data_30488 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of Rbfox2 RRM mimetic peptide CPfox5 ; _BMRB_accession_number 30488 _BMRB_flat_file_name bmr30488.str _Entry_type original _Submission_date 2018-07-03 _Accession_date 2018-07-03 _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 Sun Y.-T. . . 2 Varani G. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 105 "15N chemical shifts" 14 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-05-07 original BMRB . stop_ _Original_release_date 2018-08-10 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; A Small Cyclic beta-Hairpin Peptide Mimics the Rbfox2 RNA Recognition Motif and Binds to the Precursor miRNA 20b. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30537200 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sun Yi-Ting T. . 2 Shortridge Matthew D. . 3 Varani Gabriele . . stop_ _Journal_abbreviation Chembiochem _Journal_name_full 'Chembiochem : a European journal of chemical biology' _Journal_volume 20 _Journal_issue 7 _Journal_ISSN 1439-7633 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 931 _Page_last 939 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name CPfox5 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $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 protein _Name_common entity_1 _Molecular_mass 1925.241 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence ; GSRGFRFXPKIIFNER ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 SER 3 ARG 4 GLY 5 PHE 6 ARG 7 PHE 8 DPR 9 PRO 10 LYS 11 ILE 12 ILE 13 PHE 14 ASN 15 GLU 16 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DPR _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-PROLINE _BMRB_code DPR _PDB_code DPR _Standard_residue_derivative . _Molecular_mass 115.130 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N CD ? ? SING N H ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD HD2 ? ? SING CD HD3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ 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 . 36630 . . . . 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 '4.0 mg/mL CPfox5, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 4.0 mg/mL 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' 'potassium chloride' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _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' 20 . mM pH 6.5 . pH pressure 1 . atm temperature 298 . 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 DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.000 internal indirect . . . 0.10132912 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 TOCSY' '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 _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 GLY H H 8.301 0.00 . 2 1 1 GLY HA2 H 3.799 0.00 . 3 1 1 GLY HA3 H 4.031 0.00 . 4 1 1 GLY N N 109.971 0.00 . 5 2 2 SER H H 8.019 0.00 . 6 2 2 SER HA H 4.445 0.00 . 7 2 2 SER HB2 H 3.866 0.00 . 8 2 2 SER HB3 H 3.957 0.00 . 9 2 2 SER N N 115.069 0.00 . 10 3 3 ARG H H 8.231 0.00 . 11 3 3 ARG HA H 4.330 0.00 . 12 3 3 ARG HB2 H 1.713 0.00 . 13 3 3 ARG HB3 H 1.793 0.00 . 14 3 3 ARG HG2 H 1.533 0.00 . 15 3 3 ARG HG3 H 1.585 0.00 . 16 3 3 ARG HD2 H 3.133 0.00 . 