data_19157 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; ATOMIC-RESOLUTION STRUCTURE OF A CROSS-BETA QUADRUPLET AMYLOID FIBRIL DETERMINED BY SOLID-STATE MAGIC ANGLE SPINNING NMR AND CRYO-EM ; _BMRB_accession_number 19157 _BMRB_flat_file_name bmr19157.str _Entry_type original _Submission_date 2013-04-10 _Accession_date 2013-04-10 _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 William. . 2 Debelouchina G. T. . 3 Bayro M. J. . 4 Clare D. K. . 5 Caporini M. A. . 6 Bajaj V. S. . 7 Jaroniec C. P. . 8 Wang L. . . 9 Ladizhansky V. . . 10 Muller S. . . 11 Macphee C. E. . 12 Waudby C. A. . 13 Mott H. R. . 14 'De simone' A. . . 15 Knowles T. P.J. . 16 Saibil H. R. . 17 Vendruscolo M. . . 18 Orlova E. V. . 19 Griffin R. G. . 20 Dobson C. M. . 21 Bajaj M. . . 22 De-simone A. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 52 "15N chemical shifts" 9 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-05-14 original BMRB . stop_ _Original_release_date 2013-04-10 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; ATOMIC STRUCTURE AND HIERARCHICAL ASSEMBLY OF A CROSS-BETA 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 William. . 2 Debelouchina G. T. . 3 Bayro M. J. . 4 Clare D. K. . 5 Caporini M. A. . 6 Bajaj V. S. . 7 Jaroniec C. P. . 8 Wang L. . . 9 Ladizhansky V. . . 10 Muller S. . . 11 Macphee C. E. . 12 Waudby C. A. . 13 Mott H. R. . 14 'De simone' A. . . 15 Knowles T. P.J. . 16 Saibil H. R. . 17 Vendruscolo M. . . 18 Orlova E. V. . 19 Griffin R. G. . 20 Dobson C. M. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U. S. A.' _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 'Atomic-resolution structure of a quadruplet cross-beta amyloid fibril' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'TRANSTHYRETIN (chain A), 1' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 2' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 3' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 4' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 5' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 6' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 7' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 8' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 9' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 10' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 11' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 12' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 13' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 14' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 15' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 16' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 17' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 18' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 19' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 20' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 21' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 22' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 23' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 24' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 25' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 26' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 27' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 28' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 29' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 30' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 31' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 32' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 33' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 34' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 35' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 36' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 37' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 38' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 39' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 40' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 41' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 42' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 43' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 44' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 45' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 46' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 47' $TRANSTHYRETIN_(chain_A) 'TRANSTHYRETIN (chain A), 48' $TRANSTHYRETIN_(chain_A) stop_ _System_molecular_weight 57522.1344 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_TRANSTHYRETIN_(chain_A) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common TRANSTHYRETIN_(chain_A) _Molecular_mass 1198.3778 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence ; YTIAALLSPYS ; loop_ _Residue_seq_code _Residue_label 1 TYR 2 THR 3 ILE 4 ALA 5 ALA 6 LEU 7 LEU 8 SER 9 PRO 10 TYR 11 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 UNP TTHY_RAT P02767 . . . . . stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $TRANSTHYRETIN_(chain_A) unknown . