data_11176 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of RNA aptamer against AML1 Runt domain ; _BMRB_accession_number 11176 _BMRB_flat_file_name bmr11176.str _Entry_type original _Submission_date 2010-06-23 _Accession_date 2010-06-23 _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 Nomura Yusuke . . 2 Fujiwara Kazuya . . 3 Chiba Manabu . . 4 Fukunaga Jun-ichi . . 5 Tanaka Yoichiro . . 6 Iibuchi Hiroaki . . 7 Tanaka Taku . . 8 Nakamura Yoshikazu . . 9 Kawai Gota . . 10 Kozu Tomoko . . 11 Sakamoto Taiichi . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 105 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-06-23 original BMRB . stop_ _Original_release_date 2015-06-23 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; A novel high affinity RNA motif that mimics DNA in AML1 Runt domain binding ; _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 Nomura Yusuke . . 2 Fukunaga Jun-ichi . . 3 Tanaka Yoichiro . . 4 Fujiwara Kazuya . . 5 Chiba Manabu . . 6 Iibuchi Hiroaki . . 7 Tanaka Taku . . 8 Nakamura Yoshikazu . . 9 Kawai Gota . . 10 Sakamoto Taiichi . . 11 Kozu Tomoko . . stop_ _Journal_abbreviation . _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 . loop_ _Keyword AML1/RUNX1 'Molecular mimicry' 'NMR structure' 'RNA aptamer' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name AML22 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label AML22 $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common AML22 _Molecular_mass 7032 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGACCCACCACGGCGAGGUC CA ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 C 5 C 6 C 7 A 8 C 9 C 10 A 11 C 12 G 13 G 14 C 15 G 16 A 17 G 18 G 19 U 20 C 21 C 22 A 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 $entity . . . . . . 'artificial RNA' 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 _Details $entity 'enzymatic semisynthesis' . . . . . 'AmpliScribe T7 Transcription Kit' 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 $entity 0.6 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 0.5 mM '[U-100% 13C; U-100% 15N]' 'sodium phosphate' 10 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 0.6 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 0.5 mM '[U-100% 13C; U-100% 15N]' 'sodium phosphate' 10 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.1 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 DRX _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_no.1_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY no.1' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_no.2_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY no.2' _Sample_label $sample_3 save_ save_2D_1H-1H_NOESY_no.1_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY no.1' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_no.2_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY no.2' _Sample_label $sample_3 save_ save_2D_HCCH-TOCSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCCH-TOCSY' _Sample_label $sample_2 save_ save_2D_HCCH-COSY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCCH-COSY' _Sample_label $sample_2 save_ save_2D_HNN-COSY_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HNN-COSY' _Sample_label $sample_4 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.5 . pH pressure 1 . atm temperature 283 . 