data_4135 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assignments of a RNA Duplex Including the C-U Mismatch: Unusual Chemical Shifts of a Cytidine Amino Group in the C-U Pair. ; _BMRB_accession_number 4135 _BMRB_flat_file_name bmr4135.str _Entry_type original _Submission_date 1998-04-22 _Accession_date 1998-04-22 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; The sample used here is a double stranded RNA with two separate strands (9 base each). The sequences are as follows: 5'-CGACUCAGG-3' and 5'-CCUGCGUCG-3'. They form a duplex with 9 base-pairs in an anti-parallel manner. Consequently, the duplex includes a C-U pair at the middle of the duplex. ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tanaka Yoshiyuki . . 2 Kojima Chojiro . . 3 Yamazaki Toshio . . 4 Kodama T. S. . 5 Yasuno Kazuhiro . . 6 Miyashita Shin . . 7 Ono Akira(Mei) . . 8 Ono Akira(Sho) . . 9 Kainosho Masatsune . . 10 Kyogoku Yoshimasa . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 4 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 163 "15N chemical shifts" 1 "31P chemical shifts" 16 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-12-15 original author . stop_ _Original_release_date 2000-12-15 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Tanaka, Y., Kojima, C., Yamazaki, T., Kodama, T.S., Yasuno, K., Miyashita, S., Ono, A., Ono, A., Kainosho, M., and Kyogoku, Y., "Solution Structure of an RNA Duplex Including a C-U Base Pair," Biochemistry 39, 7074-7080 (2000). ; _Citation_title 'Solution Structure of an RNA Duplex Including a C-U Base Pair' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 20311269 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tanaka Yoshiyuki . . 2 Kojima Chojiro . . 3 Yamazaki Toshio . . 4 Kodama T. S. . 5 Yasuno Kazuhiro . . 6 Miyashita Shin . . 7 Ono Akira(Mei) . . 8 Ono Akira(Sho) . . 9 Kainosho Masatsune . . 10 Kyogoku Yoshimasa . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 39 _Journal_issue 24 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 7074 _Page_last 7080 _Year 2000 _Details . loop_ _Keyword 'the C-U mismatch' stop_ save_ ################################## # Molecular system description # ################################## save_system_RNA_duplex _Saveframe_category molecular_system _Mol_system_name 'RNA duplex including the C-U mismatch' _Abbreviation_common RNA_duplex _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label strand_A $RNA_duplex_strand_A strand_B $RNA_duplex_strand_B stop_ _System_molecular_weight 6000 _System_physical_state native _System_oligomer_state double_strand _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_RNA_duplex_strand_A _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_duplex_strand_A _Molecular_mass 3000 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence CGACUCAGG loop_ _Residue_seq_code _Residue_label 1 C 2 G 3 A 4 C 5 U 6 C 7 A 8 G 9 G stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_RNA_duplex_strand_B _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_duplex_strand_B _Molecular_mass 3000 _Mol_thiol_state . _Details . _Residue_count 9 _Mol_residue_sequence CCUGCGUCG loop_ _Residue_seq_code _Residue_label 1 C 2 C 3 U 4 G 5 C 6 G 7 U 8 C 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 _Details $RNA_duplex_strand_A . . . . . . 'chemically synthesized' $RNA_duplex_strand_B . . . . . . 