data_30548 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; RNA Duplex containing the internal loop 5'-UUCG/3'-GCUU ; _BMRB_accession_number 30548 _BMRB_flat_file_name bmr30548.str _Entry_type original _Submission_date 2018-11-29 _Accession_date 2018-11-29 _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 Berger K. D. . 2 Kennedy S. D. . 3 Turner D. H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 168 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-07-09 update BMRB 'update entry citation' 2019-02-08 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 30546 "RNA Duplex containing the internal loop 5'-GCUU/3'-UUCG" 30547 "RNA Duplex containing the internal loop 5'-GCAU/3'-UACG" stop_ _Original_release_date 2018-12-13 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30702283 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Berger K. D. . 2 Kennedy S. D. . 3 Turner D. H. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 58 _Journal_issue 8 _Journal_ASTM BICHAW _Journal_ISSN 0006-2960 _Journal_CSD 0033 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1094 _Page_last 1108 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "RNA (5'-R(*CP*GP*CP*AP*UP*UP*CP*GP*AP*CP*GP*C)-3'), RNA (5'-R(*GP*CP*GP*UP*UP*UP*CP*GP*UP*GP*CP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 entity_2 $entity_2 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common "RNA (5'-R(*CP*GP*CP*AP*UP*UP*CP*GP*AP*CP*GP*C)-3')" _Molecular_mass 3787.312 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; CGCAUUCGACGC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 C 2 2 G 3 3 C 4 4 A 5 5 U 6 6 U 7 7 C 8 8 G 9 9 A 10 10 C 11 11 G 12 12 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common "RNA (5'-R(*GP*CP*GP*UP*UP*UP*CP*GP*UP*GP*CP*G)-3')" _Molecular_mass 3821.280 _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence ; GCGUUUCGUGCG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 13 G 2 14 C 3 15 G 4 16 U 5 17 U 6 18 U 7 19 C 8 20 G 9 21 U 10 22 G 11 23 C 12 24 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 $entity_1 . 32644 . . . . $entity_2 . 32644 . . . . 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 $entity_1 'chemical synthesis' . . . . . $entity_2 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 1 mM RNA (5'-R(*CP*GP*CP*AP*UP*UP*CP*GP*AP*CP*GP*C)-3'), 1 mM RNA (5'-R(*GP*CP*GP*UP*UP*UP*CP*GP*UP*GP*CP*G)-3'), 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM none $entity_2 1 mM none 'sodium chloride' 80 mM 'natural abundance' 'sodium phosphate' 50 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_4 _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _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 'ionic strength' 130 . mM pH 6.2 . pH pressure 1 . atm temperature 293 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 0.000 internal indirect . . . 