data_27045 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solid-state NMR chemical shifts of amyloid-like fibrils formed by huntingtin exon 1 with a 44-residue polyQ domain. ; _BMRB_accession_number 27045 _BMRB_flat_file_name bmr27045.str _Entry_type original _Submission_date 2017-03-09 _Accession_date 2017-03-09 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Chemical shift assignments of huntingtin exon1 fibrils' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hoop Cody L. . 2 Kar Karunakar . . 3 Wetzel Ronald . . 4 'van der Wel' Patrick C.A. . 5 Lin Hsiang-Kai . . 6 Poirier Michelle . . 7 Boatz Jennifer C. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 130 "15N chemical shifts" 8 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-03-04 update author 'update entry citation' 2017-05-19 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 25146 'Solid-state NMR chemical shifts of amyloid-like fibrils formed by huntingtin N-terminal fragments (httNTQ30P10K2)' stop_ _Original_release_date 2017-03-09 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Fibril polymorphism affects immobilized non-amyloid flanking domains of huntingtin exon1 rather than its polyglutamine core ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28537272 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lin Hsiang-Kai K. . 2 Boatz Jennifer C. . 3 Krabbendam Inge E. . 4 Kodali Ravindra . . 5 Hou Zhipeng . . 6 Wetzel Ronald . . 7 Dolga Amalia M. . 8 Poirier Michelle A. . 9 'van der Wel' Patrick . . stop_ _Journal_abbreviation 'Nat Commun.' _Journal_volume 8 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 15462 _Page_last 15462 _Year 2017 _Details . loop_ _Keyword 'CAG expansion diseases' 'amyloid fibrils' 'protein aggregation' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_citation_2 _Saveframe_category citation _Citation_full . _Citation_title ; Polyglutamine amyloid core boundaries and flanking domain dynamics in huntingtin fragment fibrils determined by solid-state NMR ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25280367 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hoop Cody L. . 2 Lin Hsiang-Kai . . 3 Kar Karunakar . . 4 Hou Zhipeng . . 5 Poirier Michelle A. . 6 Wetzel Ronald . . 7 'van der Wel' Patrick C.A. . 8 Magyarfalvi Gabor . . 9 Lamley Jonathan M. . 10 Boatz Jennifer C. . 11 Mandal Abhishek . . 12 Lewandowski Jozef R. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full . _Journal_volume 53 _Journal_issue 42 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 6653 _Page_last 6666 _Year 2014 _Details . loop_ _Keyword 'CAG expansion diseases' 'amyloid fibrils' 'protein aggregation' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'HttExon1 fibrils' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'HttExon1, Chain A' $huntingtin_exon1_Q44 'HttExon1, Chain B' $huntingtin_exon1_Q44 stop_ _System_molecular_weight . _System_physical_state na _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function "Htt exon1 protein aggregates are implicated in Huntington's Disease" stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_huntingtin_exon1_Q44 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common huntingtin_exon1_Q44 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 120 _Mol_residue_sequence ; MATLEKLMKAFESLKSFQQQ QQQQQQQQQQQQQQQQQQQQ QQQQQQQQQQQQQQQQQQQQ QPPPPPPPPPPPQLPQPPPQ AQPLLPQPQPPPPPPPPPPG PAVAEEPLHRPSGSHHHHHH ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ALA 3 THR 4 LEU 5 GLU 6 LYS 7 LEU 8 MET 9 LYS 10 ALA 11 