20046 IAPP 51.35 19 100.00 100.00 3.57e-03 PDB 2KJ7 "Three-Dimensional Nmr Structure Of Rat Islet Amyloid Polypeptide In Dpc Micelles" 100.00 38 100.00 100.00 1.79e-16 DBJ BAA22051 "islet amyloid polypeptide [Mus musculus]" 100.00 93 100.00 100.00 1.67e-16 EMBL CAA37003 "islet amyloid polypeptide [Rattus norvegicus]" 100.00 93 100.00 100.00 2.04e-16 GB AAA37874 "islet amyloid polypeptide [Mus musculus]" 100.00 93 100.00 100.00 1.67e-16 GB AAA40730 "amylin precursor [Rattus norvegicus]" 100.00 93 100.00 100.00 2.04e-16 GB AAA41359 "islet amyloid polypeptide [Rattus norvegicus]" 100.00 93 100.00 100.00 2.04e-16 GB AAH27527 "Islet amyloid polypeptide [Mus musculus]" 100.00 93 100.00 100.00 1.67e-16 GB EDL10633 "islet amyloid polypeptide [Mus musculus]" 100.00 93 100.00 100.00 1.67e-16 REF NP_034621 "islet amyloid polypeptide precursor [Mus musculus]" 100.00 93 100.00 100.00 1.67e-16 REF NP_036718 "islet amyloid polypeptide precursor [Rattus norvegicus]" 100.00 93 100.00 100.00 2.04e-16 REF XP_006155144 "PREDICTED: islet amyloid polypeptide isoform X1 [Tupaia chinensis]" 100.00 122 97.30 97.30 2.09e-15 REF XP_006155145 "PREDICTED: islet amyloid polypeptide isoform X2 [Tupaia chinensis]" 100.00 92 97.30 97.30 1.64e-15 REF XP_006237676 "PREDICTED: islet amyloid polypeptide isoform X1 [Rattus norvegicus]" 100.00 93 100.00 100.00 2.04e-16 SP P12968 "RecName: Full=Islet amyloid polypeptide; AltName: Full=Amylin; AltName: Full=Diabetes-associated peptide; Short=DAP; Flags: Pre" 100.00 93 100.00 100.00 1.67e-16 SP P12969 "RecName: Full=Islet amyloid polypeptide; AltName: Full=Amylin; AltName: Full=Diabetes-associated peptide; Short=DAP; Flags: Pre" 100.00 93 100.00 100.00 2.04e-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 'Norway Rat' 10116 Eukaryota Metazoa Rattus norvegicus 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 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelle _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'sodium phosphate' 20 mM 'natural abundance' 'sodium azide' 0.02 % 'natural abundance' 'sodium chloride' 120 mM 'natural abundance' D2O 10 % 99.9% DPC 200 mM '98% deuterated' $entity 2.5 mM 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _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_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection 'data analysis' processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'chemical shift calculation' 'peak picking' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'geometry optimization' refinement 'structure solution' 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' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 120 . mM pH 7.3 . pH pressure 1 . atm temperature 303 . 