'chemically synthesized' 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_duplex_strand_A 'chemical synthesis' . . . . . $RNA_duplex_strand_B 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_duplex_strand_A 2.0 mM [15N4]-C14 NaHPO4 20 mM . NaCl 50 mM . stop_ save_ save_sample_two _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_duplex_strand_B 2.0 mM [15N4]-C14 NaHPO4 20 mM . NaCl 50 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_list _Saveframe_category NMR_spectrometer _Manufacturer unknown _Model unknown _Field_strength 0 _Details 'spectrometer information not available' save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 . n/a temperature 303 . K stop_ save_ save_sample_conditions_two _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 . n/a temperature 273 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _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 . ppm 0.00 external . . . . 1.0 DSS N 15 . ppm 0.00 . indirect . . . 0.101329118 DSS P 31 . ppm 0.00 . indirect . . . 0.404808636 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_chemical_shifts_one _Saveframe_category assigned_chemical_shifts _Details 'Assignment of non-exchangeable proton resonances at 30 degrees C' loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name strand_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 C H5 H 5.92 0.02 1 2 . 1 C H6 H 7.95 0.02 1 3 . 1 C H1' H 5.53 0.02 1 4 . 1 C H2' H 4.48 0.02 1 5 . 1 C H3' H 4.49 0.02 1 6 . 1 C H4' H 4.25 0.02 1 7 . 1 C H5' H 3.86 0.02 2 8 . 1 C H5'' H 3.96 0.02 2 9 . 2 G H8 H 7.73 0.02 1 10 . 2 G H1' H 5.69 0.02 1 11 . 2 G H2' H 4.64 0.02 1 12 . 2 G H3' H 4.68 0.02 1 13 . 2 G H4' H 4.47 0.02 1 14 . 2 G H5' H 4.15 0.02 2 15 . 2 G P P -3.64 0.08 1 16 . 3 A H2 H 7.73 0.02 1 17 . 3 A H8 H 7.87 0.02 1 18 . 3 A H1' H 5.92 0.02 1 19 . 3 A H2' H 4.50 0.02 1 20 . 3 A H3' H 4.56 0.02 1 21 . 3 A H4' H 4.47 0.02 1 22 . 3 A H5' H 4.13 0.02 2 23 . 3 A P P -3.99 0.08 1 24 . 4 C H5 H 5.15 0.02 1 25 . 4 C H6 H 7.27 0.02 1 26 . 4 C H1' H 5.33 0.02 1 27 . 4 C H2' H 4.03 0.02 1 28 . 4 C H3' H 4.27 0.02 1 29 . 4 C H4' H 4.31 0.02 1 30 . 4 C H5' H 3.98 0.02 2 31 . 4 C H5'' H 4.42 0.02 2 32 . 4 C P P -4.09 0.08 1 33 . 5 U H5 H 5.28 0.02 1 34 . 5 U H6 H 7.54 0.02 1 35 . 5 U H1' H 5.49 0.02 1 36 . 5 U H2' H 4.47 0.02 1 37 . 5 U H3' H 4.21 0.02 1 38 . 5 U H4' H 4.34 0.02 1 39 . 5 U H5' H 3.99 0.02 2 40 . 5 U H5'' H 4.41 0.02 2 41 . 5 U P P -4.26 0.08 5 42 . 6 C H5 H 5.75 0.02 1 43 . 6 C H6 H 7.90 0.02 1 44 . 6 C H1' H 5.47 0.02 1 45 . 6 C H2' H 4.39 0.02 1 46 . 6 C H3' H 4.57 0.02 1 47 . 6 C H4' H 4.41 0.02 1 48 . 6 C H5' H 4.06 0.02 2 49 . 6 C H5'' H 4.34 0.02 2 50 . 6 C P P -4.36 0.08 1 51 . 7 A H2 H 7.03 0.02 1 52 . 7 A H8 H 8.05 0.02 1 53 . 7 A H1' H 5.86 0.02 1 54 . 7 A H2' H 4.65 0.02 1 55 . 7 A H3' H 4.73 0.02 1 56 . 7 A H4' H 4.40 0.02 1 57 . 7 A H5' H 4.10 0.02 2 58 . 7 A H5'' H 4.51 0.02 2 59 . 7 A P P -3.99 0.08 1 60 . 8 G H8 H 6.99 0.02 1 61 . 8 G H1' H 5.42 0.02 1 62 . 8 G H2' H 4.33 0.02 1 63 . 8 G H3' H 4.28 0.02 1 64 . 8 G H4' H 4.36 0.02 1 65 . 8 G H5' H 3.97 0.02 2 66 . 8 G P P -3.72 0.08 1 67 . 9 G H8 H 7.16 0.02 1 68 . 9 G H1' H 5.74 0.02 1 69 . 9 G H2' H 3.96 0.02 1 70 . 9 G H3' H 4.12 0.02 1 71 . 9 G H4' H 4.34 0.02 1 72 . 9 G H5' H 3.93 0.02 2 73 . 9 G H5'' H 4.38 0.02 2 74 . 9 G P P -4.06 0.08 1 stop_ save_ save_assigned_chemical_shifts_two _Saveframe_category assigned_chemical_shifts _Details 'Assignment of non-exchangeable proton resonances at 30 degrees C' loop_ _Sample_label $sample_two stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name strand_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 C H5 H 5.97 0.02 1 2 . 