1.0 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_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 5.531 0.005 1 2 1 1 C H2' H 4.518 0.005 1 3 1 1 C H3' H 4.534 0.005 1 4 1 1 C H4' H 4.305 0.005 1 5 1 1 C H5 H 5.978 0.005 1 6 1 1 C H5' H 4.030 0.005 2 7 1 1 C H5'' H 3.906 0.005 2 8 1 1 C H6 H 8.061 0.005 1 9 1 1 C H41 H 8.197 0.005 1 10 1 1 C H42 H 7.029 0.005 1 11 2 2 G H1 H 13.107 0.005 1 12 2 2 G H1' H 5.745 0.005 1 13 2 2 G H2' H 4.502 0.005 1 14 2 2 G H3' H 4.695 0.005 1 15 2 2 G H4' H 4.447 0.005 1 16 2 2 G H8 H 7.788 0.005 1 17 3 3 C H1' H 5.481 0.005 1 18 3 3 C H2' H 4.556 0.005 1 19 3 3 C H3' H 4.502 0.005 1 20 3 3 C H4' H 4.412 0.005 1 21 3 3 C H5 H 5.290 0.005 1 22 3 3 C H6 H 7.692 0.005 1 23 3 3 C H41 H 8.371 0.005 1 24 3 3 C H42 H 6.793 0.005 1 25 4 4 A H1' H 5.912 0.005 1 26 4 4 A H2 H 7.298 0.005 1 27 4 4 A H2' H 4.625 0.005 1 28 4 4 A H3' H 4.464 0.005 1 29 4 4 A H4' H 4.461 0.005 1 30 4 4 A H8 H 7.875 0.005 1 31 4 4 A H61 H 7.890 0.005 1 32 4 4 A H62 H 6.450 0.005 1 33 5 5 U H1' H 5.285 0.005 1 34 5 5 U H2' H 3.940 0.005 1 35 5 5 U H3 H 11.880 0.005 1 36 5 5 U H3' H 4.342 0.005 1 37 5 5 U H5 H 5.260 0.005 1 38 5 5 U H6 H 7.423 0.005 1 39 6 6 U H1' H 5.444 0.005 1 40 6 6 U H2' H 4.415 0.005 1 41 6 6 U H3' H 4.455 0.005 1 42 6 6 U H4' H 4.342 0.005 1 43 6 6 U H5 H 5.431 0.005 1 44 6 6 U H6 H 7.932 0.005 1 45 7 7 C H1' H 5.732 0.005 1 46 7 7 C H2' H 4.597 0.005 1 47 7 7 C H3' H 4.472 0.005 1 48 7 7 C H5 H 5.604 0.005 1 49 7 7 C H6 H 7.862 0.005 1 50 7 7 C H41 H 6.518 0.005 1 51 7 7 C H42 H 6.263 0.005 1 52 8 8 G H1 H 10.574 0.005 1 53 8 8 G H1' H 5.610 0.005 1 54 8 8 G H2' H 4.754 0.005 1 55 8 8 G H3' H 4.343 0.005 1 56 8 8 G H4' H 4.481 0.005 1 57 8 8 G H8 H 7.460 0.005 1 58 8 8 G H21 H 6.106 0.005 1 59 8 8 G H22 H 6.112 0.005 1 60 9 9 A H1' H 5.847 0.005 1 61 9 9 A H2 H 7.840 0.005 1 62 9 9 A H2' H 4.465 0.005 1 63 9 9 A H3' H 4.655 0.005 1 64 9 9 A H4' H 4.436 0.005 1 65 9 9 A H8 H 7.816 0.005 1 66 10 10 C H1' H 5.392 0.005 1 67 10 10 C H2' H 4.365 0.005 1 68 10 10 C H3' H 4.364 0.005 1 69 10 10 C H5 H 5.121 0.005 1 70 10 10 C H6 H 7.451 0.005 1 71 10 10 C H41 H 8.319 0.005 1 72 10 10 C H42 H 6.872 0.005 1 73 11 11 G H1 H 13.027 0.005 1 74 11 11 G H1' H 5.712 0.005 1 75 11 11 G H2' H 4.390 0.005 1 76 11 11 G H3' H 4.526 0.005 1 77 11 11 G H4' H 4.403 0.005 1 78 11 11 G H5' H 4.461 0.005 2 79 11 11 G H5'' H 4.023 0.005 2 80 11 11 G H8 H 7.513 0.005 1 81 12 12 C H1' H 5.686 0.005 1 82 12 12 C H2' H 3.944 0.005 1 83 12 12 C H3' H 4.093 0.005 1 84 12 12 