data_25867 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; An NMR/SAXS structure of the PKI domain of the honeybee dicistrovirus, Israeli acute paralysis virus (IAPV) IRES ; _BMRB_accession_number 25867 _BMRB_flat_file_name bmr25867.str _Entry_type original _Submission_date 2015-10-27 _Accession_date 2015-10-27 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Au Hilda H. . 2 Cornilescu Gabriel . . 3 Mouzakis Kathryn D. . 4 Burke Jordan E. . 5 Ren Qian . . 6 Lee Seonghoon . . 7 Butcher Samuel E. . 8 Jan Eric . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 29 "15N chemical shifts" 29 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-03-09 update BMRB 'update entry citation' 2015-11-09 original author 'original release' stop_ _Original_release_date 2015-11-09 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26554019 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Au Hilda H. . 2 Cornilescu Gabriel . . 3 Mouzakis Kathryn D. . 4 Ren Qian . . 5 Burke Jordan E. . 6 Lee Seonghoon . . 7 Butcher Samuel E. . 8 Jan Eric . . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_volume 112 _Journal_issue 47 _Journal_ISSN 1091-6490 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first E6446 _Page_last E6455 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'PKI domain of the honeybee dicistrovirus, Israeli acute paralysis virus (IAPV) IRES' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (70-MER)' $RNA_(70-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_(70-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(70-MER) _Molecular_mass 22565.592 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 70 _Mol_residue_sequence ; GGAACAGCUGUACUGGGCAG UUACAGCAGUCGUAUGGUAA CACAUGCGGCGUUCCGAAAU ACCAUGCCUG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 2 G 3 3 A 4 4 A 5 5 C 6 6 A 7 7 G 8 8 C 9 9 U 10 10 G 11 11 U 12 12 A 13 13 C 14 14 U 15 15 G 16 16 G 17 17 G 18 18 C 19 19 A 20 20 G 21 21 U 22 22 U 23 23 A 24 24 C 25 25 A 26 26 G 27 27 C 28 28 A 29 29 G 30 30 U 31 31 C 32 32 G 33 33 U 34 34 A 35 35 U 36 36 G 37 37 G 38 38 U 39 39 A 40 40 A 41 41 C 42 42 A 43 43 C 44 44 A 45 45 U 46 46 G 47 47 C 48 48 G 49 49 G 50 50 C 51 51 G 52 52 U 53 53 U 54 54 C 55 55 C 56 56 G 57 57 A 58 58 A 59 59 A 60 60 U 61 61 A 62 62 C 63 63 C 64 64 A 65 65 U 66 66 G 67 67 C 68 68 C 69 69 U 70 70 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 $RNA_(70-MER) 'honey bee' 7460 Eukaryota Metazoa Apis mellifera 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_(70-MER) 'cell free synthesis' . . . . n/a stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.53-0.70 mM; potassium phosphate 10 mM; potassium chloride 200 mM; Ethylenediaminetetraacetic acid 50 uM' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(70-MER) . mM 0.53 0.70 '[U-13C; U-15N]-Gua' 'potassium phosphate' 10 mM . . 'natural abundance' 'potassium chloride' 200 mM . . 'natural abundance' 'Ethylenediaminetetraacetic acid' 50 uM . . 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details ; Pf1 phage 12.5 mg/mL 0.53-0.70 mM; potassium phosphate 10 mM; potassium chloride 200 mM; Ethylenediaminetetraacetic acid 50 uM ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(70-MER) . mM 0.53 0.70 '[U-13C; U-15N]-Gua' 'Pf1 phage' 12.5 mg/ml . . 'natural abundance' 'potassium phosphate' 10 mM . . 'natural abundance' 'potassium chloride' 200 mM . . 'natural abundance' 'Ethylenediaminetetraacetic acid' 50 uM . . 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_MC-SIM _Saveframe_category software _Name MC-SIM _Version 4.2.2 loop_ _Vendor _Address _Electronic_address 'Parisien, Major' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_NMRDraw _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'data analysis' 'peak picking' 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 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_TROSY-HMQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N TROSY-HMQC' _Sample_label $sample_1 save_ save_2D_1H-15N_TROSY-HMQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N TROSY-HMQC' _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' 0.225 . M pH 6.3 . pH pressure 1 . atm temperature 283 . 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 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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-15N TROSY-HMQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (70-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 2 2 G H1 H 12.145 . . 2 2 2 G N1 N 147.120 . . 3 7 7 G H1 H 12.410 . . 4 7 7 G N1 N 147.751 . . 5 9 9 U H3 H 13.345 . . 6 9 9 U N3 N 162.243 . . 7 10 10 G H1 H 12.302 . . 8 10 10 G N1 N 147.384 . . 9 11 11 U H3 H 13.927 . . 10 11 11 U N3 N 163.185 . . 11 15 15 G H1 H 10.604 . . 12 15 15 G N1 N 142.565 . . 13 16 16 G H1 H 12.574 . . 14 16 16 G N1 N 147.595 . . 15 17 17 G H1 H 13.083 . . 16 17 17 G N1 N 148.799 . . 17 20 20 G H1 H 12.691 . . 18 20 20 G N1 N 148.183 . . 19 22 22 U H3 H 14.413 . . 20 22 22 U N3 N 163.050 . . 21 26 26 G H1 H 13.179 . . 22 26 26 G N1 N 147.967 . . 23 29 29 G H1 H 13.539 . . 24 29 29 G N1 N 148.888 . . 25 30 30 U H3 H 12.445 . . 26 30 30 U N3 N 159.198 . . 27 32 32 G H1 H 12.823 . . 28 32 32 G N1 N 147.613 . . 29 33 33 U H3 H 11.802 . . 30 33 33 U N3 N 158.358 . . 31 35 35 U H3 H 13.110 . . 32 35 35 U N3 N 161.778 . . 33 36 36 G H1 H 12.748 . . 34 36 36 G N1 N 147.473 . . 35 37 37 G H1 H 10.974 . . 36 37 37 G N1 N 147.245 . . 37 38 38 U H3 H 11.302 . . 38 38 38 U N3 N 157.884 . . 39 45 45 U H3 H 13.687 . . 40 45 45 U N3 N 162.930 . . 41 46 46 G H1 H 10.831 . . 42 46 46 G N1 N 144.326 . . 43 48 48 G H1 H 12.410 . . 44 48 48 G N1 N 147.751 . . 45 49 49 G H1 H 11.579 . . 46 49 49 G N1 N 145.576 . . 47 51 51 G H1 H 12.691 . . 48 51 51 G N1 N 148.183 . . 49 52 52 U H3 H 14.332 . . 50 52 52 U N3 N 162.967 . . 51 53 53 U H3 H 13.839 . . 52 53 53 U N3 N 163.298 . . 53 65 65 U H3 H 13.687 . . 54 65 65 U N3 N 162.930 . . 55 66 66 G H1 H 12.399 . . 56 66 66 G N1 N 147.718 . . 57 69 69 U H3 H 11.875 . . 58 69 69 U N3 N 158.388 . . stop_ save_