data_20074 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Protein Fibril ; _BMRB_accession_number 20074 _BMRB_flat_file_name bmr20074.str _Entry_type new _Submission_date 2009-02-05 _Accession_date 2009-02-05 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'NFGAIL segment from human islet amyloid polypeptide' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nielsen Jakob T. . 2 Bjerring Morten . . 3 Jeppesen Martin D. . 4 Pedersen Ronnie O. . 5 Pedersen Jan M. . 6 Hein Kim L. . 7 Vosegaard Thomas . . 8 Skrydstrup Troels . . 9 Otzen Daniel E. . 10 Nielsen 'Niels Christian' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 4 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 120 "15N chemical shifts" 24 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-03-10 update BMRB 'complete entry citation' 2009-02-10 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Unique Identification of Supramolecular Structures in Amyloid Fibrils by Solid-State NMR Spectroscopy' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19130518 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nielsen Jakob T. . 2 Bjerring Morten . . 3 Jeppesen Martin . . 4 Pedersen Ronnie O. . 5 Pedersen Jan M. . 6 Hein Kim L. . 7 Vosegaard Thomas . . 8 Skrydstrup Troels . . 9 Otzen Daniel E. . 10 Nielsen 'Niels Christian' . . stop_ _Journal_abbreviation 'Angew. Chem. Int. Ed. Engl.' _Journal_volume 48 _Journal_issue 12 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2118 _Page_last 2121 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name octamer _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'subunit A1 peptide 1' $NFGAILchain 'subunit A2 peptide 1' $NFGAILchain 'subunit B1 peptide 1' $NFGAILchain 'subunit B2 peptide 1' $NFGAILchain 'subunit A1 peptide 2' $NFGAILchain 'subunit A2 peptide 2' $NFGAILchain 'subunit B1 peptide 2' $NFGAILchain 'subunit B2 peptide 2' $NFGAILchain stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'subunit A1 peptide 1' 2 'subunit A2 peptide 1' 3 'subunit B1 peptide 1' 4 'subunit B2 peptide 1' 1 'subunit A1 peptide 2' 2 'subunit A2 peptide 2' 3 'subunit B1 peptide 2' 4 'subunit B2 peptide 2' stop_ _Database_query_date . _Details 'asymmetric octamer representing continuous fibril geometry' save_ ######################## # Monomeric polymers # ######################## save_NFGAILchain _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common NFGAILchain _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence SNNFGAILSS loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -1 SER 2 0 ASN 3 1 ASN 4 2 PHE 5 3 GLY 6 4 ALA 7 5 ILE 8 6 LEU 9 7 SER 10 8 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . 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 PIR P10997 . . . . . . stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $NFGAILchain . . . . . . 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 $NFGAILchain 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL _Saveframe_category sample _Sample_type 'fibrous protein' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $NFGAILchain 2.5 mg '[U-100% 13C; U-100% 15N]' H2O . % 'natural abundance' HEPES . mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.18 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details '4 mm triple-resonance MAS probe' save_ ############################# # NMR applied experiments # ############################# save_NCA_1 _Saveframe_category NMR_applied_experiment _Experiment_name NCA _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL save_ save_NCO_2 _Saveframe_category NMR_applied_experiment _Experiment_name NCO _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL save_ save_2D_13C-13C_DARR_2.5_ms_mixing_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR 2.5 ms