data_19062 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Atomic-resolution structure of a cross-beta protofilament ; _BMRB_accession_number 19062 _BMRB_flat_file_name bmr19062.str _Entry_type original _Submission_date 2013-02-27 _Accession_date 2013-02-27 _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 Fitzpatrick Anthony W. . 2 Debelouchina Galia T. . 3 Bayro Marvin J. . 4 Clare Daniel K. . 5 Caporini Marc A. . 6 Bajaj Vikram S. . 7 Jaroniec Christopher P. . 8 Wang Luchun . . 9 Ladizhansky Vladimir . . 10 Muller Shirley . . 11 MacPhee Cait E. . 12 Waudby Christopher A. . 13 Mott Helen R. . 14 'de Simone' Alfonso . . 15 Knowles Tuomas P. . 16 Saibil Helen R. . 17 Vendruscolo Michele . . 18 Orlova Elena V. . 19 Griffin Robert G. . 20 Dobson Christopher M. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 57 "15N chemical shifts" 11 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-09-04 original author . stop_ _Original_release_date 2013-09-04 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Atomic structure and hierarchical assembly of a cross- amyloid fibril.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23513222 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Fitzpatrick Anthony W.P. . 2 Debelouchina Galia T. . 3 Bayro Marvin J. . 4 Clare Daniel K. . 5 Caporini Marc A. . 6 Bajaj Vikram S. . 7 Jaroniec Christopher P. . 8 Wang Luchun . . 9 Ladizhansky Vladimir . . 10 Muller Shirley A. . 11 MacPhee Cait E. . 12 Waudby Christopher A. . 13 Mott Helen R. . 14 'De Simone' Alfonso . . 15 Knowles Tuomas P.J. . 16 Saibil Helen R. . 17 Vendruscolo Michele . . 18 Orlova Elena V. . 19 Griffin Robert G. . 20 Dobson Christopher M. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_name_full 'Proceedings of the National Academy of Sciences of the United States of America' _Journal_volume 110 _Journal_issue 14 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5468 _Page_last 5473 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'cross-beta protofilament' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'cross-beta protofilament 1' $protofilament_part1 'cross-beta protofilament 2' $protofilament_part1 'cross-beta protofilament 3' $protofilament_part1 'cross-beta protofilament 4' $protofilament_part1 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_protofilament_part1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common protofilament_part1 _Molecular_mass 1198.378 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence YTIAALLSPYS loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 TYR 2 2 THR 3 3 ILE 4 4 ALA 5 5 ALA 6 6 LEU 7 7 LEU 8 8 SER 9 9 PRO 10 10 TYR 11 11 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $protofilament_part1 '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 $protofilament_part1 'chemical synthesis' . Escherichia coli . . 