data_20046 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; SOLUTION NMR STRUCTURE OF RAT IAPP-1-19 ; _BMRB_accession_number 20046 _BMRB_flat_file_name bmr20046.str _Entry_type new _Submission_date 2008-09-03 _Accession_date 2008-09-03 _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 . . 3 XU JIADI . . 4 VEGLIA GIANLUIGI . . 5 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" 84 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-03 update BMRB 'edit entity/assembly name' 2009-04-04 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structures of rat and human islet amyloid polypeptide IAPP(1-19) in micelles by NMR spectroscopy' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18989932 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 XU JIADI . . 4 VEGLIA GIANLUIGI . . 5 RAMAMOORTHY AYYALUSAMY . . stop_ _Journal_abbreviation Biochemistry _Journal_volume 47 _Journal_issue 48 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 12689 _Page_last 12697 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'RAT IAPP-1-19' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 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 IAPP _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence KCNTATCATQRLANFLVRS 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 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-03-04 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 16314 IAPP 100.00 37 100.00 100.00 1.81e-03 PDB 2KJ7 "Three-Dimensional Nmr Structure Of Rat Islet Amyloid Polypeptide In Dpc Micelles" 100.00 38 100.00 100.00 1.82e-03 DBJ BAA22051 "islet amyloid polypeptide [Mus musculus]" 100.00 93 100.00 100.00 1.43e-03 EMBL CAA37003 "islet amyloid polypeptide [Rattus norvegicus]" 100.00 93 100.00 100.00 1.51e-03 GB AAA37874 "islet amyloid polypeptide [Mus musculus]" 100.00 93 100.00 100.00 1.43e-03 GB AAA40730 "amylin precursor [Rattus norvegicus]" 100.00 93 100.00 100.00 1.51e-03 GB AAA41359 "islet amyloid polypeptide [Rattus norvegicus]" 100.00 93 100.00 100.00 1.51e-03 GB AAH27527 "Islet amyloid polypeptide [Mus musculus]" 100.00 93 100.00 100.00 1.43e-03 GB ACU29638 "amylin [Papio hamadryas]" 94.74 89 100.00 100.00 8.32e-03 PRF 1802238A "islet amyloid protein precursor" 100.00 89 100.00 100.00 1.58e-03 REF NP_034621 "islet amyloid polypeptide precursor [Mus musculus]" 100.00 93 100.00 100.00 1.43e-03 REF NP_036718 "islet amyloid polypeptide precursor [Rattus norvegicus]" 100.00 93 100.00 100.00 1.51e-03 REF XP_001098180 "PREDICTED: islet amyloid polypeptide isoform 1 [Macaca mulatta]" 100.00 89 100.00 100.00 1.56e-03 REF XP_001144800 "PREDICTED: islet amyloid polypeptide [Pan troglodytes]" 100.00 89 100.00 100.00 1.59e-03 REF XP_002926618 "PREDICTED: islet amyloid polypeptide [Ailuropoda melanoleuca]" 100.00 89 100.00 100.00 1.67e-03 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 1.43e-03 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 1.51e-03 stop_ save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name 1 disulfide IAPP 2 CYS SG IAPP 7 CYS SG 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 . . . . . . 