mixing' _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL save_ save_2D_13C-13C_DARR_5_ms_mixing_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR 5 ms mixing' _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL save_ save_2D_13C-13C_DARR_20_ms_mixing_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR 20 ms mixing' _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL save_ save_2D_13C-13C_DARR_40_ms_mixing_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR 40 ms mixing' _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL save_ save_2D_13C-13C_DARR_100_ms_mixing_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR 100 ms mixing' _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL save_ save_2D_13C-13C_DARR_200_ms_mixing_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR 200 ms mixing' _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 263 . K pH 7.2 . 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 DSS C 13 'methyl carbons' ppm 0.00 external indirect . . . 1.0 'liquid anhydrous ammonia' N 15 nitrogen ppm 0.00 external direct . . . 1.0 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_A1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label NCA NCO '2D 13C-13C DARR 2.5 ms mixing' '2D 13C-13C DARR 5 ms mixing' '2D 13C-13C DARR 20 ms mixing' '2D 13C-13C DARR 40 ms mixing' '2D 13C-13C DARR 100 ms mixing' '2D 13C-13C DARR 200 ms mixing' stop_ loop_ _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'subunit A1 peptide 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 3 ASN C C 172.41 0.05 1 2 1 3 ASN CA C 52.10 0.05 1 3 1 3 ASN CB C 41.84 0.05 1 4 1 3 ASN CG C 175.11 0.05 1 5 1 3 ASN N N 120.42 0.05 1 6 2 4 PHE C C 173.20 0.05 1 7 2 4 PHE CA C 56.26 0.05 1 8 2 4 PHE CB C 44.42 0.05 1 9 2 4 PHE CD1 C 131.25 0.05 4 10 2 4 PHE CD2 C 132.60 0.05 4 11 2 4 PHE CE1 C 130.62 0.05 4 12 2 4 PHE CE2 C 130.62 0.05 4 13 2 4 PHE CG C 137.79 0.05 1 14 2 4 PHE CZ C 131.78 0.05 4 15 2 4 PHE N N 125.95 0.05 1 16 3 5 GLY C C 171.41 0.05 1 17 3 5 GLY CA C 44.30 0.05 1 18 3 5 GLY N N 113.20 0.05 1 19 4 6 ALA C C 175.18 0.05 1 20 4 6 ALA CA C 50.07 0.05 1 21 4 6 ALA CB C 21.91 0.05 1 22 4 6 ALA N N 120.41 0.05 1 23 5 7 ILE C C 172.34 0.05 1 24 5 7 ILE CA C 59.35 0.05 1 25 5 7 ILE CB C 43.92 0.05 1 26 5 7 ILE CD1 C 14.91 0.05 1 27 5 7 ILE CG1 C 28.40 0.05 1 28 5 7 ILE CG2 C 17.33 0.05 1 29 5 7 ILE N N 118.22 0.05 1 30 6 8 LEU C C 174.39 0.05 1 31 6 8 LEU CA C 53.97 0.05 1 32 6 8 LEU CB C 45.22 0.05 1 33 6 8 LEU CD1 C 27.33 0.05 1 34 6 8 LEU CD2 C 23.55 0.05 1 35 6 8 LEU CG C 29.13 0.05 1 36 6 8 LEU N N 128.53 0.05 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity ',,,' ',,,,' ',,,,' ',,,,' stop_ save_ save_assigned_chem_shift_list_A1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label NCA NCO '2D 13C-13C DARR 2.5 ms mixing' '2D 13C-13C DARR 5 ms mixing' '2D 13C-13C DARR 20 ms mixing' '2D 13C-13C DARR 40 ms mixing' '2D 13C-13C DARR 100 ms mixing' '2D 13C-13C DARR 200 ms mixing' stop_ loop_ _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'subunit A2 peptide 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 3 ASN C C 172.41 0.05 1 2 1 3 ASN CA C 52.10 0.05 1 3 1 3 ASN CB C 41.84 0.05 1 4 1 3 ASN CG C 175.11 0.05 1 5 1 3 ASN N N 120.42 0.05 1 6 2 4 PHE C C 173.20 0.05 1 7 2 4 PHE CA C 56.26 0.05 1 8 2 4 PHE CB C 44.42 0.05 1 9 2 4 PHE CD1 C 131.25 0.05 4 10 2 4 PHE CD2 C 132.60 0.05 4 11 2 4 PHE CE1 C 130.62 0.05 4 12 2 4 PHE CE2 C 130.62 0.05 4 13 2 4 PHE CG C 137.79 0.05 1 14 2 4 PHE CZ C 131.78 0.05 4 15 2 4 PHE N N 125.95 0.05 1 16 3 5 GLY C C 171.41 0.05 1 17 3 5 GLY CA C 44.30 0.05 1 18 3 5 GLY N N 113.20 0.05 1 19 4 6 ALA C C 175.18 0.05 1 20 4 6 ALA CA C 50.07 0.05 1 21 4 6 ALA CB C 21.91 0.05 1 22 4 6 ALA N N 120.41 0.05 1 23 5 7 ILE C C 172.34 0.05 1 24 5 7 ILE CA C 59.28 0.05 1 25 5 7 ILE CB C 43.98 0.05 