data_25440 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H and 113Cd chemical shift assignments for the cysteins and metals of Bud31p Cd3 ; _BMRB_accession_number 25440 _BMRB_flat_file_name bmr25440.str _Entry_type original _Submission_date 2015-01-19 _Accession_date 2015-01-19 _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 'van Roon' Anne-Marie M. . 2 Yang Ji-Chun . . 3 Mathieu Daniel . . 4 Bermel Wolfgang . . 5 Nagai Kiyoshi . . 6 Neuhaus David . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 8 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 49 "113CD chemical shifts" 6 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-10-07 update author 'update entry title' 2016-02-18 update BMRB 'update entry citation' 2015-03-09 original author 'original release' stop_ _Original_release_date 2016-02-18 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; 113 Cd NMR Experiments Reveal an Unusual Metal Cluster in the Solution Structure of the Yeast Splicing Protein Bud31p ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25703931 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 'van Roon' Anne-Marie M. . 2 Yang Ji-Chun . . 3 Mathieu Daniel . . 4 Bermel Wolfgang . . 5 Nagai Kiyoshi . . 6 Neuhaus David . . stop_ _Journal_abbreviation 'Angew. Chem. Int. Ed. Engl.' _Journal_volume 54 _Journal_issue 16 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4861 _Page_last 4864 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Bud31p protein' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Bud31p polypeptide' $Bud31p_polypeptide 'Cadmium 1' $entity_CD 'Cadmium 2' $entity_CD 'Cadmium 3' $entity_CD 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_Bud31p_polypeptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Bud31p_polypeptide _Molecular_mass 18554.609 _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 159 _Mol_residue_sequence ; GGSPRIKTRRSKPAPDGFEK IKPTLTDFEIQLRDAQKDKS SKLAAKSNEQLWEIMQLHHQ RSRYIYTLYYKRKAISKDLY DWLIKEKYADKLLIAKWRKT GYEKLCCLRCIQKNETNNGS TCICRVPRAQLEEEARKKGT QVSFHQCVHCGCRGCASTD ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -1 GLY 2 0 GLY 3 1 SER 4 2 PRO 5 3 ARG 6 4 ILE 7 5 LYS 8 6 THR 9 7 ARG 10 8 ARG 11 9 SER 12 10 LYS 13 11 PRO 14 12 ALA 15 13 PRO 16 14 ASP 17 15 GLY 18 16 PHE 19 17 GLU 20 18 LYS 21 19 ILE 22 20 LYS 23 21 PRO 24 22 THR 25 23 LEU 26 24 THR 27 25 ASP 28 26 PHE 29 27 GLU 30 28 ILE 31 29 GLN 32 30 LEU 33 31 ARG 34 32 ASP 35 33 ALA 36 34 GLN 37 35 LYS 38 36 ASP 39 37 LYS 40 38 SER 41 39 SER 42 40 LYS 43 41 LEU 44 42 ALA 45 43 ALA 46 44 LYS 47 45 SER 48 46 ASN 49 47 GLU 50 48 GLN 51 49 LEU 52 50 TRP 53 51 GLU 54 52 ILE 55 53 MET 56 54 GLN 57 55 LEU 58 56 HIS 59 57 HIS 60 58 GLN 61 59 ARG 62 60 SER 63 61 ARG 64 62 TYR 65 63 ILE 66 64 TYR 67 65 THR 68 66 LEU 69 67 TYR 70 68 TYR 71 69 LYS 72 70 ARG 73 71 LYS 74 72 ALA 75 73 ILE 76 74 SER 77 75 LYS 78 76 ASP 79 77 LEU 80 78 TYR 81 79 ASP 82 80 TRP 83 81 LEU 84 82 ILE 85 83 LYS 86 84 GLU 87 85 LYS 88 86 TYR 89 87 ALA 90 88 ASP 91 89 LYS 92 90 LEU 93 91 LEU 94 92 ILE 95 93 ALA 96 94 LYS 97 95 TRP 98 96 ARG 99 97 LYS 100 98 THR 101 99 GLY 102 100 TYR 103 101 GLU 104 102 LYS 105 103 LEU 106 104 CYS 107 105 CYS 108 106 LEU 109 107 ARG 110 108 CYS 111 109 ILE 112 110 GLN 113 111 LYS 114 112 ASN 115 113 GLU 116 114 THR 117 115 ASN 118 116 ASN 119 117 GLY 120 118 SER 121 119 THR 122 120 CYS 123 121 ILE 124 122 CYS 125 123 ARG 126 124 VAL 127 125 PRO 128 126 ARG 129 127 ALA 130 128 GLN 131 129 LEU 132 130 GLU 133 131 GLU 134 