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 direct . . . 1 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 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 3 3 ASN HA H 4.89 . . 2 3 3 ASN HB2 H 2.77 . . 3 3 3 ASN HB3 H 2.94 . . 4 3 3 ASN HD21 H 6.81 . . 5 3 3 ASN HD22 H 7.66 . . 6 4 4 THR H H 7.43 . . 7 4 4 THR HA H 4.56 . . 8 4 4 THR HG2 H 1.27 . . 9 5 5 ALA H H 9.4 . . 10 5 5 ALA HA H 4.05 . . 11 5 5 ALA HB H 1.48 . . 12 6 6 THR H H 8.29 . . 13 6 6 THR HA H 4.01 . . 14 6 6 THR HB H 4.11 . . 15 6 6 THR HG2 H 1.19 . . 16 7 7 CYS H H 7.96 . . 17 7 7 CYS HA H 4.34 . . 18 7 7 CYS HB2 H 3.22 . . 19 7 7 CYS HB3 H 3.29 . . 20 8 8 ALA H H 8.26 . . 21 8 8 ALA HA H 3.99 . . 22 8 8 ALA HB H 1.45 . . 23 9 9 THR H H 8.28 . . 24 9 9 THR HA H 3.81 . . 25 9 9 THR HB H 4.21 . . 26 9 9 THR HG2 H 1.24 . . 27 10 10 GLN H H 7.82 . . 28 10 10 GLN HG2 H 2.36 . . 29 10 10 GLN HA H 4.02 . . 30 10 10 GLN HB2 H 2.13 . . 31 10 10 GLN HB3 H 2.22 . . 32 10 10 GLN HE21 H 6.80 . . 33 10 10 GLN HE22 H 7.48 . . 34 10 10 GLN HG3 H 2.50 . . 35 11 11 ARG HD2 H 3.17 . . 36 11 11 ARG HD3 H 3.24 . . 37 11 11 ARG H H 8.06 . . 38 11 11 ARG HA H 4.15 . . 39 11 11 ARG HB2 H 1.89 . . 40 11 11 ARG HB3 H 1.99 . . 41 11 11 ARG HG2 H 1.71 . . 42 11 11 ARG HG3 H 1.71 . . 43 12 12 LEU H H 8.17 . . 44 12 12 LEU HA H 4.13 . . 45 12 12 LEU HB2 H 1.70 . . 46 12 12 LEU HB3 H 1.86 . . 47 13 13 ALA H H 8.49 . . 48 13 13 ALA HA H 3.93 . . 49 13 13 ALA HB H 1.5 . . 50 14 14 ASN H H 8.17 . . 51 14 14 ASN HA H 4.4 . . 52 14 14 ASN HB2 H 2.79 . . 53 14 14 ASN HB3 H 2.9 . . 54 14 14 ASN HD21 H 6.96 . . 55 14 14 ASN HD22 H 7.71 . . 56 15 15 PHE H H 7.95 . . 57 15 15 PHE HA H 4.31 . . 58 15 15 PHE HB2 H 3.28 . . 59 15 15 PHE HB3 H 3.33 . . 60 16 16 LEU H H 8.31 . . 61 16 16 LEU HA H 3.86 . . 62 16 16 LEU HB2 H 1.95 . . 63 16 16 LEU HB3 H 2.02 . . 64 16 16 LEU HD1 H 0.88 . . 65 16 16 LEU HD2 H 0.88 . . 66 16 16 LEU HG H 1.44 . . 67 17 17 VAL H H 8.04 . . 68 17 17 VAL HA H 3.75 . . 69 17 17 VAL HB H 2.16 . . 70 17 17 VAL HG1 H 0.91 . . 71 17 17 VAL HG2 H 1.03 . . 72 18 18 ARG H H 7.99 . . 73 18 18 ARG HA H 4.16 . . 74 18 18 ARG HB2 H 1.83 . . 75 18 18 ARG HB3 H 1.83 . . 76 18 18 ARG HG2 H 1.62 . . 77 18 18 ARG HD2 H 3.16 . . 78 18 18 ARG HD3 H 3.16 . . 79 18 18 ARG HG3 H 1.68 . . 80 19 19 SER H H 8.01 . . 81 19 19 SER HA H 4.24 . . 82 19 19 SER HB2 H 3.62 . . 