data_28059 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H-15N backbone Heteronuclear NOE values for free and ssDNA complex forms of Human YB1 cold shock domain. ; _BMRB_accession_number 28059 _BMRB_flat_file_name bmr28059.str _Entry_type original _Submission_date 2020-01-02 _Accession_date 2020-01-02 _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 Fan Jing-Song . . 2 Yang Daiwen . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count heteronucl_NOE 2 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-10-08 update BMRB 'update entry citation' 2020-01-17 original author 'original release' stop_ _Original_release_date 2020-01-03 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural basis of DNA binding to human YB-1 cold shock domain regulated by phosphorylation ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 32710623 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhang Jingfeng . . 2 Fan Jing-Song S. . 3 Li Shuangli . . 4 Yang Yunhuang . . 5 Sun Peng . . 6 Zhu Qinjun . . 7 Wang Jiannan . . 8 Jiang Bin . . 9 Yang Daiwen . . 10 Liu Maili . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 48 _Journal_issue 16 _Journal_ISSN 1362-4962 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9361 _Page_last 9371 _Year 2020 _Details . loop_ _Keyword 'DNA binding' 'cold shock domain' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'CSD and ssDNA complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label CSD $CSD ssDNA $ssDNA 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_CSD _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common CSD _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 117 _Mol_residue_sequence ; MHHHHHHGGGGGGGGSSAAP AGGDKKVIATKVLGTVKWFN VRNGYGFINRNDTKEDVFVH QTAIKKNNPRKYLRSVGDGE TVEFDVVEGEKGAEAANVTG PGGVPVQGSKYAADRNH ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 28 MET 2 29 HIS 3 30 HIS 4 31 HIS 5 32 HIS 6 33 HIS 7 34 HIS 8 35 GLY 9 36 GLY 10 37 GLY 11 38 GLY 12 39 GLY 13 40 GLY 14 41 GLY 15 42 GLY 16 43 SER 17 44 SER 18 45 ALA 19 46 ALA 20 47 PRO 21 48 ALA 22 49 GLY 23 50 GLY 24 51 ASP 25 52 LYS 26 53 LYS 27 54 VAL 28 55 ILE 29 56 ALA 30 57 THR 31 58 LYS 32 59 VAL 33 60 LEU 34 61 GLY 35 62 THR 36 63 VAL 37 64 LYS 38 65 TRP 39 66 PHE 40 67 ASN 41 68 VAL 42 69 ARG 43 70 ASN 44 71 GLY 45 72 TYR 46 73 GLY 47 74 PHE 48 75 ILE 49 76 ASN 50 77 ARG 51 78 ASN 52 79 ASP 53 80 THR 54 81 LYS 55 82 GLU 56 83 ASP 57 84 VAL 58 85 PHE 59 86 VAL 60 87 HIS 61 88 GLN 62 89 THR 63 90 ALA 64 91 ILE 65 92 LYS 66 93 LYS 67 94 ASN 68 95 ASN 69 96 PRO 70 97 ARG 71 98 LYS 72 99 TYR 73 100 LEU 74 101 ARG 75 102 SER 76 103 VAL 77 104 GLY 78 105 ASP 79 106 GLY 80 107 GLU 81 108 THR 82 109 VAL 83 110 GLU 84 111 PHE 85 112 ASP 86 113 VAL 87 114 VAL 88 115 GLU 89 116 GLY 90 117 GLU 91 118 LYS 92 119 GLY 93 120 ALA 94 121 GLU 95 122 ALA 96 123 ALA 97 124 ASN 98 