data_25996 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the J-K region of EMCV IRES ; _BMRB_accession_number 25996 _BMRB_flat_file_name bmr25996.str _Entry_type original _Submission_date 2016-03-16 _Accession_date 2016-06-10 _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 Imai Shunsuke . . 2 D'Souza Victoria . . 3 Wagner Gerhard . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 90 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-10-12 update BMRB 'update entry citation' 2016-08-08 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 25999 'Solution structure of the St domain of EMCV IRES' 26000 'Solution structure of the delta-J-delta-K domain of EMCV IRES' 26997 'Solution structure of the J domain of EMCV IRES' 26998 'Solution structure of the K domain of EMCV IRES' stop_ _Original_release_date 2016-08-08 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; An accurately preorganized IRES RNA structure enables eIF4G capture for initiation of viral translation ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27525590 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Imai Shunsuke . . 2 Hellen Christopher . . 3 D'Souza Victoria . . 4 Wagner Gerhard . . stop_ _Journal_abbreviation 'Nat. Struct. Mol. Biol.' _Journal_volume 23 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 859 _Page_last 864 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'J-K region of EMCV IRES' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (108-MER)' $RNA_(108-MER) 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_RNA_(108-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(108-MER) _Molecular_mass 34838.840 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 108 _Mol_residue_sequence ; GGGGCUGAAGGAUGCCCAGA AGGUACCCCAUUGUAUGGGA UCUGAUCUGGGGCCUCGGUG CACAUGCUUUACAUGUGUUU AGUCGAGGUUAAAAAACGUC UAGGCCCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 . G 2 . G 3 . G 4 . G 5 . C 6 . U 7 . G 8 687 A 9 688 A 10 689 G 11 690 G 12 691 A 13 692 U 14 693 G 15 694 C 16 695 C 17 696 C 18 697 A 19 698 G 20 699 A 21 700 A 22 701 G 23 702 G 24 703 U 25 704 A 26 705 C 27 706 C 28 707 C 29 708 C 30 709 A 31 710 U 32 711 U 33 712 G 34 713 U 35 714 A 36 715 U 37 716 G 38 717 G 39 718 G 40 719 A 41 720 U 42 721 C 43 722 U 44 723 G 45 724 A 46 725 U 47 726 C 48 727 U 49 728 G 50 729 G 51 730 G 52 731 G 53 732 C 54 733 C 55 734 U 56 735 C 57 736 G 58 737 G 59 738 U 60 739 G 61 740 C 62 741 A 63 742 C 64 743 A 65 744 U 66 745 G 67 746 C 68 747 U 69 748 U 70 749 U 71 750 A 72 751 C 73 752 A 74 753 U 75 754 G 76 755 U 77 756 G 78 757 U 79 758 U 80 759 U 81 760 A 82 761 G 83 762 U 84 763 C 85 764 G 86 765 A 87 766 G 88 767 G 89 768 U 90 769 U 91 770 A 92 771 A 93 772 A 94 773 A 95 774 A 96 775 A 97 776 C 98 777 G 99 778 U 100 779 C 101 780 U 102 781 A 103 782 G 104 783 G 105 784 C 106 785 C 107 786 C 108 787 C 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 $RNA_(108-MER) 'Encephalomyocarditis virus' 12104 Viruses . Cardiovirus 'Cardiovirus A' 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_(108-MER) 'enzymatic semisynthesis' . . . . . 