data_30546 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; RNA Duplex containing the internal loop 5'-GCUU/3'-UUCG ; _BMRB_accession_number 30546 _BMRB_flat_file_name bmr30546.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" 148 "13C chemical shifts" 24 "31P chemical shifts" 7 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 30547 "RNA Duplex containing the internal loop 5'-GCAU/3'-UACG" 30548 "RNA Duplex containing the internal loop 5'-UUCG/3'-GCUU" 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*GP*CP*UP*UP*AP*CP*GP*C)-3'), RNA (5'-R(*GP*CP*GP*UP*GP*CP*UP*UP*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*GP*CP*UP*UP*AP*CP*GP*C)-3')" _Molecular_mass 3787.312 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; CGCAGCUUACGC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 C 2 2 G 3 3 C 4 4 A 5 5 G 6 6 C 7 7 U 8 8 U 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*GP*CP*UP*UP*UP*GP*CP*G)-3')" _Molecular_mass 3821.280 _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence ; GCGUGCUUUGCG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 13 G 2 14 C 3 15 G 4 16 U 5 17 G 6 18 C 7 19 U 8 20 U 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*GP*CP*UP*UP*AP*CP*GP*C)-3'), 1 mM RNA (5'-R(*GP*CP*GP*UP*GP*CP*UP*UP*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 'data analysis' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name vnmr _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task collection stop_ _Details . save_ save_software_4 _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_5 _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_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 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_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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 298 . 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 C 13 'methyl protons' ppm 0.000 internal indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0.000 internal indirect . . . 1.0 DSS P 31 'methyl protons' ppm 0.000 internal 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_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' 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 5.588 0.005 1 2 1 1 C H2' H 4.574 0.005 1 3 1 1 C H3' H 4.556 0.005 1 4 1 1 C H4' H 4.341 0.005 1 5 1 1 C H5 H 5.988 0.005 1 6 1 1 C H5' H 4.053 0.005 2 7 1 1 C H5'' H 3.939 0.005 2 8 1 1 C H6 H 8.052 0.005 1 9 1 1 C H41 H 8.124 0.005 1 10 1 1 C H42 H 6.908 0.005 1 11 1 1 C C6 C 142.903 0.2 1 12 2 2 G H1 H 13.060 0.005 1 13 2 2 G H1' H 5.784 0.005 1 14 2 2 G H2' H 4.572 0.005 1 15 2 2 G H3' H 4.696 0.005 1 16 2 2 G H4' H 4.511 0.005 1 17 2 2 G H8 H 7.798 0.005 1 18 2 2 G C8 C 136.544 0.2 1 19 2 2 G P P -3.925 0.02 1 20 3 3 C H1' H 5.508 0.005 1 21 3 3 C H2' H 4.564 0.005 1 22 3 3 C H3' H 4.538 0.005 1 23 3 3 C H4' H 4.444 0.005 1 24 3 3 C H5 H 5.283 0.005 1 25 3 3 C H6 H 7.663 0.005 1 26 3 3 C H41 H 8.369 0.005 1 27 3 3 C H42 H 6.771 0.005 1 28 3 3 C C6 C 136.283 0.2 1 29 4 4 A H1' H 5.976 0.005 1 30 4 4 A H2 H 7.165 0.005 1 31 4 4 A H2' H 4.731 0.005 1 32 4 4 A H3' H 4.624 0.005 1 33 4 4 A H8 H 7.952 0.005 1 34 4 4 A C8 C 139.283 0.2 1 35 4 4 A P P -3.579 0.02 1 36 5 5 G H1' H 5.390 0.005 1 37 5 5 G H2' H 4.369 0.005 1 38 5 5 G H3' H 4.193 0.005 1 39 5 5 G H4' H 4.431 0.005 1 40 5 5 G H8 H 6.992 0.005 1 41 5 5 G C8 C 136.283 0.2 1 42 5 5 G P P -4.272 0.02 1 43 6 6 C H1' H 5.607 0.005 1 44 6 6 C H2' H 4.128 0.005 1 45 6 6 C H5 H 5.093 0.005 1 46 6 6 C H6 H 7.402 0.005 1 47 6 6 C H41 H 7.362 0.005 1 48 6 6 C H42 H 6.537 0.005 1 49 6 6 C C6 C 141.345 0.2 1 50 7 7 U H1' H 5.632 0.005 1 51 7 7 U H2' H 4.349 0.005 1 52 7 7 U H5 H 5.357 0.005 1 53 7 7 U H6 H 7.673 0.005 1 54 7 7 U C6 C 141.895 0.2 1 55 8 8 U H1' H 5.863 0.005 1 56 8 8 U H2' H 4.385 