data_25106 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural dynamics of double-helical RNA having CAG motif ; _BMRB_accession_number 25106 _BMRB_flat_file_name bmr25106.str _Entry_type original _Submission_date 2014-07-23 _Accession_date 2014-07-23 _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 KUMAR AMIT . . 2 TAWANI ARPITA . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 33 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-01-26 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 25107 DNA-quercetin stop_ _Original_release_date 2015-01-26 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural Insight reveals dynamics in repeating r(CAG) transcript found in Huntington s disease (HD) and Spinocerebellar ataxias (SCAs)' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 KUMAR AMIT . . 2 TAWANI ARPITA . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'CAG RNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3')_1' $RNA_(5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3') 'RNA (5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3')_2' $RNA_(5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3') 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_RNA_(5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3') _Molecular_mass 2885.816 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence CCGCAGCGG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 C 2 2 C 3 3 G 4 4 C 5 5 A 6 6 G 7 7 C 8 8 G 9 9 G 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 $RNA_(5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3') . . . . . . 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 $RNA_(5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3') 'chemical synthesis' . . . . . 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 $RNA_(5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3') 2.35 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' 'Phosphate buffer' 10 mM 'natural abundance' NaCl 100 mM 'natural abundance' EDTA 0.05 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 400 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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 308 . K pH 7.2 . pH pressure 1 . atm 'ionic strength' 0.018 . M 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 H 1 'methyl protons' ppm 0 internal direct . . . 1 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_ _Software_label $DISCOVER stop_ loop_ _Experiment_label '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 'RNA (5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3')_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 C H1' H 5.515 0.093 1 2 1 1 C H5 H 5.608 0.000 1 3 1 1 C H6 H 7.982 0.000 1 4 2 2 C H1' H 5.606 0.000 1 5 2 2 C H5 H 5.981 0.000 1 6 2 2 C H6 H 8.052 0.000 1 7 3 3 G H1 H 12.639 0.011 1 8 3 3 G H1' H 5.658 0.000 1 9 3 3 G H8 H 7.588 0.003 1 10 3 3 G H21 H 8.448 0.000 1 11 3 3 G H22 H 6.730 0.000 1 12 4 4 C H1' H 5.441 0.003 1 13 4 4 C H5 H 5.192 0.000 1 14 4 4 C H6 H 7.557 0.005 1 15 5 5 A H1' H 6.054 0.002 1 16 5 5 A H2 H 7.904 0.002 1 17 5 5 A H8 H 8.184 0.000 1 18 6 6 G H1 H 13.289 0.041 1 19 6 6 G H1' H 5.561 0.000 1 20 6 6 G H8 H 7.178 0.025 1 21 7 7 C H1' H 5.508 0.016 1 22 7 7 C H5 H 5.058 0.000 1 23 7 7 C H6 H 7.663 0.003 1 24 8 8 G H1 H 12.398 1.455 1 25 8 8 G H1' H 5.706 0.000 1 26 8 8 G H8 H 7.419 0.003 1 27 8 8 G H21 H 8.339 0.000 1 28 8 8 G H22 H 6.008 0.444 1 29 9 9 G H1 H 12.472 0.014 1 30 9 9 G H1' H 5.776 0.000 1 31 9 9 G H8 H 7.313 0.003 1 32 9 9 G H21 H 8.334 0.000 1 33 9 9 G H22 H 6.757 0.000 1 stop_ save_