data_34265 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the r(UGGUGGU)4 RNA quadruplex ; _BMRB_accession_number 34265 _BMRB_flat_file_name bmr34265.str _Entry_type original _Submission_date 2018-04-25 _Accession_date 2018-04-25 _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 Andralojc W. . . 2 Gdaniec Z. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 3 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 169 "13C chemical shifts" 44 "31P chemical shifts" 7 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-08-13 update BMRB 'update entry citation' 2018-10-26 original author 'original release' stop_ _Original_release_date 2018-10-23 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30341177 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Andralojc W. . . 2 Malgowska M. . . 3 Sarzynska J. . . 4 Pasternak K. . . 5 Szpotkowski K. . . 6 Kierzek R. . . 7 Gdaniec Z. . . stop_ _Journal_abbreviation RNA _Journal_volume 25 _Journal_issue 1 _Journal_ASTM RNARFU _Journal_ISSN 1469-9001 _Journal_CSD 2122 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 121 _Page_last 134 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "RNA (5'-R(*UP*GP*GP*UP*GP*GP*U)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, 1' $entity_1 'entity_1, 2' $entity_1 'entity_1, 3' $entity_1 'entity_1, 4' $entity_1 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 entity_1 _Molecular_mass 2254.363 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence ; UGGUGGU ; loop_ _Residue_seq_code _Residue_label 1 U 2 G 3 G 4 U 5 G 6 G 7 U 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 . 32630 . . . . 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' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2.0 mM 'natural abundance' 'phosphate buffer' 10 mM 'natural abundance' 'potassium chloride' 50 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '2.0 mM pUGGUGGU, 10 mM phosphate buffer, 0.05 mM potassium chloride, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2.0 mM 'natural abundance' 'phosphate buffer' 10 mM 'natural abundance' 'potassium chloride' 0.05 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 stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 700 _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_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-31P_COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P COSY' _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' 0.06 . M pH 6.8 . pH pressure 1 . atm temperature 298 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.06 . M pH 6.8 . pH pressure 1 . atm temperature 278 . K stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.06 . M pH 6.8 . pH pressure 1 . bar temperature 333 . 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 TSP C 13 'methyl protons' ppm 0.000 internal indirect . . . 