PHE 12 GLU 13 SER 14 LEU 15 LYS 16 SER 17 PHE 18 GLN 19 GLN 20 GLN 21 GLN 22 GLN 23 GLN 24 GLN 25 GLN 26 GLN 27 GLN 28 GLN 29 GLN 30 GLN 31 GLN 32 GLN 33 GLN 34 GLN 35 GLN 36 GLN 37 GLN 38 GLN 39 GLN 40 GLN 41 GLN 42 GLN 43 GLN 44 GLN 45 GLN 46 GLN 47 GLN 48 GLN 49 GLN 50 GLN 51 GLN 52 GLN 53 GLN 54 GLN 55 GLN 56 GLN 57 GLN 58 GLN 59 GLN 60 GLN 61 GLN 62 PRO 63 PRO 64 PRO 65 PRO 66 PRO 67 PRO 68 PRO 69 PRO 70 PRO 71 PRO 72 PRO 73 GLN 74 LEU 75 PRO 76 GLN 77 PRO 78 PRO 79 PRO 80 GLN 81 ALA 82 GLN 83 PRO 84 LEU 85 LEU 86 PRO 87 GLN 88 PRO 89 GLN 90 PRO 91 PRO 92 PRO 93 PRO 94 PRO 95 PRO 96 PRO 97 PRO 98 PRO 99 PRO 100 GLY 101 PRO 102 ALA 103 VAL 104 ALA 105 GLU 106 GLU 107 PRO 108 LEU 109 HIS 110 ARG 111 PRO 112 SER 113 GLY 114 SER 115 HIS 116 HIS 117 HIS 118 HIS 119 HIS 120 HIS 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 _Details $huntingtin_exon1_Q44 Human 9606 Eukaryota Metazoa Homo sapiens 'exon1 fragment of mutant huntingtin protein' 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 $huntingtin_exon1_Q44 'recombinant technology' . Escherichia coli . pMal_c2x stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type fiber _Details 'Uniformly 13C,15N labeled' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $huntingtin_exon1_Q44 5 mg '[U-99% 13C; U-99% 15N]' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . CCPN . . stop_ loop_ _Task 'chemical shift assignment' collection stop_ _Details . save_ save_CcpNMR_Analysis _Saveframe_category software _Name CcpNMR_Analysis _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . CCPN . . stop_ loop_ _Task 'chemical shift assignment' collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_13C-13C_DARR_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR' _Sample_label $sample_1 save_ save_2D_13C-13C_DARR_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR' _Sample_label $sample_1 save_ save_2D_13C-13C_INEPT/TOBSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C INEPT/TOBSY' _Sample_label $sample_1 save_ save_2D_13C-13C_PDSD_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C PDSD' _Sample_label $sample_1 save_ save_1H-13C_DIPSHIFT_5 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C DIPSHIFT' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_275_K _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 275 . 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_chainA _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $CcpNMR_Analysis stop_ loop_ _Experiment_label '2D 13C-13C DARR' '2D 13C-13C INEPT/TOBSY' '2D 13C-13C PDSD' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $275_K _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'HttExon1, Chain A' _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 MET CB C 34.5 0.3 1 2 1 1 MET CG C 25.3 0.3 1 3 1 1 MET CE C 17.0 0.3 1 4 2 2 ALA C C 177.5 0.3 1 5 2 2 ALA CA C 52.6 0.3 1 6 2 2 ALA CB C 19.4 0.3 1 7 3 3 THR CA C 70.0 0.5 1 8 3 3 THR CB C 69.0 0.5 1 9 3 3 THR CG2 C 21.5 0.3 1 10 4 4 LEU CA C 57.5 0.3 1 11 4 4 LEU CB C 40.9 0.3 1 12 4 4 LEU CG C 26.3 0.3 1 13 4 4 LEU CD1 C 23.7 0.3 2 14 5 5 GLU CD C 183.5 0.3 1 15 5 5 GLU CA C 58.9 0.3 1 16 5 5 GLU CB C 29.0 0.3 1 17 5 5 GLU CG C 36.4 0.3 1 18 6 6 LYS C C 179.6 0.3 1 19 6 6 LYS CA C 59.5 0.3 1 20 6 6 LYS CB C 32.6 0.3 1 21 6 6 LYS CG C 25.8 0.3 1 22 6 6 LYS CD C 29.3 0.3 1 23 6 6 LYS CE C 42.3 0.3 1 24 7 7 LEU CA C 57.9 0.3 1 25 7 7 LEU CB C 41.7 0.3 1 26 7 7 LEU CG C 26.9 0.3 1 27 7 7 LEU CD1 C 23.7 0.3 2 28 7 7 LEU CD2 C 23.7 0.3 2 29 10 10 ALA CA C 55.0 0.3 1 30 10 10 ALA CB C 18.2 0.3 1 