C H4' H 4.123 0.005 1 85 12 12 C H5 H 5.210 0.005 1 86 12 12 C H6 H 7.462 0.005 1 87 12 12 C H41 H 8.305 0.005 1 88 12 12 C H42 H 6.903 0.005 1 stop_ save_ save_assigned_chemical_shifts_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_2 _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 13 1 G H1' H 5.668 0.005 1 2 13 1 G H2' H 4.710 0.005 1 3 13 1 G H3' H 4.518 0.005 1 4 13 1 G H4' H 4.311 0.005 1 5 13 1 G H5' H 3.982 0.005 2 6 13 1 G H5'' H 3.852 0.005 2 7 13 1 G H8 H 7.998 0.005 1 8 14 2 C H1' H 5.628 0.005 1 9 14 2 C H2' H 4.641 0.005 1 10 14 2 C H3' H 4.545 0.005 1 11 14 2 C H4' H 4.443 0.005 1 12 14 2 C H5 H 5.259 0.005 1 13 14 2 C H6 H 7.813 0.005 1 14 14 2 C H41 H 8.554 0.005 1 15 14 2 C H42 H 6.636 0.005 1 16 15 3 G H1 H 13.095 0.005 1 17 15 3 G H1' H 5.738 0.005 1 18 15 3 G H2' H 4.513 0.005 1 19 15 3 G H3' H 4.468 0.005 1 20 15 3 G H8 H 7.537 0.005 1 21 16 4 U H1' H 5.494 0.005 1 22 16 4 U H2' H 4.616 0.005 1 23 16 4 U H3 H 14.403 0.005 1 24 16 4 U H3' H 4.469 0.005 1 25 16 4 U H4' H 4.424 0.005 1 26 16 4 U H5 H 5.074 0.005 1 27 16 4 U H6 H 7.596 0.005 1 28 17 5 U H1' H 5.527 0.005 1 29 17 5 U H2' H 4.102 0.005 1 30 17 5 U H3 H 12.045 0.005 1 31 17 5 U H3' H 4.426 0.005 1 32 17 5 U H5 H 5.685 0.005 1 33 17 5 U H6 H 7.857 0.005 1 34 18 6 U H1' H 5.459 0.005 1 35 18 6 U H2' H 4.437 0.005 1 36 18 6 U H3' H 4.461 0.005 1 37 18 6 U H4' H 4.362 0.005 1 38 18 6 U H5 H 5.435 0.005 1 39 18 6 U H6 H 7.944 0.005 1 40 19 7 C H1' H 5.729 0.005 1 41 19 7 C H2' H 4.586 0.005 1 42 19 7 C H3' H 4.468 0.005 1 43 19 7 C H5 H 5.639 0.005 1 44 19 7 C H6 H 7.889 0.005 1 45 19 7 C H41 H 6.606 0.005 1 46 19 7 C H42 H 6.370 0.005 1 47 20 8 G H1 H 11.513 0.005 1 48 20 8 G H1' H 5.661 0.005 1 49 20 8 G H2' H 4.623 0.005 1 50 20 8 G H3' H 4.236 0.005 1 51 20 8 G H4' H 4.451 0.005 1 52 20 8 G H8 H 7.477 0.005 1 53 20 8 G H21 H 6.309 0.005 1 54 20 8 G H22 H 6.305 0.005 1 55 21 9 U H1' H 5.400 0.005 1 56 21 9 U H2' H 4.459 0.005 1 57 21 9 U H3 H 13.832 0.005 1 58 21 9 U H3' H 4.546 0.005 1 59 21 9 U H4' H 4.404 0.005 1 60 21 9 U H5 H 5.238 0.005 1 61 21 9 U H6 H 7.706 0.005 1 62 22 10 G H1 H 12.408 0.005 1 63 22 10 G H1' H 5.730 0.005 1 64 22 10 G H2' H 4.450 0.005 1 65 22 10 G H3' H 4.612 0.005 1 66 22 10 G H4' H 4.410 0.005 1 67 22 10 G H8 H 7.680 0.005 1 68 23 11 C H1' H 5.446 0.005 1 69 23 11 C H2' H 4.280 0.005 1 70 23 11 C H3' H 4.412 0.005 1 71 23 11 C H4' H 4.345 0.005 1 72 23 11 C H5 H 5.185 0.005 1 73 23 11 C H6 H 7.573 0.005 1 74 23 11 C H41 H 8.366 0.005 1 75 23 11 C H42 H 6.777 0.005 1 76 24 12 G H1' H 5.789 0.005 1 77 24 12 G H2' H 4.025 0.005 1 78 24 12 G H3' H 4.236 0.005 1 79 24 12 G H4' H 4.163 0.005 1 80 24 12 G H8 H 7.529 0.005 1 stop_ save_