1 26 5 7 ILE CD1 C 15.19 0.05 1 27 5 7 ILE CG1 C 28.73 0.05 1 28 5 7 ILE CG2 C 16.30 0.05 1 29 5 7 ILE N N 118.22 0.05 1 30 6 8 LEU C C 174.39 0.05 1 31 6 8 LEU CA C 53.97 0.05 1 32 6 8 LEU CB C 45.22 0.05 1 33 6 8 LEU CD1 C 27.33 0.05 1 34 6 8 LEU CD2 C 23.55 0.05 1 35 6 8 LEU CG C 29.13 0.05 1 36 6 8 LEU N N 128.53 0.05 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity ',,,' ',,,,' ',,,,' ',,,,' stop_ save_ save_assigned_chem_shift_list_A1_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label NCA NCO '2D 13C-13C DARR 2.5 ms mixing' '2D 13C-13C DARR 5 ms mixing' '2D 13C-13C DARR 20 ms mixing' '2D 13C-13C DARR 40 ms mixing' '2D 13C-13C DARR 100 ms mixing' '2D 13C-13C DARR 200 ms mixing' stop_ loop_ _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'subunit B1 peptide 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 3 ASN C C 171.67 0.05 1 2 1 3 ASN CA C 51.95 0.05 1 3 1 3 ASN CB C 41.62 0.05 1 4 1 3 ASN CG C 174.78 0.05 1 5 1 3 ASN N N 119.69 0.05 1 6 2 4 PHE C C 175.27 0.05 1 7 2 4 PHE CA C 55.56 0.05 1 8 2 4 PHE CB C 42.79 0.05 1 9 2 4 PHE CD1 C 131.27 0.05 4 10 2 4 PHE CD2 C 131.27 0.05 4 11 2 4 PHE CE1 C 132.60 0.05 4 12 2 4 PHE CE2 C 132.60 0.05 4 13 2 4 PHE CG C 137.04 0.05 1 14 2 4 PHE CZ C 131.72 0.05 4 15 2 4 PHE N N 120.36 0.05 1 16 3 5 GLY C C 168.74 0.05 1 17 3 5 GLY CA C 48.06 0.05 1 18 3 5 GLY N N 115.53 0.05 1 19 4 6 ALA C C 174.31 0.05 1 20 4 6 ALA CA C 49.51 0.05 1 21 4 6 ALA CB C 21.09 0.05 1 22 4 6 ALA N N 127.05 0.05 1 23 5 7 ILE C C 173.57 0.05 1 24 5 7 ILE CA C 59.89 0.05 1 25 5 7 ILE CB C 41.33 0.05 1 26 5 7 ILE CD1 C 15.25 0.05 1 27 5 7 ILE CG1 C 28.09 0.05 1 28 5 7 ILE CG2 C 16.65 0.05 1 29 5 7 ILE N N 119.52 0.05 1 30 6 8 LEU C C 175.01 0.05 1 31 6 8 LEU CA C 54.47 0.05 1 32 6 8 LEU CB C 44.11 0.05 1 33 6 8 LEU CD1 C 25.87 0.05 1 34 6 8 LEU CD2 C 23.20 0.05 1 35 6 8 LEU CG C 29.33 0.05 1 36 6 8 LEU N N 126.79 0.05 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity ',,,' ',,,,' ',,,,' ',,,,' stop_ save_ save_assigned_chem_shift_list_A1_4 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label NCA NCO '2D 13C-13C DARR 2.5 ms mixing' '2D 13C-13C DARR 5 ms mixing' '2D 13C-13C DARR 20 ms mixing' '2D 13C-13C DARR 40 ms mixing' '2D 13C-13C DARR 100 ms mixing' '2D 13C-13C DARR 200 ms mixing' stop_ loop_ _Sample_label $SNNFGAILSS_U_13C,_15N-_labeled_for_NFGAIL stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'subunit B2 peptide 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 3 ASN C C 171.67 0.05 1 2 1 3 ASN CA C 51.95 0.05 1 3 1 3 ASN CB C 41.62 0.05 1 4 1 3 ASN CG C 174.78 0.05 1 5 1 3 ASN N N 119.69 0.05 1 6 2 4 PHE C C 175.27 0.05 1 7 2 4 PHE CA C 55.56 0.05 1 8 2 4 PHE CB C 42.79 0.05 1 9 2 4 PHE CD1 C 131.27 0.05 4 10 2 4 PHE CD2 C 131.27 0.05 4 11 2 4 PHE CE1 C 132.60 0.05 4 12 2 4 PHE CE2 C 132.60 0.05 4 13 2 4 PHE CG C 137.04 0.05 1 14 2 4 PHE CZ C 131.72 0.05 4 15 2 4 PHE N N 120.36 0.05 1 16 3 5 GLY C C 168.97 0.05 1 17 3 5 GLY CA C 48.06 0.05 1 18 3 5 GLY N N 115.53 0.05 1 19 4 6 ALA C C 174.31 0.05 1 20 4 6 ALA CA C 49.51 0.05 1 21 4 6 ALA CB C 21.09 0.05 1 22 4 6 ALA N N 127.76 0.05 1 23 5 7 ILE C C 173.57 0.05 1 24 5 7 ILE CA C 59.85 0.05 1 25 5 7 ILE CB C 41.97 0.05 1 26 5 7 ILE CD1 C 15.13 0.05 1 27 5 7 ILE CG1 C 28.13 0.05 1 28 5 7 ILE CG2 C 16.60 0.05 1 29 5 7 ILE N N 119.52 0.05 1 30 6 8 LEU C C 175.01 0.05 1 31 6 8 LEU CA C 54.47 0.05 1 32 6 8 LEU CB C 44.11 0.05 1 33 6 8 LEU CD1 C 25.87 0.05 1 34 6 8 LEU CD2 C 23.20 0.05 1 35 6 8 LEU CG C 29.33 0.05 1 36 6 8 LEU N N 126.79 0.05 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity ',,,' ',,,,' ',,,,' ',,,,' stop_ save_ save_constraint_statistics _Saveframe_category constraint_statistics _Text_data_format . _Text_data . _NOE_interproton_distance_evaluation . _NOE_pseudoatom_corrections . _Details . save_