0.25144953 TSP H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 TSP 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-31P COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_3 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 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 U H1' H 5.354 0.01 1 2 1 1 U H2' H 4.057 0.01 1 3 1 1 U H3' H 4.563 0.01 1 4 1 1 U H4' H 4.328 0.01 1 5 1 1 U H5 H 5.635 0.01 1 6 1 1 U H5' H 4.036 0.01 2 7 1 1 U H5'' H 4.168 0.01 2 8 1 1 U H6 H 7.890 0.01 1 9 1 1 U C1' C 93.814 0.20 1 10 1 1 U C2' C 74.986 0.20 1 11 1 1 U C3' C 74.375 0.20 1 12 1 1 U C4' C 84.071 0.20 1 13 1 1 U C5 C 104.002 0.20 1 14 1 1 U C5' C 65.480 0.20 1 15 1 1 U C6 C 144.572 0.20 1 16 1 1 U P P -1.237 0.05 1 17 2 2 G H1' H 5.839 0.01 1 18 2 2 G H2' H 4.940 0.01 1 19 2 2 G H3' H 4.885 0.01 1 20 2 2 G H4' H 4.596 0.01 1 21 2 2 G H5' H 4.225 0.01 2 22 2 2 G H5'' H 4.374 0.01 2 23 2 2 G H8 H 8.250 0.01 1 24 2 2 G C1' C 87.245 0.20 1 25 2 2 G C2' C 75.827 0.20 1 26 2 2 G C3' C 77.781 0.20 1 27 2 2 G C4' C 85.258 0.20 1 28 2 2 G C5' C 67.735 0.20 1 29 2 2 G C8 C 139.023 0.20 1 30 2 2 G P P -4.322 0.05 1 31 3 3 G H1' H 6.074 0.01 1 32 3 3 G H2' H 4.910 0.01 1 33 3 3 G H3' H 4.436 0.01 1 34 3 3 G H4' H 4.696 0.01 1 35 3 3 G H5' H 4.492 0.01 2 36 3 3 G H5'' H 4.384 0.01 2 37 3 3 G H8 H 7.937 0.01 1 38 3 3 G C1' C 93.248 0.20 1 39 3 3 G C2' C 75.009 0.20 1 40 3 3 G C3' C 74.788 0.20 1 41 3 3 G C4' C 83.786 0.20 1 42 3 3 G C5' C 69.983 0.20 1 43 3 3 G C8 C 139.114 0.20 1 44 3 3 G P P -2.220 0.05 1 45 4 4 U H1' H 5.421 0.01 1 46 4 4 U H2' H 4.226 0.01 1 47 4 4 U H3' H 4.401 0.01 1 48 4 4 U H4' H 4.518 0.01 1 49 4 4 U H5 H 4.549 0.01 1 50 4 4 U H5' H 4.200 0.01 2 51 4 4 U H5'' H 4.669 0.01 2 52 4 4 U H6 H 7.447 0.01 1 53 4 4 U C1' C 95.963 0.20 1 54 4 4 U C2' C 74.484 0.20 1 55 4 4 U C3' C 73.066 0.20 1 56 4 4 U C4' C 82.769 0.20 1 57 4 4 U C5 C 101.196 0.20 1 58 4 4 U C5' C 64.691 0.20 1 59 4 4 U P P -3.401 0.05 1 60 5 5 G H1' H 5.877 0.01 1 61 5 5 G H2' H 4.303 0.01 1 62 5 5 G H3' H 4.993 0.01 1 63 5 5 G H4' H 4.494 0.01 1 64 5 5 G H5' H 4.183 0.01 2 65 5 5 G H5'' H 4.707 0.01 2 66 5 5 G H8 H 8.417 0.01 1 67 5 5 G C1' C 92.290 0.20 1 68 5 5 G C2' C 75.376 0.20 1 69 5 5 G C3' C 72.516 0.20 1 70 5 5 G C4' C 81.548 0.20 1 71 5 5 G C5' C 64.393 0.20 1 72 5 5 G C8 C 138.825 0.20 1 73 5 5 G P P -5.103 0.05 1 74 6 6 G H1' H 6.236 0.01 1 75 6 6 G H2' H 4.174 0.01 1 76 6 6 G H3' H 4.593 0.01 1 77 6 6 G H4' H 4.435 0.01 1 78 6 6 G H5' H 4.174 0.01 2 79 6 6 G H5'' H 4.664 0.01 2 80 6 6 G H8 H 7.606 0.01 1 81 6 6 G C1' C 91.610 0.20 1 82 6 6 G C2' C 77.461 0.20 1 83 6 6 G C3' C 72.270 0.20 1 84 6 6 G C4' C 81.735 0.20 1 85 6 6 G C5' C 64.794 0.20 1 86 6 6 G C8 C 135.483 0.20 1 87 6 6 G P P -3.945 0.05 1 88 7 7 U H1' H 5.908 0.01 1 89 7 7 U H2' H 3.939 0.01 1 90 7 7 U H3' H 4.365 0.01 1 91 7 7 U H4' H 4.269 0.01 1 92 7 7 U H5 H 5.071 0.01 1 93 7 7 U H5' H 4.092 0.01 2 94 7 7 U H6 H 7.779 0.01 1 95 7 7 U C1' C 88.617 0.20 1 96 7 7 U C2' C 78.392 0.20 1 97 7 7 U C3' C 73.344 0.20 1 98 7 7 U C4' C 87.488 0.20 1 99 7 7 U C5 C 103.481 0.20 1 100 7 7 U C5' C 67.286 0.20 1 101 7 7 U C6 C 143.790 0.20 1 102 7 7 U P P -3.130 0.05 1 stop_ save_ save_assigned_chemical_shifts_2 _Saveframe_category assigned_chemical_shifts _Details . 