125 VAL 99 126 THR 100 127 GLY 101 128 PRO 102 129 GLY 103 130 GLY 104 131 VAL 105 132 PRO 106 133 VAL 107 134 GLN 108 135 GLY 109 136 SER 110 137 LYS 111 138 TYR 112 139 ALA 113 140 ALA 114 141 ASP 115 142 ARG 116 143 ASN 117 144 HIS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_ssDNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common ssDNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 7 _Mol_residue_sequence ; AACACCT ; loop_ _Residue_seq_code _Residue_label 1 DA 2 DA 3 DC 4 DA 5 DC 6 DC 7 DT 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 $CSD Human 9606 Eukaryota Metazoa Homo sapiens 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 $CSD 'recombinant technology' . Escherichia coli . pet32a 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 $CSD 1 mM '[U-100% 15N]' 'phosphate buffer' 20 mM 'natural abundance' NaCl 50 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'ssDNA complex' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $CSD 1 mM '[U-100% 15N]' 'phosphate buffer' 20 mM 'natural abundance' NaCl 50 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-15N_heteronuckear_NOE_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N heteronuckear NOE' _Sample_label $sample_1 save_ save_1H-15N_heteronuckear_NOE_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N heteronuckear NOE' _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 0.1 mM pH 7.4 0.1 pH pressure 1 . atm temperature 298 0.1 K stop_ save_ save_heteronuclear_noe_list_1 _Saveframe_category heteronuclear_NOE _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '1H-15N heteronuckear NOE' stop_ loop_ _Sample_label . stop_ _Sample_conditions_label $sample_conditions_1 _Spectrometer_frequency_1H 600 _Mol_system_component_name CSD _Atom_one_atom_name N _Atom_two_atom_name H _Heteronuclear_NOE_value_type 'peak height' _NOE_reference_value 200000 _NOE_reference_description 'difference peaks have difference ref intensities in the ref spectrum.' _Text_data_format . _Text_data . loop_ _Residue_seq_code _Residue_label _Heteronuclear_NOE_value _Heteronuclear_NOE_value_error 27 VAL 0.606 0.006 28 ILE 0.734 0.005 29 ALA 0.746 0.005 30 THR 0.717 0.006 31 LYS 0.760 0.007 32 VAL 0.762 0.006 33 LEU 0.727 0.006 34 GLY 0.751 0.008 35 THR 0.755 0.008 36 VAL 0.768 0.008 37 LYS 0.766 0.011 38 TRP 0.765 0.007 39 PHE 0.737 0.007 40 ASN 0.735 0.009 42 ARG 0.646 0.007 43 ASN 0.727 0.007 44 GLY 0.747 0.007 45 TYR 0.794 0.005 46 GLY 0.773 0.007 47 PHE 0.797 0.008 48 ILE 0.760 0.009 49 ASN 0.773 0.005 50 ARG 0.763 0.007 51 ASN 0.770 0.007 52 ASP 0.764 0.004 53 THR 0.731 0.006 55 GLU 0.768 0.006 56 ASP 0.739 0.005 57 VAL 0.739 0.007 58 PHE 0.717 0.007 59 VAL 0.764 0.007 60 HIS 0.767 0.009 61 GLN 0.772 0.004 62 THR 0.779 0.013 63 ALA 0.698 0.004 64 ILE 0.785 0.006 65 LYS 0.759 0.016 70 ARG 0.726 0.008 71 LYS 0.703 0.022 73 LEU 