17 3 3 ARG HD3 H 3.133 0.00 . 18 3 3 ARG HE H 7.102 0.00 . 19 3 3 ARG N N 121.432 0.00 . 20 4 4 GLY H H 8.265 0.00 . 21 4 4 GLY HA2 H 3.813 0.00 . 22 4 4 GLY HA3 H 3.196 0.00 . 23 4 4 GLY N N 110.210 0.00 . 24 5 5 PHE H H 8.349 0.00 . 25 5 5 PHE HA H 4.655 0.00 . 26 5 5 PHE HB2 H 2.911 0.00 . 27 5 5 PHE HB3 H 2.911 0.00 . 28 5 5 PHE HD1 H 7.098 0.00 . 29 5 5 PHE HD2 H 7.098 0.00 . 30 5 5 PHE N N 120.756 0.00 . 31 6 6 ARG H H 8.277 0.00 . 32 6 6 ARG HA H 4.587 0.00 . 33 6 6 ARG HB2 H 1.568 0.00 . 34 6 6 ARG HB3 H 1.666 0.00 . 35 6 6 ARG HG2 H 1.394 0.00 . 36 6 6 ARG HG3 H 1.488 0.00 . 37 6 6 ARG HD2 H 3.035 0.00 . 38 6 6 ARG HD3 H 3.092 0.00 . 39 6 6 ARG HE H 7.149 0.00 . 40 6 6 ARG N N 122.624 0.00 . 41 7 7 PHE H H 8.766 0.00 . 42 7 7 PHE HA H 4.969 0.00 . 43 7 7 PHE HB2 H 2.766 0.01 . 44 7 7 PHE HB3 H 2.966 0.00 . 45 7 7 PHE HD1 H 7.206 0.00 . 46 7 7 PHE HD2 H 7.206 0.00 . 47 7 7 PHE N N 125.820 0.00 . 48 8 8 DPR HA H 4.579 0.00 . 49 8 8 DPR HB2 H 2.154 0.00 . 50 8 8 DPR HD2 H 3.382 0.00 . 51 8 8 DPR HD3 H 3.507 0.00 . 52 8 8 DPR HG2 H 1.803 0.00 . 53 9 9 PRO HA H 4.448 0.00 . 54 9 9 PRO HB2 H 2.175 0.00 . 55 9 9 PRO HB3 H 2.051 0.00 . 56 9 9 PRO HG2 H 1.862 0.00 . 57 9 9 PRO HG3 H 2.019 0.01 . 58 9 9 PRO HD2 H 3.630 0.00 . 59 9 9 PRO HD3 H 3.912 0.00 . 60 10 10 LYS H H 7.690 0.00 . 61 10 10 LYS HA H 4.456 0.00 . 62 10 10 LYS HB2 H 1.820 0.00 . 63 10 10 LYS HB3 H 1.820 0.00 . 64 10 10 LYS HG2 H 1.374 0.01 . 65 10 10 LYS HG3 H 1.374 0.01 . 66 10 10 LYS HD2 H 1.643 0.00 . 67 10 10 LYS HD3 H 1.643 0.00 . 68 10 10 LYS HE2 H 2.926 0.00 . 69 10 10 LYS HE3 H 2.926 0.00 . 70 10 10 LYS N N 120.825 0.00 . 71 11 11 ILE H H 8.154 0.00 . 72 11 11 ILE HA H 4.377 0.00 . 73 11 11 ILE HB H 1.578 0.00 . 74 11 11 ILE HG12 H 0.836 0.00 . 75 11 11 ILE HG13 H 1.332 0.00 . 76 11 11 ILE HG2 H 0.692 0.00 . 77 11 11 ILE HD1 H 0.404 0.00 . 78 11 11 ILE N N 122.793 0.00 . 79 12 12 ILE H H 8.599 0.00 . 80 12 12 ILE HA H 4.241 0.00 . 81 12 12 ILE HB H 1.575 0.00 . 82 12 12 ILE HG12 H 1.049 0.00 . 83 12 12 ILE HG13 H 1.223 0.00 . 84 12 12 ILE HG2 H 0.761 0.00 . 85 12 12 ILE HD1 H 0.647 0.00 . 86 12 12 ILE N N 126.555 0.00 . 87 13 13 PHE H H 8.564 0.00 . 88 13 13 PHE HA H 4.741 0.00 . 89 13 13 PHE HB2 H 2.873 0.00 . 90 13 13 PHE HB3 H 3.014 0.00 . 91 13 13 PHE HD1 H 7.095 0.00 . 92 13 13 PHE HD2 H 7.095 0.00 . 93 13 13 PHE HE1 H 7.194 0.00 . 94 13 13 PHE HE2 H 7.194 0.00 . 95 13 13 PHE N N 124.083 0.00 . 96 14 14 ASN H H 8.538 0.00 . 97 14 14 ASN HA H 4.679 0.00 . 98 14 14 ASN HB2 H 2.803 0.00 . 99 14 14 ASN HB3 H 2.864 0.00 . 100 14 14 ASN HD21 H 7.556 0.00 . 101 14 14 ASN HD22 H 6.763 0.00 . 102 14 14 ASN N N 120.360 0.00 . 103 15 15 GLU H H 8.487 0.00 . 104 15 15 GLU HA H 4.228 0.00 . 105 15 15 GLU HB2 H 1.968 0.00 . 106 15 15 GLU HB3 H 2.041 0.00 . 107 15 15 GLU HG2 H 2.227 0.00 . 108 15 15 GLU HG3 H 2.227 0.00 . 109 15 15 GLU N N 119.634 0.00 . 110 16 16 ARG H H 8.411 0.00 . 111 16 16 ARG HA H 4.169 0.00 . 112 16 16 ARG HB2 H 1.758 0.00 . 113 16 16 ARG HB3 H 1.841 0.00 . 114 16 16 ARG HG2 H 1.548 0.00 . 115 16 16 ARG HG3 H 1.604 0.00 . 116 16 16 ARG HD2 H 3.136 0.00 . 117 16 16 ARG HD3 H 3.136 0.00 . 118 16 16 ARG HE H 7.148 0.00 . 119 16 16 ARG N N 120.309 0.00 . stop_ save_