data_50268 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Small Molecule Targeting IRES Domain Inhibits Enterovirus 71 Replication via an Allosteric Mechanism that Stabilizes a Ternary Complex ; _BMRB_accession_number 50268 _BMRB_flat_file_name bmr50268.str _Entry_type original _Submission_date 2020-05-10 _Accession_date 2020-05-10 _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 Davila-Calderon Jesse . . 2 Patwardhan Neeraj . . 3 Chiu Liang-Yuan . . 4 Sugarman Andrew . . 5 Cai Zhengguo . . 6 Penutmutchu Srinivasa R. . 7 Li Mei-Ling . . 8 Brewer Gary . . 9 Hargrove Amanda E. . 10 Tolbert Blanton S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 119 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-10-01 update BMRB 'update entry citation' 2020-06-10 original author 'original release' stop_ _Original_release_date 2020-05-11 save_ ############################# # Citation for this entry # ############################# save_citations_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 32963221 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Davila-Calderon Jesse . . 2 Patwardhan Neeraj . . 3 Chiu Liang-Yuan . . 4 Sugarman Andrew . . 5 Cai Zhengguo . . 6 Penutmutchu Srinivasa R. . 7 Li Mei-Ling . . 8 Brewer Gary . . 9 Hargrove Amanda E. . 10 Tolbert Blanton S. . stop_ _Journal_abbreviation 'Nat. Commun.' _Journal_name_full 'Nature communications' _Journal_volume 11 _Journal_issue 1 _Journal_ISSN 2041-1723 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4775 _Page_last 4775 _Year 2020 _Details . save_ ################################## # Molecular system description # ################################## save_assembly_1 _Saveframe_category molecular_system _Mol_system_name 'EV71 SL2 DMA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'EV71 RNA(41-MER)' $entity_1 stop_ _System_molecular_weight 13140.855 _System_physical_state native _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 . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 41 _Mol_residue_sequence ; GGAUCAAUAGCAGGUGUGGC ACACCAGUCAUACCUUGAUC C ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 U 5 C 6 A 7 A 8 U 9 A 10 G 11 C 12 A 13 G 14 G 15 U 16 G 17 U 18 G 19 G 20 C 21 A 22 C 23 A 24 C 25 C 26 A 27 G 28 U 29 C 30 A 31 U 32 A 33 C 34 C 35 U 36 U 37 G 38 A 39 U 40 C 41 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source_1 _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain _Gene_mnemonic $entity_1 'Enterovirus A71' 138948 Viruses . Enterovirus 'Enterovirus A71' A "5'UTR SL2" stop_ save_ ######################### # Experimental source # ######################### save_experimental_source_1 _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 'SL2: DMA135=1:4 molar ratio' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 200 uM "[Selective Deuteration; Fully Deuteration for U and C; Selective Deuteration for A and G with 2H at (3',4',5'5'')]" DMA135 800 uM '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_1 200 uM '[Selective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP]' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details 'SL2 only' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 200 uM "[Selective Deuteration; Fully Deuteration for U and C; Selective Deuteration for A and G with 2H at (3',4',5'5'')]" stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details 'SL2: DMA135=1:4 molar ratio' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 200 uM '[Selective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP]' DMA135 800 uM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version . loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name NMRFAM-SPARKY _Version . loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name HADDOCK _Version . loop_ _Task Docking stop_ _Details . save_ save_software_4 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Task collection stop_ _Details . save_ save_software_5 _Saveframe_category software _Name NMRViewJ _Version . loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_6 _Saveframe_category software _Name NMRPipe _Version . loop_ _Task processing stop_ _Details . save_ save_software_7 _Saveframe_category software _Name NMRDraw _Version . loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _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_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_4 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_3 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 303 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'The DMSO protons is set as 2.5 ppm.' 