data_11489 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; RNA aptamer against prion protein in complex with the partial binding peptide ; _BMRB_accession_number 11489 _BMRB_flat_file_name bmr11489.str _Entry_type original _Submission_date 2012-03-08 _Accession_date 2012-03-11 _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 Mashima Tsukasa . . 2 Nishikawa Fumiko . . 3 Kamatari Yuji O . 4 Fujiwara Hiromichi . . 5 Nishikawa Satoshi . . 6 Kuwata Kazuo . . 7 Katahira Masato . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 153 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-11 original author . stop_ _Original_release_date 2013-02-11 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Anti-prion activity of an RNA aptamer and its structural basis' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23180780 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mashima Tsukasa . . 2 Nishikawa Fumiko . . 3 Kamatari Yuji O . 4 Fujiwara Hiromichi . . 5 Saimura Masayuki . . 6 Nagata Takashi . . 7 Kodaki Tsutomu . . 8 Nishikawa Satoshi . . 9 Kuwata Kazuo . . 10 Katahira Masato . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 41 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1355 _Page_last 1362 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'RNA aptamer against prion protein' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')_1' $RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') 'RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')_2' $RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') entity_2_1 $P16 entity_2_2 $P16 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_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') _Molecular_mass 4033.540 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GGAGGAGGAGGA loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 G 5 G 6 A 7 G 8 G 9 A 10 G 11 G 12 A stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_P16 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common P16 _Molecular_mass 1387.577 _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence GQWNKPSKPKTN loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 25 GLY 2 26 GLN 3 27 TRP 4 28 ASN 5 29 LYS 6 30 PRO 7 31 SER 8 32 LYS 9 33 PRO 10 34 LYS 11 35 THR 12 36 ASN 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_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') . . . . . . $P16 cow 9913 Eukaryota Metazoa . . 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_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') 'chemical synthesis' . . . . . $P16 'chemical synthesis' . . . . . 