83 19 19 SER HB3 H 3.67 . . 84 20 20 SER H H 7.96 . . 85 20 20 SER HA H 4.19 . . 86 20 20 SER HB2 H 3.86 . . 87 20 20 SER HB3 H 3.86 . . 88 21 21 ASN H H 8.04 . . 89 21 21 ASN HA H 4.59 . . 90 21 21 ASN HB2 H 2.77 . . 91 21 21 ASN HB3 H 2.77 . . 92 21 21 ASN HD21 H 6.87 . . 93 21 21 ASN HD22 H 7.53 . . 94 22 22 ASN H H 8.13 . . 95 22 22 ASN HB2 H 2.68 . . 96 22 22 ASN HB3 H 2.83 . . 97 22 22 ASN HD21 H 6.89 . . 98 22 22 ASN HD22 H 7.59 . . 99 23 23 LEU H H 7.96 . . 100 23 23 LEU HA H 4.3 . . 101 23 23 LEU HB2 H 1.58 . . 102 23 23 LEU HB3 H 1.68 . . 103 23 23 LEU HD1 H 0.81 . . 104 23 23 LEU HD2 H 0.87 . . 105 23 23 LEU HG H 1.38 . . 106 24 24 GLY H H 8.04 . . 107 24 24 GLY HA2 H 3.56 . . 108 24 24 GLY HA3 H 3.56 . . 109 25 25 PRO HA H 4.43 . . 110 25 25 PRO HB2 H 1.96 . . 111 25 25 PRO HB3 H 2.23 . . 112 26 26 VAL H H 8.18 . . 113 26 26 VAL HA H 4.05 . . 114 26 26 VAL HB H 2.07 . . 115 26 26 VAL HG1 H 0.92 . . 116 26 26 VAL HG2 H 0.92 . . 117 27 27 LEU H H 8.04 . . 118 27 27 LEU HA H 3.98 . . 119 27 27 LEU HB2 H 1.59 . . 120 27 27 LEU HB3 H 1.68 . . 121 27 27 LEU HD1 H 0.87 . . 122 27 27 LEU HD2 H 0.87 . . 123 27 27 LEU HG H 1.49 . . 124 28 28 PRO HA H 4.64 . . 125 28 28 PRO HB2 H 2 . . 126 28 28 PRO HB3 H 2.3 . . 127 29 29 PRO HA H 4.47 . . 128 29 29 PRO HB2 H 1.99 . . 129 29 29 PRO HB3 H 2.25 . . 130 29 29 PRO HD2 H 3.75 . . 131 29 29 PRO HD3 H 3.75 . . 132 29 29 PRO HG2 H 1.91 . . 133 29 29 PRO HG3 H 1.91 . . 134 30 30 THR H H 8.12 . . 135 30 30 THR HA H 4.27 . . 136 30 30 THR HB H 4.16 . . 137 30 30 THR HG2 H 1.15 . . 138 31 31 ASN H H 8.44 . . 139 31 31 ASN HB2 H 2.73 . . 140 31 31 ASN HB3 H 2.8 . . 141 31 31 ASN HD21 H 6.83 . . 142 31 31 ASN HD22 H 7.57 . . 143 32 32 VAL HG1 H 0.9 . . 144 32 32 VAL HG2 H 0.9 . . 145 32 32 VAL H H 8.09 . . 146 32 32 VAL HA H 4.06 . . 147 32 32 VAL HB H 2.09 . . 148 33 33 GLY H H 8.47 . . 149 33 33 GLY HA2 H 3.94 . . 150 33 33 GLY HA3 H 3.94 . . 151 34 34 SER H H 8.04 . . 152 34 34 SER HA H 4.41 . . 153 34 34 SER HB2 H 4.04 . . 154 34 34 SER HB3 H 4.04 . . 155 35 35 ASN H H 8.46 . . 156 35 35 ASN HA H 4.37 . . 157 35 35 ASN HB2 H 2.72 . . 158 35 35 ASN HB3 H 2.76 . . 159 35 35 ASN HD21 H 6.85 . . 160 35 35 ASN HD22 H 7.55 . . 161 36 36 THR H H 7.99 . . 162 36 36 THR HA H 4.02 . . 163 36 36 THR HB H 4.15 . . 164 36 36 THR HG2 H 1.02 . . 165 37 37 TYR H H 8.06 . . 166 37 37 TYR HA H 4.47 . . 167 37 37 TYR HB2 H 2.87 . . 168 37 37 TYR HB3 H 3.03 . . 169 37 37 TYR HD1 H 7.08 . . 170 37 37 TYR HD2 H 7.08 . . 171 37 37 TYR HE1 H 6.76 . . 172 37 37 TYR HE2 H 6.76 . . stop_ save_