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $TRANSTHYRETIN_(chain_A) 'chemical synthesis' . . . . n/a . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solid _Details n/a loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $TRANSTHYRETIN_(chain_A) na mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AutoDep _Saveframe_category software _Name AutoDep _Version 4.3 _Details . save_ save_CNSsolve _Saveframe_category software _Name CNSSOLVE _Version any loop_ _Vendor _Address _Electronic_address BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- . . stop_ _Details ; REFINEMENT DETAILS CAN BE FOUND IN THE CNSSOLVE CITATION ABOVE. OWING TO PROTEIN DATA BANK CONVENTIONS, PDB FILES CAN ONLY CONTAIN UP TO 62 INDEPENDENT CHAINS. THEREFORE, THE COORDINATES IN THIS ENTRY REPRESENT ONLY A SHORT SECTION OF THE FIBRIL. TO OBTAIN COORDINATES OF THE LONGER FIBRIL STRUCTURE, PLEASE CONTACT CMD44@CAM.AC.UK, MV245@CAM.AC.UK OR AWPFITZPATRICK@GMAIL.COM. ; save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Bruker_Custom_built-750 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Custom built' _Field_strength 750 _Details . save_ save_VARIAN_CUSTOM_BUILT-500 _Saveframe_category NMR_spectrometer _Manufacturer VARIAN _Model 'CUSTOM BUILT' _Field_strength 500 _Details . 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_ save_1D_DQ-DRAWS_5 _Saveframe_category NMR_applied_experiment _Experiment_name '1D DQ-DRAWS' _Sample_label $sample_1 save_ save_REDOR_6 _Saveframe_category NMR_applied_experiment _Experiment_name REDOR _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'pH [0.0], temp [288.15], pressure [1], ionStrength [0.0]' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH . . pH pressure 1.000 . atm temperature 288.150 . 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 adamantane C 13 'methine carbon' ppm 31.47 external indirect . . . 1.0 adamantane N 15 'methine carbon' ppm 31.47 external indirect . . . . 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 _Saveframe_category assigned_chemical_shifts _Details 'Origin nmrStar file /ebi/msd/pdb_root/Processing/prepare/3zpk/ebi/shifts.mr.txt.csh' 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 'TRANSTHYRETIN (chain A), 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 172.0 0.02 1 2 1 1 TYR CA C 56.3 0.02 1 3 1 1 TYR CB C 36.5 0.02 1 4 1 1 TYR CG C 124.5 0.02 1 5 1 1 TYR CZ C 160.0 0.02 1 6 2 2 THR C C 173.5 0.02 1 7 2 2 THR CA C 62.6 0.02 1 8 2 2 THR CB C 72.5 0.02 1 9 2 2 THR CG2 C 20.0 0.02 1 10 2 2 THR N N 117.0 0.02 1 11 3 3 ILE C C 174.1 0.02 1 12 3 3 ILE CA C 60.2 0.02 1 13 3 3 ILE CB C 41.8 0.02 1 14 3 3 ILE CG1 C 28.2 0.02 1 15 3 3 ILE CG2 C 17.0 0.02 1 16 3 3 ILE CD1 C 14.6 0.02 1 17 3 3 ILE N N 127.0 0.02 1 18 4 4 ALA C C 174.5 0.02 1 19 4 4 ALA CA C 49.9 0.02 1 20 4 4 ALA CB C 22.1 0.02 1 21 4 4 ALA N N 128.0 0.02 1 22 5 5 ALA C C 173.3 0.02 1 23 5 5 ALA CA C 50.3 0.02 1 24 5 5 ALA CB C 22.9 0.02 1 25 5 5 ALA N N 125.1 0.02 1 26 6 6 LEU C C 174.2 0.02 1 27 6 6 LEU CA C 54.4 0.02 1 28 6 6 LEU CB C 45.5 0.02 1 29 6 6 LEU CG C 29.4 0.02 1 30 6 6 LEU CD1 C 23.9 0.02 2 31 6 6 LEU CD2 C 28.2 0.02 2 32 6 6 LEU N N 127.0 0.02 1 33 7 7 LEU C C 173.9 0.02 1 34 7 7 LEU CA C 54.1 0.02 1 35 7 7 LEU CB C 44.3 0.02 1 36 7 7 LEU CG C 29.9 0.02 1 37 7 7 LEU CD1 C 27.7 0.02 2 38 7 7 LEU CD2 C 25.3 0.02 2 39 7 7 LEU N N 127.5 0.02 1 40 8 8 SER C C 173.6 0.02 1 41 8 8 SER CA C 55.4 0.02 1 42 8 8 SER CB C 63.2 0.02 1 43 8 8 SER N N 117.2 0.02 1 44 9 9 PRO C C 174.8 0.02 1 45 9 9 PRO CA C 62.6 0.02 1 46 9 9 PRO CB C 32.6 0.02 1 47 9 9 PRO CG C 28.0 0.02 1 48 9 9 PRO CD C 49.6 0.02 1 49 9 9 PRO N N 135.8 0.02 1 50 10 10 TYR C C 173.6 0.02 1 51 10 10 TYR CA C 57.7 0.02 1 52 10 10 TYR CB C 43.8 0.02 1 53 10 10 TYR CG C 128.7 0.02 1 54 10 10 TYR CD1 C 133.6 0.02 3 55 10 10 TYR CD2 C 133.6 0.02 3 56 10 10 TYR CE1 C 118.3 0.02 3 57 10 10 TYR CE2 C 118.3 0.02 3 58 10 10 TYR CZ C 157.4 0.02 1 59 10 10 TYR N N 127.3 0.02 1 60 11 11 SER C C 181.9 0.02 1 61 11 11 SER CA C 57.8 0.02 1 stop_ save_