31 19 19 GLN C C 175.9 0.3 1 32 19 19 GLN CA C 56.1 0.3 1 33 19 19 GLN CB C 34.2 0.3 1 34 19 19 GLN CG C 34.2 0.3 1 35 19 19 GLN CD C 178.6 0.3 1 36 19 19 GLN N N 119.4 0.3 1 37 19 19 GLN NE2 N 108.3 0.3 1 38 40 40 GLN CG C 33.9 0.3 1 39 40 40 GLN CD C 180.3 0.3 1 40 43 43 GLN C C 174.1 0.3 1 41 43 43 GLN CA C 53.9 0.3 1 42 43 43 GLN CB C 31.7 0.3 1 43 43 43 GLN CG C 30.2 0.3 1 44 43 43 GLN CD C 177.6 0.3 1 45 43 43 GLN N N 116.9 0.3 1 46 43 43 GLN NE2 N 105.7 0.3 1 47 63 63 PRO CA C 61.2 0.3 1 48 63 63 PRO CB C 30.7 0.3 1 49 63 63 PRO CG C 27.4 0.3 1 50 63 63 PRO CD C 50.2 0.3 1 51 75 75 PRO C C 177.0 0.3 1 52 75 75 PRO CA C 63.0 0.3 1 53 75 75 PRO CB C 32.1 0.3 1 54 75 75 PRO CG C 27.5 0.3 1 55 75 75 PRO CD C 50.3 0.3 1 56 103 103 VAL CA C 61.8 0.3 1 57 103 103 VAL CB C 33.0 0.3 1 58 105 105 GLU C C 175.1 0.3 1 59 105 105 GLU CA C 56.2 0.3 1 60 105 105 GLU CB C 30.6 0.3 1 61 105 105 GLU CG C 36.4 0.3 1 62 105 105 GLU CD C 184.1 0.3 1 63 106 106 GLU CA C 56.0 0.3 1 64 106 106 GLU CB C 29.8 0.3 1 65 106 106 GLU CG C 36.1 0.3 1 66 106 106 GLU CD C 184.1 0.3 1 67 110 110 ARG CB C 30.3 0.3 1 68 110 110 ARG CG C 27.0 0.3 1 69 110 110 ARG CD C 43.0 0.3 1 stop_ save_ save_assigned_chem_shift_list_chainB _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $CcpNMR_Analysis stop_ loop_ _Experiment_label '2D 13C-13C DARR' '2D 13C-13C INEPT/TOBSY' '2D 13C-13C PDSD' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $275_K _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'HttExon1, Chain B' _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 MET CB C 34.5 0.3 1 2 1 1 MET CG C 25.3 0.3 1 3 1 1 MET CE C 17.0 0.3 1 4 2 2 ALA C C 177.5 0.3 1 5 2 2 ALA CA C 52.6 0.3 1 6 2 2 ALA CB C 19.4 0.3 1 7 3 3 THR CA C 70.0 0.5 1 8 3 3 THR CB C 69.0 0.5 1 9 3 3 THR CG2 C 21.5 0.3 1 10 4 4 LEU CA C 57.5 0.3 1 11 4 4 LEU CB C 40.9 0.3 1 12 4 4 LEU CG C 26.3 0.3 1 13 4 4 LEU CD1 C 23.7 0.3 2 14 5 5 GLU CD C 183.5 0.3 1 15 5 5 GLU CA C 58.9 0.3 1 16 5 5 GLU CB C 29.0 0.3 1 17 5 5 GLU CG C 36.4 0.3 1 18 6 6 LYS C C 179.6 0.3 1 19 6 6 LYS CA C 59.5 0.3 1 20 6 6 LYS CB C 32.6 0.3 1 21 6 6 LYS CG C 25.8 0.3 1 22 6 6 LYS CD C 29.3 0.3 1 23 6 6 LYS CE C 42.3 0.3 1 24 7 7 LEU CA C 57.9 0.3 1 25 7 7 LEU CB C 41.7 0.3 1 26 7 7 LEU CG C 26.9 0.3 1 27 7 7 LEU CD1 C 23.7 0.3 2 28 7 7 LEU CD2 C 23.7 0.3 2 29 10 10 ALA CA C 55.0 0.3 1 30 10 10 ALA CB C 18.2 0.3 1 31 19 19 GLN C C 174.1 0.3 1 32 19 19 GLN CA C 53.9 0.3 1 33 19 19 GLN CB C 31.7 0.3 1 34 19 19 GLN CG C 30.2 0.3 1 35 19 19 GLN CD C 177.6 0.3 1 36 19 19 GLN N N 116.9 0.3 1 37 19 19 GLN NE2 N 105.7 0.3 1 38 40 40 GLN CG C 33.9 0.3 1 39 40 40 GLN CD C 180.3 0.3 1 40 43 43 GLN C C 175.9 0.3 1 41 43 43 GLN CA C 56.1 0.3 1 42 43 43 GLN CB C 34.2 0.3 1 43 43 43 GLN CG C 34.2 0.3 1 44 43 43 GLN CD C 178.6 0.3 1 45 43 43 GLN N N 119.4 0.3 1 46 43 43 GLN NE2 N 108.3 0.3 1 47 63 63 PRO CA C 61.2 0.3 1 48 63 63 PRO CB C 30.7 0.3 1 49 63 63 PRO CG C 27.4 0.3 1 50 63 63 PRO CD C 50.2 0.3 1 51 75 75 PRO C C 177.0 0.3 1 52 75 75 PRO CA C 63.0 0.3 1 53 75 75 PRO CB C 32.1 0.3 1 54 75 75 PRO CG C 27.5 0.3 1 55 75 75 PRO CD C 50.3 0.3 1 56 103 103 VAL CA C 61.8 0.3 1 57 103 103 VAL CB C 33.0 0.3 1 58 105 105 GLU C C 175.1 0.3 1 59 105 105 GLU CA C 56.2 0.3 1 60 105 105 GLU CB C 30.6 0.3 1 61 105 105 GLU CG C 36.4 0.3 1 62 105 105 GLU CD C 184.1 0.3 1 63 106 106 GLU CA C 56.0 0.3 1 64 106 106 GLU CB C 29.8 0.3 1 65 106 106 GLU CG C 36.1 0.3 1 66 106 106 GLU CD C 184.1 0.3 1 67 110 110 ARG CB C 30.3 0.3 1 68 110 110 ARG CG C 27.0 0.3 1 69 110 110 ARG CD C 43.0 0.3 1 stop_ save_