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_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') 1 mM 'natural abundance' $P16 1 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' 'potassium chloride' 10 mM 'natural abundance' DSS 0.01 mM 'natural abundance' 'sodium azide' 3 mM 'natural abundance' H2O 95 % . D2O 5 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') 1 mM 'natural abundance' $P16 1 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' 'potassium chloride' 10 mM 'natural abundance' DSS 0.01 mM 'natural abundance' 'sodium azide' 3 mM 'natural abundance' D2O 100 % . stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.26 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ 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' 'peak picking' stop_ _Details . save_ save_NMRPipe _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_TALOS _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _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_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_JRHMBC_10 _Saveframe_category NMR_applied_experiment _Experiment_name JRHMBC _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 temperature 278 . K pH 6.2 . pH pressure 1 . atm 'ionic strength' 20 . mM stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 303 . K pH 6.2 . pH pressure 1 . atm 'ionic strength' 20 . mM 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 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_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_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')_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 G H1' H 5.556 0.03 1 2 1 1 G H2' H 4.944 0.03 1 3 1 1 G H3' H 4.96 0.03 1 4 1 1 G H4' H 4.727 0.03 1 5 1 1 G H5' H 4.211 0.03 2 6 1 1 G H5'' H 4.273 0.03 2 7 1 1 G H8 H 7.418 0.03 1 8 2 2 G H1' H 5.447 0.03 1 9 2 2 G H2' H 4.292 0.03 1 10 2 2 G H3' H 4.559 0.03 1 11 2 2 G H4' H 3.137 0.03 1 12 2 2 G H5' H 3.097 0.03 2 13 2 2 G H5'' H 3.752 0.03 2 14 2 2 G H8 H 7.848 0.03 1 15 3 3 A H1' H 5.707 0.03 1 16 3 3 A H2 H 8.509 0.03 1 17 3 3 A H2' H 4.435 0.03 1 18 3 3 A H3' H 5.111 0.03 1 19 3 3 A H4' H 4.493 0.03 1 20 3 3 A H5' H 3.878 0.03 2 21 3 3 A H5'' H 4.287 0.03 2 22 3 3 A H8 H 7.78 0.03 1 23 4 4 G H1' H 5.78 0.03 1 24 4 4 G H2' H 5.534 0.03 1 25 4 4 G H4' H 4.787 0.03 1 26 4 4 G H5' H 4.568 0.03 2 27 4 4 G H5'' H 4.61 0.03 2 28 4 4 G H8 H 7.721 0.03 1 29 5 5 G H1' H 6.276 0.03 1 30 5 5 G H2' H 4.966 0.03 1 31 5 5 G H3' H 4.825 0.03 1 32 5 5 G H4' H 4.825 0.03 1 33 5 5 G H5' H 4.227 0.03 2 34 5 5 G H5'' H 4.647 0.03 2 35 5 5 G H8 H 8.083 0.03 1 36 6 6 A H1' H 6.334 0.03 1 37 6 6 A H2 H 9.041 0.03 1 38 6 6 A H2' H 5.895 0.03 1 39 6 6 A H3' H 5.302 0.03 1 40 6 6 A H4' H 4.855 0.03 1 41 6 6 A H5' H 4.685 0.03 1 42 6 6 A H5'' H 4.685 0.03 1 43 6 6 A H8 H 8.384 0.03 1 44 7 7 G H1' H 5.609 0.03 1 45 7 7 G H2' H 5.168 0.03 1 46 7 7 G H3' H 5.081 0.03 1 47 7 7 G H4' H 5.012 0.03 1 48 7 7 G H5' H 4.349 0.03 2 49 7 7 G H5'' H 4.513 0.03 2 50 7 7 G H8 H 8.17 0.03 1 51 8 8 G H1' H 5.41 0.03 1 52 8 8 G H2' H 4.305 0.03 1 53 8 8 G H3' H 4.499 0.03 1 54 8 8 G H4' H 3.108 0.03 1 55 8 8 G H5' H 2.888 0.03 2 56 8 8 G H5'' H 3.716 0.03 2 57 8 8 G H8 H 7.902 0.03 1 58 9 9 A H1' H 5.714 0.03 1 59 9 9 A H2 H 8.492 0.03 1 60 9 9 A H2' H 4.342 0.03 1 61 9 9 A H3' H 5.228 0.03 1 62 9 9 A H4' H 4.46 0.03 1 63 9 9 A H5' H 