0.648 0.015 74 ARG 0.673 0.006 75 SER 0.751 0.014 77 GLY 0.758 0.043 78 ASP 0.711 0.004 79 GLY 0.765 0.008 80 GLU 0.758 0.006 81 THR 0.755 0.007 82 VAL 0.775 0.009 83 GLU 0.801 0.009 84 PHE 0.780 0.007 85 ASP 0.770 0.004 86 VAL 0.756 0.008 87 VAL 0.785 0.009 88 GLU 0.713 0.006 89 GLY 0.490 0.006 90 GLU 0.497 0.022 91 LYS 0.443 0.009 92 GLY 0.473 0.005 93 ALA 0.648 0.004 94 GLU 0.731 0.008 95 ALA 0.793 0.006 96 ALA 0.771 0.007 97 ASN 0.758 0.006 98 VAL 0.775 0.006 99 THR 0.790 0.009 100 GLY 0.762 0.012 102 GLY 0.765 0.007 103 GLY 0.766 0.007 104 VAL 0.728 0.014 106 VAL 0.728 0.016 107 GLN 0.720 0.062 108 GLY 0.734 0.018 109 SER 0.755 0.017 111 TYR 0.535 0.020 stop_ save_ save_heteronuclear_noe_list_2 _Saveframe_category heteronuclear_NOE _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '1H-15N heteronuckear NOE' stop_ loop_ _Sample_label . stop_ _Sample_conditions_label $sample_conditions_1 _Spectrometer_frequency_1H 700 _Mol_system_component_name CSD _Atom_one_atom_name N _Atom_two_atom_name H _Heteronuclear_NOE_value_type 'peak height' _NOE_reference_value 200000 _NOE_reference_description 'same as list_1' _Text_data_format . _Text_data . loop_ _Residue_seq_code _Residue_label _Heteronuclear_NOE_value _Heteronuclear_NOE_value_error 27 VAL 0.767 0.003 28 ILE 0.769 0.006 29 ALA 0.824 0.003 30 THR 0.795 0.003 31 LYS 0.837 0.003 32 VAL 0.843 0.003 33 LEU 0.828 0.003 34 GLY 0.863 0.003 35 THR 0.858 0.003 36 VAL 0.866 0.003 37 LYS 0.810 0.005 38 TRP 0.814 0.003 39 PHE 0.805 0.003 40 ASN 0.834 0.004 41 VAL 0.826 0.004 42 ARG 0.796 0.003 43 ASN 0.806 0.003 44 GLY 0.819 0.003 45 TYR 0.875 0.003 46 GLY 0.894 0.004 47 PHE 0.830 0.003 48 ILE 0.854 0.004 49 ASN 0.826 0.004 50 ARG 0.789 0.004 51 ASN 0.806 0.003 52 ASP 0.833 0.001 53 THR 0.799 0.003 54 LYS 0.867 0.003 55 GLU 0.842 0.003 56 ASP 0.781 0.003 57 VAL 0.841 0.004 58 PHE 0.829 0.003 59 VAL 0.847 0.003 60 HIS 0.814 0.005 61 GLN 0.833 0.004 62 THR 0.819 0.003 63 ALA 0.855 0.003 64 ILE 0.802 0.003 65 LYS 0.810 0.005 66 LYS 0.803 0.004 67 ASN 0.775 0.012 68 ASN 0.819 0.005 70 ARG 0.782 0.003 71 LYS 0.763 0.007 72 TYR 0.778 0.007 73 LEU 0.810 0.005 75 SER 0.830 0.003 76 VAL 0.867 0.003 77 GLY 0.864 0.004 78 ASP 0.775 0.002 79 GLY 0.791 0.004 80 GLU 0.866 0.002 81 THR 0.812 0.003 82 VAL 0.821 0.003 83 GLU 0.799 0.004 84 PHE 0.833 0.003 85 ASP 0.833 0.001 86 VAL 0.827 0.003 87 VAL 0.783 0.005 88 GLU 0.783 0.004 89 GLY 0.625 0.003 90 GLU 0.631 0.008 91 LYS 0.588 0.005 92 GLY 0.676 0.002 93 ALA 0.759 0.003 94 GLU 0.739 0.005 95 ALA 0.782 0.003 96 ALA 0.795 0.004 97 ASN 0.835 0.004 98 VAL 0.855 0.003 99 THR 0.844 0.005 100 GLY 0.801 0.004 102 GLY 0.854 0.004 103 GLY 0.816 0.003 104 VAL 0.761 0.002 106 VAL 0.869 0.003 107 GLN 0.821 0.004 108 GLY 0.807 0.004 109 SER 0.841 0.005 110 LYS 0.807 0.024 111 TYR 0.782 0.004 112 ALA 0.783 0.003 113 ALA 0.774 0.005 stop_ save_