0.005 1 57 8 8 U H3' H 4.446 0.005 1 58 8 8 U H4' H 4.443 0.005 1 59 8 8 U H5 H 5.858 0.005 1 60 8 8 U H6 H 7.885 0.005 1 61 8 8 U C6 C 142.405 0.2 1 62 9 9 A H1' H 5.997 0.005 1 63 9 9 A H2 H 7.525 0.005 1 64 9 9 A H2' H 4.700 0.005 1 65 9 9 A H3' H 4.668 0.005 1 66 9 9 A H4' H 4.578 0.005 1 67 9 9 A H8 H 8.384 0.005 1 68 9 9 A C8 C 136.165 0.2 1 69 9 9 A P P -3.778 0.02 1 70 10 10 C H1' H 5.490 0.005 1 71 10 10 C H2' H 4.433 0.005 1 72 10 10 C H3' H 4.450 0.005 1 73 10 10 C H5 H 5.200 0.005 1 74 10 10 C H6 H 7.558 0.005 1 75 10 10 C H41 H 8.273 0.005 1 76 10 10 C H42 H 6.644 0.005 1 77 10 10 C C6 C 140.842 0.2 1 78 11 11 G H1 H 13.060 0.005 1 79 11 11 G H1' H 5.735 0.005 1 80 11 11 G H2' H 4.413 0.005 1 81 11 11 G H3' H 4.573 0.005 1 82 11 11 G H4' H 4.438 0.005 1 83 11 11 G H8 H 7.552 0.005 1 84 11 11 G C8 C 136.153 0.2 1 85 12 12 C H1' H 5.719 0.005 1 86 12 12 C H2' H 3.984 0.005 1 87 12 12 C H3' H 4.125 0.005 1 88 12 12 C H4' H 4.171 0.005 1 89 12 12 C H5 H 5.237 0.005 1 90 12 12 C H6 H 7.490 0.005 1 91 12 12 C H41 H 8.243 0.005 1 92 12 12 C H42 H 6.842 0.005 1 93 12 12 C C6 C 141.292 0.2 1 stop_ save_ save_assigned_chemical_shifts_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' 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 12.830 0.005 1 2 13 1 G H1' H 5.689 0.005 1 3 13 1 G H2' H 4.743 0.005 1 4 13 1 G H3' H 4.544 0.005 1 5 13 1 G H4' H 4.325 0.005 1 6 13 1 G H5' H 4.011 0.005 2 7 13 1 G H5'' H 3.883 0.005 2 8 13 1 G H8 H 8.008 0.005 1 9 13 1 G C8 C 138.760 0.2 1 10 14 2 C H1' H 5.650 0.005 1 11 14 2 C H2' H 4.628 0.005 1 12 14 2 C H3' H 4.579 0.005 1 13 14 2 C H4' H 4.483 0.005 1 14 14 2 C H5 H 5.275 0.005 1 15 14 2 C H6 H 7.824 0.005 1 16 14 2 C H41 H 8.511 0.005 1 17 14 2 C H42 H 6.566 0.005 1 18 14 2 C C6 C 141.409 0.2 1 19 15 3 G H1 H 12.940 0.005 1 20 15 3 G H1' H 5.776 0.005 1 21 15 3 G H2' H 4.484 0.005 1 22 15 3 G H3' H 4.574 0.005 1 23 15 3 G H8 H 7.592 0.005 1 24 15 3 G C8 C 136.420 0.2 1 25 16 4 U H1' H 5.571 0.005 1 26 16 4 U H2' H 4.649 0.005 1 27 16 4 U H3 H 13.700 0.005 1 28 16 4 U H5 H 5.170 0.005 1 29 16 4 U H6 H 7.674 0.005 1 30 16 4 U C6 C 143.711 0.2 1 31 17 5 G H1' H 5.686 0.005 1 32 17 5 G H2' H 4.521 0.005 1 33 17 5 G H8 H 7.619 0.005 1 34 17 5 G C8 C 136.721 0.2 1 35 18 6 C H1' H 5.477 0.005 1 36 18 6 C H2' H 4.213 0.005 1 37 18 6 C H3' H 4.325 0.005 1 38 18 6 C H5 H 5.136 0.005 1 39 18 6 C H6 H 7.394 0.005 1 40 18 6 C H41 H 7.362 0.005 1 41 18 6 C H42 H 6.520 0.005 1 42 18 6 C C6 C 141.003 0.2 1 43 18 6 C P P -4.127 0.02 1 44 19 7 U H1' H 5.619 0.005 1 45 19 7 U H2' H 4.444 0.005 1 46 19 7 U H3' H 4.351 0.005 1 47 19 7 U H4' H 4.441 0.005 1 48 19 7 U H5 H 5.355 0.005 1 49 19 7 U H6 H 7.621 0.005 1 50 19 7 U C6 C 141.872 0.2 1 51 19 7 U P P -3.850 0.02 1 52 20 8 U H1' H 5.997 0.005 1 53 20 8 U H2' H 4.296 0.005 1 54 20 8 U H3' H 4.575 0.005 1 55 20 8 U H4' H 4.415 0.005 1 56 20 8 U H5 H 5.832 0.005 1 57 20 8 U H6 H 7.936 0.005 1 58 20 8 U C6 C 142.231 0.2 1 59 21 9 U H1' H 5.799 0.005 1 60 21 9 U H2' H 4.676 0.005 1 61 21 9 U H3 H 13.700 0.005 1 62 21 9 U H3' H 4.640 0.005 1 63 21 9 U H4' H 4.514 0.005 1 64 21 9 U H5 H 5.803 0.005 1 65 21 9 U H6 H 7.864 0.005 1 66 21 9 U C6 C 143.331 0.2 1 67 21 9 U P P -3.393 0.02 1 68 22 10 G H1 H 12.390 0.005 1 69 22 10 G H1' H 5.827 0.005 1 70 22 10 G H2' H 4.537 0.005 1 71 22 10 G H3' H 4.442 0.005 1 72 22 10 G H8 H 7.898 0.005 1 73 22 10 G C8 C 137.463 0.2 1 74 23 11 C H1' H 5.491 0.005 1 75 23 11 C H2' H 4.311 0.005 1 76 23 11 C H5 H 5.187 0.005 1 77 23 11 C H6 H 7.602 0.005 1 78 23 11 C H41 H 8.316 0.005 1 79 23 11 C H42 H 6.643 0.005 1 80 23 11 C C6 C 140.645 0.2 1 81 24 12 G H1' H 5.829 0.005 1 82 24 12 G H2' H 4.087 0.005 1 83 24 12 G H3' H 4.281 0.005 1 84 24 12 G H4' H 4.218 0.005 1 85 24 12 G H8 H 7.577 0.005 1 86 24 12 G C8 C 137.288 0.2 1 stop_ save_