1 C H6 H 8.08 0.02 1 3 . 1 C H1' H 5.47 0.02 1 4 . 1 C H2' H 4.41 0.02 1 5 . 1 C H3' H 4.43 0.02 1 6 . 1 C H4' H 4.28 0.02 1 7 . 1 C H5' H 3.87 0.02 2 8 . 1 C H5'' H 4.01 0.02 2 9 . 2 C H5 H 5.57 0.02 1 10 . 2 C H6 H 7.95 0.02 1 11 . 2 C H1' H 5.55 0.02 1 12 . 2 C H2' H 4.36 0.02 1 13 . 2 C H3' H 4.54 0.02 1 14 . 2 C H4' H 4.41 0.02 1 15 . 2 C H5' H 4.08 0.02 2 16 . 2 C P P -4.41 0.08 1 17 . 3 U H5 H 5.40 0.02 1 18 . 3 U H6 H 7.81 0.02 1 19 . 3 U H1' H 5.47 0.02 1 20 . 3 U H2' H 4.49 0.02 1 21 . 3 U H3' H 4.54 0.02 1 22 . 3 U H4' H 4.35 0.02 1 23 . 3 U H5' H 4.08 0.02 2 24 . 3 U H5'' H 4.41 0.02 2 25 . 3 U P P -4.14 0.08 5 26 . 4 G H8 H 7.68 0.02 1 27 . 4 G H1' H 5.69 0.02 1 28 . 4 G H2' H 4.04 0.02 1 29 . 4 G H3' H 4.61 0.02 1 30 . 4 G H4' H 4.38 0.02 1 31 . 4 G H5' H 4.08 0.02 2 32 . 4 G P P -3.91 0.08 5 33 . 5 C H5 H 5.00 0.02 1 34 . 5 C H6 H 7.47 0.02 1 35 . 5 C H1' H 5.59 0.02 1 36 . 5 C H2' H 4.48 0.02 1 37 . 5 C H3' H 4.30 0.02 1 38 . 5 C H4' H 4.28 0.02 1 39 . 5 C H5' H 4.42 0.02 2 40 . 5 C P P -4.20 0.08 1 41 . 6 G H8 H 7.35 0.02 1 42 . 6 G H1' H 5.59 0.02 1 43 . 6 G H2' H 4.49 0.02 1 44 . 6 G H3' H 4.29 0.02 1 45 . 6 G H4' H 4.39 0.02 1 46 . 6 G H5' H 4.02 0.02 2 47 . 6 G H5'' H 4.24 0.02 2 48 . 6 G P P -3.50 0.08 5 49 . 7 U H5 H 4.98 0.02 1 50 . 7 U H6 H 7.79 0.02 1 51 . 7 U H1' H 5.48 0.02 1 52 . 7 U H2' H 4.42 0.02 1 53 . 7 U H3' H 4.44 0.02 1 54 . 7 U H4' H 4.36 0.02 1 55 . 7 U H5' H 4.02 0.02 2 56 . 7 U P P -4.81 0.08 5 57 . 8 C H5 H 5.57 0.02 1 58 . 8 C H6 H 7.73 0.02 1 59 . 8 C H1' H 5.54 0.02 1 60 . 8 C H2' H 4.26 0.02 1 61 . 8 C H3' H 4.42 0.02 1 62 . 8 C H4' H 4.34 0.02 1 63 . 8 C H5' H 4.02 0.02 2 64 . 8 C P P -4.09 0.08 1 65 . 9 G H8 H 7.57 0.02 1 66 . 9 G H1' H 5.73 0.02 1 67 . 9 G H2' H 4.03 0.02 1 68 . 9 G H3' H 4.22 0.02 1 69 . 9 G H4' H 4.15 0.02 1 70 . 9 G H5' H 3.98 0.02 2 71 . 9 G H5'' H 4.38 0.02 2 72 . 9 G P P -3.97 0.08 1 stop_ save_ save_assigned_chemical_shifts_three _Saveframe_category assigned_chemical_shifts _Details 'Assignment of exchangeable and other proton resonances at 0 degrees C' loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_two _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name strand_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 C H41 H 8.23 0.02 1 2 . 1 C H42 H 6.99 0.02 1 3 . 2 G H1 H 12.43 0.02 1 4 . 3 A H61 H 8.33 0.02 1 5 . 3 A H62 H 6.66 0.02 1 6 . 4 C H41 H 8.34 0.02 1 7 . 4 C H42 H 7.04 0.02 1 8 . 4 C HO2' H 6.28 0.02 1 9 . 6 C H41 H 8.35 0.02 1 10 . 6 C H42 H 7.18 0.02 1 11 . 7 A H61 H 7.90 0.02 1 12 . 7 A H62 H 6.26 0.02 1 13 . 8 G H1 H 13.15 0.02 1 14 . 8 G H21 H 8.41 0.02 1 15 . 8 G H22 H 6.03 0.02 1 16 . 9 G H1 H 13.31 0.02 1 stop_ save_ save_assigned_chemical_shifts_four _Saveframe_category assigned_chemical_shifts _Details 'Assignment of exchangeable and other proton resonances at 0 degrees C' loop_ _Sample_label $sample_two stop_ _Sample_conditions_label $sample_conditions_two _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name strand_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 C H41 H 8.43 0.02 1 2 . 1 C H42 H 7.18 0.02 1 3 . 2 C H41 H 8.51 0.02 1 4 . 2 C H42 H 7.04 0.02 1 5 . 3 U H3 H 13.51 0.02 1 6 . 4 G H1 H 12.35 0.02 1 7 . 4 G HO2' H 6.45 0.02 1 8 . 5 C H41 H 6.51 0.02 2 9 . 5 C H42 H 6.11 0.02 2 10 . 5 C N4 N 96.00 1.2 1 11 . 6 G H1 H 13.21 0.02 1 12 . 6 G H21 H 8.31 0.02 1 13 . 6 G H22 H 6.23 0.02 1 14 . 7 U H3 H 14.56 0.02 1 15 . 8 C H41 H 8.34 0.02 1 16 . 8 C H42 H 6.93 0.02 1 17 . 8 C HO2' H 6.78 0.02 1 18 . 9 G H1 H 12.81 0.02 1 stop_ save_