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 $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 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 U H1' H 5.310 0.01 1 2 1 1 U H2' H 3.970 0.01 1 3 1 1 U H3' H 4.555 0.01 1 4 1 1 U H4' H 4.308 0.01 1 5 1 1 U H5 H 5.628 0.01 1 6 1 1 U H5' H 4.018 0.01 2 7 1 1 U H5'' H 4.188 0.01 2 8 1 1 U H6 H 7.958 0.01 1 9 2 2 G H1' H 5.833 0.01 1 10 2 2 G H2' H 4.980 0.01 1 11 2 2 G H3' H 4.894 0.01 1 12 2 2 G H4' H 4.589 0.01 1 13 2 2 G H5' H 4.177 0.01 2 14 2 2 G H5'' H 4.391 0.01 2 15 2 2 G H8 H 8.318 0.01 1 16 3 3 G H1' H 6.133 0.01 1 17 3 3 G H2' H 4.901 0.01 1 18 3 3 G H3' H 4.419 0.01 1 19 3 3 G H4' H 4.698 0.01 1 20 3 3 G H5' H 4.374 0.01 2 21 3 3 G H5'' H 4.512 0.01 2 22 3 3 G H8 H 8.023 0.01 1 23 4 4 U H1' H 5.406 0.01 1 24 4 4 U H2' H 4.235 0.01 1 25 4 4 U H3' H 4.402 0.01 1 26 4 4 U H4' H 4.508 0.01 1 27 4 4 U H5 H 4.488 0.01 1 28 4 4 U H5' H 4.208 0.01 2 29 4 4 U H5'' H 4.696 0.01 2 30 4 4 U H6 H 7.455 0.01 1 31 5 5 G H1' H 5.845 0.01 1 32 5 5 G H2' H 4.312 0.01 1 33 5 5 G H3' H 4.986 0.01 1 34 5 5 G H4' H 4.504 0.01 1 35 5 5 G H5' H 4.169 0.01 2 36 5 5 G H5'' H 4.708 0.01 2 37 5 5 G H8 H 8.433 0.01 1 38 6 6 G H1' H 6.232 0.01 1 39 6 6 G H2' H 4.168 0.01 1 40 6 6 G H3' H 4.571 0.01 1 41 6 6 G H4' H 4.438 0.01 1 42 6 6 G H5' H 4.152 0.01 2 43 6 6 G H5'' H 4.655 0.01 2 44 6 6 G H8 H 7.592 0.01 1 45 7 7 U H1' H 5.891 0.01 1 46 7 7 U H2' H 3.907 0.01 1 47 7 7 U H3' H 4.354 0.01 1 48 7 7 U H4' H 4.256 0.01 1 49 7 7 U H5 H 5.071 0.01 1 50 7 7 U H5' H 4.072 0.01 2 51 7 7 U H6 H 7.773 0.01 1 stop_ save_ save_assigned_chemical_shifts_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 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 U H1' H 5.299 0.01 1 2 1 1 U H2' H 3.928 0.01 1 3 1 1 U H3 H 10.857 0.01 1 4 1 1 U H3' H 4.581 0.01 1 5 1 1 U H4' H 4.303 0.01 1 6 1 1 U H5 H 5.641 0.01 1 7 1 1 U H5' H 4.042 0.01 2 8 1 1 U H5'' H 4.228 0.01 2 9 1 1 U H6 H 8.004 0.01 1 10 2 2 G H1 H 11.244 0.01 1 11 2 2 G H1' H 5.826 0.01 1 12 2 2 G H2' H 5.023 0.01 1 13 2 2 G H3' H 4.913 0.01 1 14 2 2 G H4' H 4.597 0.01 1 15 2 2 G H5' H 4.164 0.01 2 16 2 2 G H5'' H 4.410 0.01 2 17 2 2 G H8 H 8.383 0.01 1 18 2 2 G H21 H 9.869 0.01 1 19 2 2 G H22 H 6.925 0.01 1 20 3 3 G H1 H 11.302 0.01 1 21 3 3 G H1' H 6.176 0.01 1 22 3 3 G H2' H 4.918 0.01 1 23 3 3 G H3' H 4.419 0.01 1 24 3 3 G H4' H 4.725 0.01 1 25 3 3 G H5' H 4.532 0.01 2 26 3 3 G H5'' H 4.384 0.01 2 27 3 3 G H8 H 8.107 0.01 1 28 3 3 G H21 H 9.729 0.01 1 29 4 4 U H1' H 5.396 0.01 1 30 4 4 U H2' H 4.258 0.01 1 31 4 4 U H3 H 9.967 0.01 1 32 4 4 U H3' H 4.421 0.01 1 33 4 4 U H4' H 4.522 0.01 1 34 4 4 U H5 H 4.447 0.01 1 35 4 4 U H5' H 4.178 0.01 2 36 4 4 U H6 H 7.462 0.01 1 37 4 4 U HO2' H 6.867 0.01 1 38 5 5 G H1 H 11.474 0.01 1 39 5 5 G H1' H 5.842 0.01 1 40 5 5 G H2' H 4.335 0.01 1 41 5 5 G H3' H 4.999 0.01 1 42 5 5 G H5' H 4.178 0.01 2 43 5 5 G H5'' H 4.732 0.01 2 44 5 5 G H8 H 8.445 0.01 1 45 5 5 G H21 H 10.075 0.01 1 46 5 5 G H22 H 6.132 0.01 1 47 5 5 G HO2' H 6.731 0.01 1 48 6 6 G H1 H 11.400 0.01 1 49 6 6 G H1' H 6.242 0.01 1 50 6 6 G H2' H 4.185 0.01 1 51 6 6 G H3' H 4.575 0.01 1 52 6 6 G H4' H 4.448 0.01 1 53 6 6 G H5' H 4.160 0.01 2 54 6 6 G H5'' H 4.674 0.01 2 55 6 6 G H8 H 7.596 0.01 1 56 6 6 G H21 H 9.625 0.01 1 57 6 6 G H22 H 7.429 0.01 1 58 6 6 G HO2' H 6.740 0.01 1 59 7 7 U H1' H 5.891 0.01 1 60 7 7 U H2' H 3.907 0.01 1 61 7 7 U H3 H 11.209 0.01 1 62 7 7 U H3' H 4.365 0.01 1 63 7 7 U H4' H 4.260 0.01 1 64 7 7 U H5 H 5.085 0.01 1 65 7 7 U H5' H 4.076 0.01 2 66 7 7 U H6 H 7.781 0.01 1 67 7 7 U HO2' H 7.077 0.01 1 stop_ save_