3.77 0.03 2 64 9 9 A H5'' H 4.293 0.03 2 65 9 9 A H8 H 7.875 0.03 1 66 10 10 G H1' H 5.864 0.03 1 67 10 10 G H2' H 4.612 0.03 1 68 10 10 G H3' H 4.654 0.03 1 69 10 10 G H4' H 4.739 0.03 1 70 10 10 G H8 H 7.792 0.03 1 71 11 11 G H1' H 5.423 0.03 1 72 11 11 G H2' H 4.556 0.03 1 73 11 11 G H3' H 4.905 0.03 1 74 11 11 G H4' H 4.825 0.03 1 75 11 11 G H5' H 4.316 0.03 2 76 11 11 G H5'' H 4.705 0.03 2 77 11 11 G H8 H 7.992 0.03 1 78 12 12 A H1' H 5.958 0.03 1 79 12 12 A H2 H 7.831 0.03 1 80 12 12 A H2' H 4.436 0.03 1 81 12 12 A H3' H 4.403 0.03 1 82 12 12 A H4' H 4.409 0.03 1 83 12 12 A H5' H 4.279 0.03 2 84 12 12 A H5'' H 4.411 0.03 2 85 12 12 A H8 H 8.114 0.03 1 stop_ save_ save_assigned_chem_shift_list_1_3 _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_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name entity_2_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 25 1 GLY HA2 H 3.673 0.03 2 2 25 1 GLY HA3 H 3.621 0.03 2 3 26 2 GLN HA H 3.919 0.03 1 4 26 2 GLN HB2 H 1.627 0.03 1 5 26 2 GLN HB3 H 1.627 0.03 1 6 26 2 GLN HG2 H 1.905 0.03 1 7 26 2 GLN HG3 H 1.905 0.03 1 8 27 3 TRP HA H 4.129 0.03 1 9 27 3 TRP HB2 H 2.793 0.03 2 10 27 3 TRP HB3 H 2.652 0.03 2 11 27 3 TRP HD1 H 6.519 0.03 1 12 27 3 TRP HE3 H 6.978 0.03 1 13 27 3 TRP HZ2 H 6.848 0.03 1 14 27 3 TRP HZ3 H 6.459 0.03 1 15 27 3 TRP HH2 H 6.581 0.03 1 16 28 4 ASN HA H 4.151 0.03 1 17 28 4 ASN HB2 H 2.209 0.03 2 18 28 4 ASN HB3 H 2.164 0.03 2 19 29 5 LYS HA H 3.934 0.03 1 20 29 5 LYS HB2 H 1.428 0.03 2 21 29 5 LYS HB3 H 1.294 0.03 2 22 29 5 LYS HG2 H 1.066 0.03 1 23 29 5 LYS HG3 H 1.066 0.03 1 24 29 5 LYS HD2 H 1.405 0.03 1 25 29 5 LYS HD3 H 1.405 0.03 1 26 29 5 LYS HE2 H 2.752 0.03 1 27 29 5 LYS HE3 H 2.752 0.03 1 28 30 6 PRO HA H 4.197 0.03 1 29 30 6 PRO HB2 H 2.072 0.03 2 30 30 6 PRO HB3 H 1.704 0.03 2 31 30 6 PRO HG2 H 1.713 0.03 1 32 30 6 PRO HG3 H 1.713 0.03 1 33 30 6 PRO HD2 H 3.424 0.03 2 34 30 6 PRO HD3 H 3.264 0.03 2 35 31 7 SER HA H 4.302 0.03 1 36 31 7 SER HB2 H 3.729 0.03 1 37 31 7 SER HB3 H 3.729 0.03 1 38 32 8 LYS HA H 4.555 0.03 1 39 32 8 LYS HB2 H 1.762 0.03 2 40 32 8 LYS HB3 H 1.661 0.03 2 41 32 8 LYS HG2 H 1.399 0.03 1 42 32 8 LYS HG3 H 1.399 0.03 1 43 32 8 LYS HD2 H 1.65 0.03 1 44 32 8 LYS HD3 H 1.65 0.03 1 45 32 8 LYS HE2 H 2.954 0.03 1 46 32 8 LYS HE3 H 2.954 0.03 1 47 33 9 PRO HA H 4.36 0.03 1 48 33 9 PRO HB2 H 2.253 0.03 2 49 33 9 PRO HB3 H 1.849 0.03 2 50 33 9 PRO HG2 H 1.984 0.03 2 51 33 9 PRO HG3 H 1.948 0.03 2 52 33 9 PRO HD2 H 3.762 0.03 2 53 33 9 PRO HD3 H 3.575 0.03 2 54 34 10 LYS HA H 4.361 0.03 1 55 34 10 LYS HB2 H 1.86 0.03 2 56 34 10 LYS HB3 H 1.759 0.03 2 57 34 10 LYS HG2 H 1.48 0.03 2 58 34 10 LYS HG3 H 1.432 0.03 2 59 34 10 LYS HD2 H 1.673 0.03 1 60 34 10 LYS HD3 H 1.673 0.03 1 61 34 10 LYS HE2 H 2.996 0.03 1 62 34 10 LYS HE3 H 2.996 0.03 1 63 35 11 THR HA H 4.354 0.03 1 64 35 11 THR HB H 4.255 0.03 1 65 35 11 THR HG2 H 1.169 0.03 1 66 36 12 ASN HA H 4.47 0.03 1 67 36 12 ASN HB2 H 2.757 0.03 2 68 36 12 ASN HB3 H 2.686 0.03 2 stop_ save_