132 GLU 135 133 ALA 136 134 ARG 137 135 LYS 138 136 LYS 139 137 GLY 140 138 THR 141 139 GLN 142 140 VAL 143 141 SER 144 142 PHE 145 143 HIS 146 144 GLN 147 145 CYS 148 146 VAL 149 147 HIS 150 148 CYS 151 149 GLY 152 150 CYS 153 151 ARG 154 152 GLY 155 153 CYS 156 154 ALA 157 155 SER 158 156 THR 159 157 ASP stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_CD _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 'CADMIUM ION' _BMRB_code CD _PDB_code CD _Molecular_mass 112.411 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CD CD CD . 2 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Gene_mnemonic $Bud31p_polypeptide "Baker's yeast" 4932 Eukaryota Fungi Saccharomyces cerevisiae BUD31 stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Variant _Vector_name _Details $Bud31p_polypeptide 'recombinant technology' . Escherichia coli BL21(DE3) 'RIL CodonPlus' pRK172 ; Protein Was Expressed As an N Terminal Glutathione S Transferase Fusion Protein ; 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 $Bud31p_polypeptide 2.6 mM 'natural abundance' 'sodium phosphate' 20 mM 'natural abundance' 'sodium chloride' 150 mM 'natural abundance' DTT 5 mM [U-2H] D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 3.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.115 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance AVIII' _Field_strength 850 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance AVIII' _Field_strength 500 _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_113Cd-113Cd_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 113Cd-113Cd COSY' _Sample_label $sample_1 save_ save_2D_113Cd-1H_HSQC_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 113Cd-1H HSQC NOESY' _Sample_label $sample_1 save_ save_2D_113Cd-1H_HMQC-RELAY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 113Cd-1H HMQC-RELAY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_(natural_abundance)_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic (natural abundance)' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_(natural_abundance)_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic (natural abundance)' _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' 0.27 . M pH 6.5 . pH pressure 1 . atm temperature 298 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.27 . M pH 6.5 . pH pressure 1 . atm temperature 308 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details '113Cd chemical shifts' 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 _Reference_correction_type TSP Cd 113 'methyl protons' ppm 0 external indirect . 'separate tube (no insert) similar to the experimental sample tube' . 0.222819519 . TSP H 1 'methyl protons' ppm 0 external direct . 'separate tube (no insert) similar to the experimental sample tube' . 1.0 none 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 TOCSY' '2D 1H-1H NOESY' '2D 113Cd-113Cd COSY' '2D 113Cd-1H HSQC NOESY' '2D 1H-13C HSQC aliphatic (natural abundance)' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Bud31p polypeptide' _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 1 104 106 CYS HA H 4.483 0.020 1 2 104 106 CYS HB2 H 3.337 0.020 1 3 104 106 CYS HB3 H 3.134 0.020 1 4 105 107 CYS HA H 4.795 0.020 1 5 105 107 CYS HB2 H 2.765 0.020 2 6 105 107 CYS HB3 H 2.861 0.020 2 7 108 110 CYS HA H 4.139 0.020 1 8 108 110 CYS HB2 H 3.086 0.020 1 9 108 110 CYS HB3 H 2.651 0.020 1 10 120 122 CYS HA H 4.190 0.020 1 11 120 122 CYS HB2 H 3.310 0.020 1 12 120 122 CYS HB3 