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 $protofilament_part1 15 mg/mL '[U-100% 13C; U-100% 15N]' acetonitrile 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNSSOLVE _Saveframe_category software _Name CNSSOLVE _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model N/A _Field_strength 900 _Details 'Equipped with a triple-channel 3.2 mm E-free MAS probe.' save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer N/A _Model N/A _Field_strength 750 _Details 'Custom-built spectrometer utilizing a triple-channel 3.2 mm Bruker E-free MAS probe.' save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer N/A _Model N/A _Field_strength 500 _Details 'Custom-built spectrometer equipped with a 4 mm 1H/13C/15N Varian-Chemagnetix probe.' save_ ############################# # NMR applied experiments # ############################# save_1D_DQ-DRAWS_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1D DQ-DRAWS' _Sample_label $sample_1 save_ save_REDOR_2 _Saveframe_category NMR_applied_experiment _Experiment_name REDOR _Sample_label $sample_1 save_ save_ZF-TEDOR_3 _Saveframe_category NMR_applied_experiment _Experiment_name ZF-TEDOR _Sample_label $sample_1 save_ save_2D_PDSD_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D PDSD' _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 pH 2 . pH pressure 1 . atm temperature 298 . 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 C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 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 '1D DQ-DRAWS' REDOR ZF-TEDOR '2D PDSD' 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 'cross-beta protofilament 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 1 TYR C C 172.000 0.02 1 2 1 1 TYR CA C 56.300 0.02 1 3 1 1 TYR CB C 36.500 0.02 1 4 1 1 TYR CG C 124.500 0.02 1 5 1 1 TYR CD1 C 134.500 0.02 3 6 1 1 TYR CD2 C 133.400 0.02 3 7 1 1 TYR CE1 C 118.700 0.02 3 8 1 1 TYR CE2 C 117.800 0.02 3 9 1 1 TYR CZ C 160.000 0.02 1 10 1 1 TYR N N 39.200 0.02 1 11 2 2 THR C C 173.500 0.02 1 12 2 2 THR CA C 62.600 0.02 1 13 2 2 THR CB C 72.500 0.02 1 14 2 2 THR CG2 C 20.000 0.02 1 15 2 2 THR N N 117.000 0.02 1 16 3 3 ILE C C 174.100 0.02 1 17 3 3 ILE CA C 60.200 0.02 1 18 3 3 ILE CB C 41.800 0.02 1 19 3 3 ILE CG1 C 28.200 0.02 1 20 3 3 ILE CG2 C 17.000 0.02 1 21 3 3 ILE CD1 C 14.600 0.02 1 22 3 3 ILE N N 127.000 0.02 1 23 4 4 ALA C C 174.500 0.02 1 24 4 4 ALA CA C 49.900 0.02 1 25 4 4 ALA CB C 22.100 0.02 1 26 4 4 ALA N N 128.000 0.02 1 27 5 5 ALA C C 173.300 0.02 1 28 5 5 ALA CA C 50.300 0.02 1 29 5 5 ALA CB C 22.900 0.02 1 30 5 5 ALA N N 125.100 0.02 1 31 6 6 LEU C C 174.200 0.02 1 32 6 6 LEU CA C 54.400 0.02 1 33 6 6 LEU CB C 45.500 0.02 1 34 6 6 LEU CG C 29.400 0.02 1 35 6 6 LEU CD1 C 23.900 0.02 2 36 6 6 LEU CD2 C 28.200 0.02 2 37 6 6 LEU N N 127.000 0.02 1 38 7 7 LEU C C 173.900 0.02 1 39 7 7 LEU CA C 54.100 0.02 1 40 7 7 LEU CB C 44.300 0.02 1 41 7 7 LEU CG C 29.900 0.02 1 42 7 7 LEU CD1 C 27.700 0.02 2 43 7 7 LEU CD2 C 25.300 0.02 2 44 7 7 LEU N N 127.500 0.02 1 45 8 8 SER C C 173.600 0.02 1 46 8 8 SER CA C 55.400 0.02 1 47 8 8 SER CB C 63.200 0.02 1 48 8 8 SER N N 117.200 0.02 1 49 9 9 PRO C C 174.800 0.02 1 50 9 9 PRO CA C 62.600 0.02 1 51 9 9 PRO CB C 32.600 0.02 1 52 9 9 PRO CG C 28.000 0.02 1 53 9 9 PRO CD C 49.600 0.02 1 54 9 9 PRO N N 135.800 0.02 1 55 10 10 TYR C C 173.600 0.02 1 56 10 10 TYR CA C 57.700 0.02 1 57 10 10 TYR CB C 43.800 0.02 1 58 10 10 TYR CG C 128.700 0.02 1 59 10 10 TYR CD1 C 133.600 0.02 3 60 10 10 TYR CD2 C 133.600 0.02 3 61 10 10 TYR CE1 C 118.300 0.02 3 62 10 10 TYR CE2 C 118.300 0.02 3 63 10 10 TYR CZ C 157.400 0.02 1 64 10 10 TYR N N 127.300 0.02 1 65 11 11 SER C C 181.900 0.02 1 66 11 11 SER CA C 57.800 0.02 1 67 11 11 SER CB C 000.000 0.00 1 68 11 11 SER N N 000.000 0.00 1 stop_ save_