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 water H 1 protons ppm 4.7 internal 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details ; Assignments for DMA: 120 2 1 DMA H8 H 1 2.9065 . . 1 121 2 1 DMA H9 H 1 2.9065 . . 1 122 2 1 DMA H10 H 1 2.9065 . . 1 123 2 1 DMA H11 H 1 2.9065 . . 1 124 2 1 DMA H12 H 1 2.9065 . . 1 125 2 1 DMA H13 H 1 2.9065 . . 1 ; loop_ _Software_label $software_4 stop_ loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 $sample_4 $sample_3 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'EV71 RNA(41-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 1 1 G H1' H 5.7693 . 1 2 1 1 G H2' H 4.919 . 1 3 1 1 G H8 H 8.0965 . 1 4 2 2 G H1' H 5.8309 . 1 5 2 2 G H2' H 4.919 . 1 6 2 2 G H8 H 7.5556 . 1 7 3 3 A H1' H 5.9374 . 1 8 3 3 A H2 H 7.7052 . 1 9 3 3 A H2' H 4.5152 . 1 10 3 3 A H8 H 7.7589 . 1 11 4 4 U H1' H 5.4307 . 1 12 4 4 U H2' H 4.3148 . 1 13 4 4 U H6 H 7.5058 . 1 14 5 5 C H1' H 5.5206 . 1 15 5 5 C H2' H 4.2347 . 1 16 5 5 C H6 H 7.6918 . 1 17 6 6 A H1' H 5.7169 . 1 18 6 6 A H2 H 6.8399 . 1 19 6 6 A H8 H 7.8142 . 1 20 7 7 A H1' H 5.4921 . 1 21 7 7 A H2 H 7.6522 . 1 22 7 7 A H8 H 7.4506 . 1 23 9 9 A H1' H 5.7235 . 1 24 9 9 A H2 H 7.8729 . 1 25 9 9 A H8 H 8.0206 . 1 26 10 10 G H1' H 5.4139 . 1 27 10 10 G H8 H 7.6502 . 1 28 12 12 A H1' H 5.7453 . 1 29 12 12 A H2 H 7.5287 . 1 30 12 12 A H8 H 8.1796 . 1 31 13 13 G H1' H 5.6196 . 1 32 13 13 G H8 H 7.2797 . 1 33 14 14 G H1' H 5.7356 . 1 34 14 14 G H2' H 4.5963 . 1 35 14 14 G H8 H 7.1393 . 1 36 15 15 U H1' H 5.6125 . 1 37 15 15 U H2' H 4.6435 . 1 38 15 15 U H6 H 7.6216 . 1 39 16 16 G H1' H 5.7499 . 1 40 16 16 G H2' H 4.6435 . 1 41 16 16 G H8 H 7.8828 . 1 42 17 17 U H1' H 5.4034 . 1 43 17 17 U H2' H 4.4607 . 1 44 17 17 U H6 H 7.6009 . 1 45 18 18 G H1' H 5.7403 . 1 46 18 18 G H2' H 4.4885 . 1 47 18 18 G H8 H 7.6581 . 1 48 19 19 G H1' H 5.6690 . 1 49 19 19 G H2' H 4.5602 . 1 50 19 19 G H8 H 7.1719 . 1 51 20 20 C H1' H 5.4042 . 1 52 20 20 C H2' H 4.5343 . 1 53 20 20 C H6 H 7.3783 . 1 54 21 21 A H1' H 5.8282 . 1 55 21 21 A H2 H 8.1402 . 1 56 21 21 A H8 H 7.9272 . 1 57 22 22 C H1' H 5.3542 . 1 58 22 22 C H2' H 3.9409 . 1 59 22 22 C H6 H 7.3848 . 1 60 23 23 A H1' H 5.8454 . 1 61 23 23 A H2 H 7.9808 . 1 62 23 23 A H8 H 8.2427 . 1 63 24 24 C H1' H 5.3562 . 1 64 24 24 C H2' H 4.2991 . 1 65 24 24 C H6 H 7.4208 . 1 66 25 25 C H1' H 5.5748 . 1 67 25 25 C H2' H 4.3174 . 1 68 25 25 C H6 H 7.6746 . 1 69 26 26 A H1' H 5.9484 . 1 70 26 26 A H2 H 7.4214 . 1 71 26 26 A H2' H 4.3068 . 1 72 26 26 A H8 H 8.2240 . 1 73 27 27 G H1' H 5.4408 . 1 74 27 27 G H2' H 4.3490 . 1 75 27 27 G H8 H 7.5897 . 1 76 28 28 U H1' H 5.5159 . 1 77 28 28 U H2' H 4.1411 . 1 78 28 28 U H6 H 7.7205 . 1 79 29 29 C H1' H 5.6092 . 1 80 29 29 C H2' H 4.6041 . 1 81 29 29 C H6 H 7.8899 . 1 82 30 30 A H1' H 5.7739 . 1 83 30 30 A H2 H 7.2592 . 1 84 30 30 A H2' H 4.6323 . 1 85 30 30 A H8 H 7.9033 . 1 86 31 31 U H1' H 5.2334 . 1 87 31 31 U H2' H 4.1062 . 1 88 31 31 U H6 H 7.5364 . 1 89 32 32 A H1' H 5.8678 . 1 90 32 32 A H2 H 7.3525 . 1 91 32 32 A H2' H 4.5849 . 1 92 32 32 A H8 H 8.324 . 1 93 33 33 C H1' H 5.3655 . 1 94 33 33 C H2' H 4.2397 . 1 95 33 33 C H6 H 7.4759 . 1 96 34 34 C H1' H 5.4975 . 1 97 34 34 C H2' H 4.5137 . 1 98 34 34 C H6 H 7.7370 . 1 99 35 35 U H1' H 5.8994 . 1 100 35 35 U H2' H 4.3533 . 1 101 35 35 U H6 H 7.7573 . 1 102 36 36 U H1' H 5.7697 . 1 103 36 36 U H6 H 7.8874 . 1 104 37 37 G H1' H 5.7368 . 1 105 37 37 G H2' H 4.4291 . 1 106 37 37 G H8 H 7.8406 . 1 107 38 38 A H1' H 5.8936 . 1 108 38 38 A H2 H 7.6534 . 1 109 38 38 A H2' H 4.4704 . 1 110 38 38 A H8 H 7.8214 . 1 111 39 39 U H1' H 5.4357 . 1 112 39 39 U H2' H 4.3426 . 1 113 39 39 U H6 H 7.5691 . 1 114 40 40 C H1' H 5.5406 . 1 115 40 40 C H2' H 4.1986 . 1 116 40 40 C H6 H 7.7894 . 1 117 41 41 C H1' H 5.7055 . 1 118 41 41 C H2' H 3.9571 . 1 119 41 41 C H6 H 7.6143 . 1 stop_ save_