H 3.170 0.020 1 13 122 124 CYS HA H 4.207 0.020 1 14 122 124 CYS HB2 H 3.707 0.020 1 15 122 124 CYS HB3 H 2.982 0.020 1 16 145 147 CYS HA H 4.936 0.020 1 17 145 147 CYS HB2 H 3.478 0.020 1 18 145 147 CYS HB3 H 3.084 0.020 1 19 148 150 CYS HA H 4.797 0.020 1 20 148 150 CYS HB2 H 3.236 0.020 1 21 148 150 CYS HB3 H 2.638 0.020 1 22 150 152 CYS HA H 3.897 0.020 1 23 150 152 CYS HB2 H 3.403 0.020 1 24 150 152 CYS HB3 H 3.167 0.020 1 25 153 155 CYS HA H 4.880 0.020 1 26 153 155 CYS HB2 H 3.506 0.020 1 27 153 155 CYS HB3 H 2.338 0.020 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 113Cd-113Cd COSY' '2D 113Cd-1H HSQC NOESY' '2D 1H-13C HSQC aliphatic (natural abundance)' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Cadmium 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 1000 1 CD CD CD 33.826 0.100 1 stop_ save_ save_assigned_chem_shift_list_1_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 113Cd-113Cd COSY' '2D 113Cd-1H HSQC NOESY' '2D 1H-13C HSQC aliphatic (natural abundance)' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Cadmium 2' _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 1001 1 CD CD CD 41.727 0.100 1 stop_ save_ save_assigned_chem_shift_list_1_4 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 113Cd-113Cd COSY' '2D 113Cd-1H HSQC NOESY' '2D 1H-13C HSQC aliphatic (natural abundance)' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Cadmium 3' _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 1002 1 CD CD CD 58.415 0.100 1 stop_ save_ save_assigned_chem_shift_list_2_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 113Cd-1H HMQC-RELAY' '2D 1H-13C HSQC aliphatic (natural abundance)' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Bud31p polypeptide' _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 1 104 106 CYS HB2 H 3.340 0.020 1 2 104 106 CYS HB3 H 3.148 0.020 1 3 105 107 CYS HB2 H 2.745 0.020 2 4 108 110 CYS HA H 4.136 0.020 1 5 108 110 CYS HB2 H 3.083 0.020 1 6 108 110 CYS HB3 H 2.646 0.020 1 7 120 122 CYS HB2 H 3.298 0.020 1 8 120 122 CYS HB3 H 3.185 0.020 1 9 122 124 CYS HA H 4.202 0.020 1 10 122 124 CYS HB2 H 3.715 0.020 1 11 122 124 CYS HB3 H 2.977 0.020 1 12 145 147 CYS HA H 4.927 0.020 1 13 145 147 CYS HB2 H 3.477 0.020 1 14 145 147 CYS HB3 H 3.093 0.020 1 15 148 150 CYS HA H 4.781 0.020 1 16 148 150 CYS HB2 H 3.232 0.020 1 17 148 150 CYS HB3 H 2.626 0.020 1 18 150 152 CYS HA H 3.877 0.020 1 19 150 152 CYS HB2 H 3.418 0.020 1 20 153 155 CYS HA H 4.874 0.020 1 21 153 155 CYS HB2 H 3.503 0.020 1 22 153 155 CYS HB3 H 2.338 0.020 1 stop_ save_ save_assigned_chem_shift_list_2_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 113Cd-1H HMQC-RELAY' '2D 1H-13C HSQC aliphatic (natural abundance)' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Cadmium 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 1000 1 CD CD CD 33.517 0.100 1 stop_ save_ save_assigned_chem_shift_list_2_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 113Cd-1H HMQC-RELAY' '2D 1H-13C HSQC aliphatic (natural abundance)' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Cadmium 2' _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 1001 1 CD CD CD 39.143 0.100 1 stop_ save_ save_assigned_chem_shift_list_2_4 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 113Cd-1H HMQC-RELAY' '2D 1H-13C HSQC aliphatic (natural abundance)' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Cadmium 3' _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 1002 1 CD CD CD 56.389 0.100 1 stop_ save_