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 H 1 'methyl protons' ppm 0 external indirect . . . 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_ _Experiment_label '2D 1H-1H NOESY no.1' '2D 1H-1H NOESY no.2' stop_ loop_ _Sample_label $sample_1 $sample_3 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name AML22 _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 G H1' H 5.85 0.02 1 2 1 1 G H2' H 4.795 0.02 1 3 1 1 G H3' H 4.66 0.02 1 4 1 1 G H8 H 8.164 0.02 1 5 2 2 G H1' H 5.71 0.02 1 6 2 2 G H2' H 4.505 0.02 1 7 2 2 G H3' H 4.451 0.02 1 8 2 2 G H8 H 7.382 0.02 1 9 3 3 A H1' H 5.917 0.02 1 10 3 3 A H2 H 7.745 0.02 1 11 3 3 A H2' H 4.497 0.02 1 12 3 3 A H3' H 4.576 0.02 1 13 3 3 A H8 H 7.819 0.02 1 14 4 4 C H1' H 5.311 0.02 1 15 4 4 C H2' H 4.3 0.02 1 16 4 4 C H3' H 4.241 0.02 1 17 4 4 C H5 H 5.161 0.02 1 18 4 4 C H6 H 7.365 0.02 1 19 5 5 C H1' H 5.441 0.02 1 20 5 5 C H2' H 4.461 0.02 1 21 5 5 C H3' H 4.636 0.02 1 22 5 5 C H5 H 5.443 0.02 1 23 5 5 C H6 H 7.545 0.02 1 24 6 6 C H1' H 5.411 0.02 1 25 6 6 C H2' H 4.243 0.02 1 26 6 6 C H3' H 4.587 0.02 1 27 6 6 C H5 H 5.629 0.02 1 28 6 6 C H6 H 7.893 0.02 1 29 7 7 A H1' H 5.684 0.02 1 30 7 7 A H2 H 7.851 0.02 1 31 7 7 A H2' H 4.42 0.02 1 32 7 7 A H3' H 4.536 0.02 1 33 7 7 A H8 H 8.218 0.02 1 34 8 8 C H1' H 5.308 0.02 1 35 8 8 C H2' H 4.181 0.02 1 36 8 8 C H3' H 4.25 0.02 1 37 8 8 C H5 H 5.484 0.02 1 38 8 8 C H6 H 7.374 0.02 1 39 9 9 C H1' H 5.713 0.02 1 40 9 9 C H2' H 3.795 0.02 1 41 9 9 C H3' H 4.356 0.02 1 42 9 9 C H5 H 5.684 0.02 1 43 9 9 C H6 H 7.578 0.02 1 44 10 10 A H1' H 6.054 0.02 1 45 10 10 A H2 H 8.184 0.02 1 46 10 10 A H2' H 5.049 0.02 1 47 10 10 A H3' H 4.063 0.02 1 48 10 10 A H4' H 4.46 0.02 1 49 10 10 A H8 H 8.685 0.02 1 50 11 11 C H1' H 5.849 0.02 1 51 11 11 C H2' H 4.004 0.02 1 52 11 11 C H3' H 4.398 0.02 1 53 11 11 C H5 H 5.951 0.02 1 54 11 11 C H6 H 7.579 0.02 1 55 12 12 G H1' H 5.878 0.02 1 56 12 12 G H2' H 4.658 0.02 1 57 12 12 G H3' H 5.528 0.02 1 58 12 12 G H8 H 7.735 0.02 1 59 13 13 G H1' H 4.265 0.02 1 60 13 13 G H2' H 4.466 0.02 1 61 13 13 G H3' H 4.369 0.02 1 62 13 13 G H8 H 8.215 0.02 1 63 14 14 C H1' H 5.442 0.02 1 64 14 14 C H2' H 3.993 0.02 1 65 14 14 C H3' H 4.639 0.02 1 66 14 14 C H5 H 5.52 0.02 1 67 14 14 C H6 H 7.76 0.02 1 68 15 15 G H1' H 5.846 0.02 1 69 15 15 G H2' H 4.497 0.02 1 70 15 15 G H3' H 4.746 0.02 1 71 15 15 G H8 H 7.836 0.02 1 72 16 16 A H1' H 6.105 0.02 1 73 16 16 A H2 H 8.125 0.02 1 74 16 16 A H2' H 4.761 0.02 1 75 16 16 A H3' H 4.659 0.02 1 76 16 16 A H4' H 4.543 0.02 1 77 16 16 A H8 H 8.297 0.02 1 78 17 17 G H1' H 5.323 0.02 1 79 17 17 G H2' H 4.691 0.02 1 80 17 17 G H3' H 4.082 0.02 1 81 17 17 G H8 H 7.47 0.02 1 82 18 18 G H1' H 5.75 0.02 1 83 18 18 G H2' H 4.433 0.02 1 84 18 18 G H3' H 4.029 0.02 1 85 18 18 G H8 H 7.3 0.02 1 86 19 19 U H1' H 5.55 0.02 1 87 19 19 U H2' H 4.499 0.02 1 88 19 19 U H3' H 4.021 0.02 1 89 19 19 U H5 H 5.018 0.02 1 90 19 19 U H6 H 7.768 0.02 1 91 20 20 C H1' H 5.521 0.02 1 92 20 20 C H2' H 4.374 0.02 1 93 20 20 C H3' H 4.341 0.02 1 94 20 20 C H5 H 5.557 0.02 1 95 20 20 C H6 H 7.838 0.02 1 96 21 21 C H1' H 5.342 0.02 1 97 21 21 C H2' H 4.366 0.02 1 98 21 21 C H3' H 4.365 0.02 1 99 21 21 C H5 H 5.399 0.02 1 100 21 21 C H6 H 7.58 0.02 1 101 22 22 A H1' H 5.863 0.02 1 102 22 22 A H2 H 7.194 0.02 1 103 22 22 A H2' H 3.951 0.02 1 104 22 22 A H3' H 4.199 0.02 1 105 22 22 A H8 H 7.918 0.02 1 stop_ save_