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 'recombinant technology' . . . . . 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 1.625 mM 'natural abundance' DPC 200 mM '[U-100% 2H]' 'sodium azide' 0.02 % 'natural abundance' 'sodium phosphate' 20 mM 'natural abundance' 'sodium chloride' 120 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 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' 'chemical shift calculation' 'data analysis' 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 refinement 'structure solution' stop_ _Details . save_ save_TALOS _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task refinement 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_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 temperature 303 . K pH 7.3 . pH 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 4.704 internal direct . . . 0 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 HB2 H 2.84 . 1 2 3 3 ASN HB3 H 3.02 . 1 3 3 3 ASN HD21 H 7.72 . 1 4 3 3 ASN HD22 H 6.85 . 1 5 4 4 THR H H 7.47 . 1 6 4 4 THR HG2 H 1.35 . 1 7 5 5 ALA H H 9.49 . 1 8 5 5 ALA HA H 4.12 . 1 9 5 5 ALA HB H 1.56 . 1 10 7 7 CYS H H 8.02 . 1 11 7 7 CYS HA H 4.4 . 1 12 7 7 CYS HB2 H 3.28 . 1 13 7 7 CYS HB3 H 3.36 . 1 14 8 8 ALA H H 8.3 . 1 15 8 8 ALA HA H 4.05 . 1 16 8 8 ALA HB H 1.52 . 1 17 9 9 THR H H 8.31 . 1 18 9 9 THR HA H 3.89 . 1 19 9 9 THR HB H 4.28 . 1 20 9 9 THR HG2 H 1.31 . 1 21 10 10 GLN H H 7.88 . 1 22 10 10 GLN HA H 4.08 . 1 23 10 10 GLN HB2 H 2.2 . 1 24 10 10 GLN HB3 H 2.29 . 1 25 10 10 GLN HE21 H 7.51 . 1 26 10 10 GLN HE22 H 6.84 . 1 27 10 10 GLN HG2 H 2.42 . 1 28 10 10 GLN HG3 H 2.57 . 1 29 11 11 ARG H H 8.11 . 1 30 11 11 ARG HA H 4.2 . 1 31 11 11 ARG HB2 H 1.96 . 1 32 11 11 ARG HB3 H 2.06 . 1 33 11 11 ARG HD2 H 3.25 . 1 34 11 11 ARG HD3 H 3.31 . 1 35 11 11 ARG HG2 H 1.79 . 1 36 11 11 ARG HG3 H 1.79 . 1 37 12 12 LEU H H 8.19 . 1 38 12 12 LEU HA H 4.2 . 1 39 12 12 LEU HB2 H 1.92 . 1 40 12 12 LEU HB3 H 1.92 . 1 41 12 12 LEU HD1 H 1.01 . 1 42 12 12 LEU HD2 H 1.01 . 1 43 12 12 LEU HG H 1.79 . 1 44 13 13 ALA H H 8.5 . 1 45 13 13 ALA HA H 4.02 . 1 46 13 13 ALA HB H 1.57 . 1 47 14 14 ASN H H 8.16 . 1 48 14 14 ASN HA H 4.48 . 1 49 14 14 ASN HB2 H 2.84 . 1 50 14 14 ASN HB3 H 2.95 . 1 51 14 14 ASN HD21 H 7.73 . 1 52 14 14 ASN HD22 H 6.99 . 1 53 15 15 PHE H H 7.94 . 1 54 15 15 PHE HA H 4.4 . 1 55 15 15 PHE HB2 H 3.37 . 1 56 15 15 PHE HB3 H 3.37 . 1 57 15 15 PHE HD1 H 7.24 . 1 58 15 15 PHE HD2 H 7.24 . 1 59 15 15 PHE HE1 H 7.28 . 1 60 15 15 PHE HE2 H 7.28 . 1 61 16 16 LEU H H 8.19 . 1 62 16 16 LEU HA H 3.98 . 1 63 16 16 LEU HB2 H 1.98 . 1 64 16 16 LEU HB3 H 2.06 . 1 65 16 16 LEU HD1 H 0.96 . 1 66 16 16 LEU HD2 H 0.96 . 1 67 16 16 LEU HG H 1.56 . 1 68 17 17 VAL H H 7.89 . 1 69 17 17 VAL HA H 3.97 . 1 70 17 17 VAL HB H 2.25 . 1 71 17 17 VAL HG1 H 0.99 . 1 72 17 17 VAL HG2 H 1.09 . 1 73 18 18 ARG H H 7.89 . 1 74 18 18 ARG HA H 4.29 . 1 75 18 18 ARG HB2 H 1.9 . 1 76 18 18 ARG HB3 H 1.9 . 1 77 18 18 ARG HD2 H 3.22 . 1 78 18 18 ARG HD3 H 3.34 . 1 79 18 18 ARG HG2 H 1.72 . 1 80 18 18 ARG HG3 H 1.72 . 1 81 19 19 SER H H 7.92 . 1 82 19 19 SER HA H 4.28 . 1 83 19 19 SER HB2 H 3.76 . 1 84 19 19 SER HB3 H 3.76 . 1 stop_ save_