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 $RNA_(108-MER) 0.5 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' 'sodium chloride' 10 mM 'natural abundance' D2O 100 % [U-2H] stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(108-MER) 0.5 mM "[U-2H, {H1',H2',H2,H8}-Ade]" 'potassium phosphate' 10 mM 'natural abundance' 'sodium chloride' 10 mM 'natural abundance' D2O 100 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_CARA _Saveframe_category software _Name CARA _Version . loop_ _Vendor _Address _Electronic_address 'Keller and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _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_2 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' 20 . mM pH 6.5 . pH pressure 1 . atm temperature 308 . 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 direct . . . 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' stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (108-MER)' _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 1 687 8 A H1' H 5.69 0 1 2 687 8 A H2 H 7.48 0 1 3 687 8 A H2' H 4.41 0 1 4 687 8 A H8 H 7.92 0 1 5 688 9 A H1' H 5.87 0 1 6 688 9 A H2' H 4.78 0 1 7 688 9 A H8 H 8.24 0 1 8 691 12 A H1' H 5.92 0 1 9 691 12 A H2 H 7.78 0 1 10 691 12 A H2' H 4.45 0 1 11 691 12 A H8 H 7.64 0 1 12 697 18 A H1' H 5.78 0 1 13 697 18 A H2 H 6.82 0 1 14 697 18 A H2' H 4.53 0 1 15 697 18 A H8 H 7.90 0 1 16 699 20 A H1' H 5.75 0 1 17 699 20 A H2 H 7.40 0 1 18 699 20 A H2' H 4.42 0 1 19 699 20 A H8 H 7.62 0 1 20 700 21 A H1' H 5.59 0 1 21 700 21 A H2 H 7.66 0 1 22 700 21 A H8 H 7.69 0 1 23 704 25 A H1' H 5.81 0 1 24 704 25 A H2 H 7.79 0 1 25 704 25 A H8 H 8.01 0 1 26 709 30 A H1' H 5.85 0 1 27 709 30 A H2 H 7.38 0 1 28 709 30 A H2' H 4.40 0 1 29 709 30 A H8 H 7.93 0 1 30 714 35 A H1' H 5.81 0 1 31 714 35 A H2 H 7.84 0 1 32 714 35 A H2' H 4.76 0 1 33 714 35 A H8 H 8.34 0 1 34 719 40 A H1' H 5.97 0 1 35 719 40 A H2 H 8.10 0 1 36 719 40 A H2' H 4.53 0 1 37 719 40 A H8 H 7.76 0 1 38 724 45 A H1' H 5.78 0 1 39 724 45 A H2' H 4.53 0 1 40 724 45 A H8 H 8.14 0 1 41 741 62 A H1' H 5.88 0 1 42 741 62 A H2 H 7.29 0 1 43 741 62 A H2' H 4.47 0 1 44 741 62 A H8 H 7.97 0 1 45 743 64 A H1' H 5.85 0 1 46 743 64 A H2 H 7.23 0 1 47 743 64 A H2' H 4.27 0 1 48 743 64 A H8 H 7.93 0 1 49 750 71 A H1' H 6.03 0 1 50 750 71 A H2 H 8.10 0 1 51 750 71 A H2' H 4.81 0 1 52 750 71 A H8 H 8.50 0 1 53 752 73 A H1' H 5.92 0 1 54 752 73 A H2 H 7.28 0 1 55 752 73 A H2' H 4.44 0 1 56 752 73 A H8 H 8.00 0 1 57 760 81 A H1' H 5.83 0 1 58 760 81 A H2 H 7.84 0 1 59 760 81 A H2' H 4.58 0 1 60 760 81 A H8 H 8.13 0 1 61 765 86 A H1' H 5.84 0 1 62 765 86 A H2 H 7.32 0 1 63 765 86 A H2' H 4.40 0 1 64 765 86 A H8 H 7.65 0 1 65 770 91 A H1' H 5.74 0 1 66 770 91 A H2 H 7.68 0 1 67 770 91 A H8 H 8.13 0 1 68 771 92 A H1' H 5.63 0 1 69 771 92 A H2' H 4.47 0 1 70 771 92 A H8 H 7.94 0 1 71 772 93 A H1' H 5.57 0 1 72 772 93 A H2 H 7.68 0 1 73 772 93 A H2' H 4.46 0 1 74 772 93 A H8 H 7.87 0 1 75 773 94 A H1' H 5.59 0 1 76 773 94 A H2 H 7.68 0 1 77 773 94 A H2' H 4.49 0 1 78 773 94 A H8 H 7.85 0 1 79 774 95 A H1' H 5.61 0 1 80 774 95 A H2 H 7.72 0 1 81 774 95 A H2' H 4.54 0 1 82 774 95 A H8 H 7.85 0 1 83 775 96 A H1' H 5.57 0 1 84 775 96 A H2 H 7.87 0 1 85 775 96 A H2' H 4.48 0 1 86 775 96 A H8 H 7.85 0 1 87 781 102 A H1' H 5.80 0 1 88 781 102 A H2 H 7.39 0 1 89 781 102 A H2' H 4.64 0 1 90 781 102 A H8 H 8.07 0 1 stop_ save_