data_6653 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of a Zap1 Zinc-Responsive Domain Provides Insights into Metalloregulatory Transcriptional Repression in Saccharomyces cerevisiae ; _BMRB_accession_number 6653 _BMRB_flat_file_name bmr6653.str _Entry_type original _Submission_date 2005-06-03 _Accession_date 2005-06-03 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Single zinc finger (zzf1L) of zzf1-2 used for comparative study.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wang Zhonghua . . 2 Feng Linda S. . 3 Venkataraman Krishna . . 4 Matskevich Viktor A. . 5 Parasuram Priya . . 6 Laity John H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 26 "13C chemical shifts" 89 "15N chemical shifts" 26 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2006-04-24 original author . stop_ _Original_release_date 2006-04-24 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Structure of a Zap1 Zinc-responsive Domain Provides Insights into Metalloregulatory Transcriptional Repression in Saccharomyces cerevisiae. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16483601 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wang Zhonghua . . 2 Feng Linda S. . 3 Matskevich Viktor A. . 4 Venkataraman Krishna . . 5 Parasuram Priya . . 6 Laity John H. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 357 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1167 _Page_last 1183 _Year 2006 _Details . save_ ####################################### # Cited references within the entry # ####################################### save_Reference_1 _Saveframe_category citation _Citation_full . _Citation_title ; Zap1p, a metalloregulatory protein involved in zinc-responsive transcriptional regulation in Saccharomyces cerevisiae. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhao Hui . . 2 Eide David J . stop_ _Journal_abbreviation 'Mol. Cell' _Journal_name_full . _Journal_volume 17 _Journal_issue 9 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 5044 _Page_last 5052 _Year 1997 _Details . save_ save_Reference_2 _Saveframe_category citation _Citation_full . _Citation_title ; Zinc fingers can act as Zn(II) sensors to regulate transcriptional activation domain function ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 14517251 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bird Amanda J. . 2 McCall McCall . . 3 Kramer Michelle . . 4 Blankman Elizabeth . . 5 Winge Dennis R. . 6 Eide David J. . stop_ _Journal_abbreviation 'EMBO J.' _Journal_name_full . _Journal_volume 22 _Journal_issue 19 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 5137 _Page_last 5146 _Year 2003 _Details . save_ save_Reference_3 _Saveframe_category citation _Citation_full . _Citation_title 'NMRView: A computer program for the visualization and analysis of NMR Data' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Johnson B. A. . 2 Blevins R. A. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full . _Journal_volume 6 _Journal_issue . _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 603 _Page_last 614 _Year 1994 _Details . save_ save_Reference_4 _Saveframe_category citation _Citation_full . _Citation_title 'NMRPipe: a multidimensional spectral processing system based on UNIX pipes' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8520220 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Delaglio F. . . 2 Grzesiek S. . . 3 Vuister G. W. . 4 Zhu G. . . 5 Pfeifer J. . . 6 Bax A. . . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full . _Journal_volume 6 _Journal_issue 3 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 277 _Page_last 293 _Year 1995 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name zzf1L _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label '38 amino acid polypeptide' $Zap1_zinc_finger_1_and_linker Zinc $ZN stop_ _System_molecular_weight 4456 _System_physical_state native _System_oligomer_state 'protein-ligand system' _System_paramagnetic no _System_thiol_state 'free and other bound' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component diamagnetic Zinc stop_ loop_ _Biological_function 'Transcription factor' 'metalloregulatory protein' stop_ _Database_query_date . _Details 'finger 1 and linker of zap1 protein' save_ ######################## # Monomeric polymers # ######################## save_Zap1_zinc_finger_1_and_linker _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common zzf1L _Molecular_mass . _Mol_thiol_state 'free and other bound' loop_ _Biological_function 'Transcription factor' 'metalloregulatory protein' stop_ _Details 'One Cys2His2 zinc finger with a linker' ############################## # Polymer residue sequence # ############################## _Residue_count 38 _Mol_residue_sequence ; DLKCKWKECPESCSSLFDLQ RHLLKDHVSQDFKHPMEP ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 2 ASP 2 3 LEU 3 4 LYS 4 5 CYS 5 6 LYS 6 7 TRP 7 8 LYS 8 9 GLU 9 10 CYS 10 11 PRO 11 12 GLU 12 13 SER 13 14 CYS 14 15 SER 15 16 SER 16 17 LEU 17 18 PHE 18 19 ASP 19 20 LEU 20 21 GLN 21 22 ARG 22 23 HIS 23 24 LEU 24 25 LEU 25 26 LYS 26 27 ASP 27 28 HIS 28 29 VAL 29 30 SER 30 31 GLN 31 32 ASP 32 33 PHE 33 34 LYS 34 35 HIS 35 36 PRO 36 37 MET 37 38 GLU 38 39 PRO stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type non-polymer _Name_common "ZN (ZINC ION)" _BMRB_code . _PDB_code ZN _Molecular_mass 65.409 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Aug 8 10:36:42 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons ZN ZN ZN . 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 $Zap1_zinc_finger_1_and_linker yeast 4932 Eukaryota Fungi Saccharomyces cerevisiae 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_type _Vector_name _Vendor_name $Zap1_zinc_finger_1_and_linker 'recombinant technology' 'E. coli' Escherichia coli BL21 DE3 plasmid p21a-zzf1L Novagen stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'zzf1L, Zn(II), MES, DSS, NaN2,THP' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Zap1_zinc_finger_1_and_linker 0.8 mM '[U-13C; U-15N]' $ZN 0.9 mM . MES 20 mM . 'Tri(2-carboxyethyl)-phosphine hydrochloride' 0.5 mM . DSS 0.2 mM . NaN2 1 mM . stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NMRView _Version 5.0.4 loop_ _Task 'Data analysis' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name NMRPipe _Version 97.027.12.56 loop_ _Task 'Raw spectral data processing' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_14.1_T_Varian_Inova_600Mhz _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Inova _Field_strength 600 _Details 'triple resonance {1H,15N,13C} probe' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N_HSQC' _Sample_label $sample_1 save_ save_3D_HNCACB_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_3D_CBCA(CO)NH_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _Sample_label $sample_1 save_ save_3D_HNCO_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC _Saveframe_category NMR_applied_experiment _Experiment_name 2D_1H-15N_HSQC _BMRB_pulse_sequence_accession_number . _Details BioPack save_ save_3D_HNCACB _Saveframe_category NMR_applied_experiment _Experiment_name 3D_HNCACB _BMRB_pulse_sequence_accession_number . _Details BioPack save_ save_3D_CBCA(CO)NH _Saveframe_category NMR_applied_experiment _Experiment_name 3D_CBCA(CO)NH _BMRB_pulse_sequence_accession_number . _Details BioPack save_ save_3D_HNCO _Saveframe_category NMR_applied_experiment _Experiment_name 3D_HNCO _BMRB_pulse_sequence_accession_number . _Details BioPack save_ ####################### # Sample conditions # ####################### save_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.9 0.03 pH temperature 293 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_referencing _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 0.0 internal direct . . . 1.0 DSS C 13 'methyl protons' ppm 0.0 . indirect . . . 0.251449530 DSS N 15 'methyl protons' ppm 0.0 . 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_1 stop_ loop_ _Experiment_label '2D 1H-15N_HSQC' '3D HNCACB' '3D CBCA(CO)NH' '3D HNCO' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $conditions_1 _Chem_shift_reference_set_label $chemical_shift_referencing _Mol_system_component_name '38 amino acid 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 2 1 ASP C C 175.1 0.080 1 2 2 1 ASP CA C 54.451 0.310 1 3 2 1 ASP CB C 41.792 0.310 1 4 3 2 LEU H H 8.793 0.015 1 5 3 2 LEU C C 175.367 0.080 1 6 3 2 LEU CA C 54.249 0.310 1 7 3 2 LEU CB C 42.602 0.310 1 8 3 2 LEU N N 123.703 0.140 1 9 4 3 LYS H H 8.239 0.015 1 10 4 3 LYS C C 175.569 0.080 1 11 4 3 LYS CA C 55.160 0.310 1 12 4 3 LYS CB C 33.336 0.310 1 13 4 3 LYS N N 123.701 0.140 1 14 5 4 CYS H H 8.051 0.015 1 15 5 4 CYS CA C 61.945 0.310 1 16 5 4 CYS CB C 30.348 0.310 1 17 5 4 CYS N N 126.953 0.140 1 18 9 8 GLU C C 175.334 0.080 1 19 9 8 GLU CA C 56.882 0.310 1 20 9 8 GLU CB C 28.222 0.310 1 21 10 9 CYS H H 8.186 0.015 1 22 10 9 CYS CA C 57.894 0.310 1 23 10 9 CYS CB C 31.766 0.310 1 24 10 9 CYS N N 124.974 0.140 1 25 11 10 PRO C C 177.279 0.080 1 26 11 10 PRO CA C 63.565 0.310 1 27 11 10 PRO CB C 32.981 0.310 1 28 12 11 GLU H H 8.947 0.015 1 29 12 11 GLU C C 176.642 0.080 1 30 12 11 GLU CA C 58.553 0.310 1 31 12 11 GLU CB C 31.108 0.310 1 32 12 11 GLU N N 124.125 0.140 1 33 13 12 SER H H 8.637 0.015 1 34 13 12 SER C C 173.455 0.080 1 35 13 12 SER CA C 58.198 0.310 1 36 13 12 SER CB C 65.691 0.310 1 37 13 12 SER N N 118.894 0.140 1 38 14 13 CYS H H 8.815 0.015 1 39 14 13 CYS C C 174.764 0.080 1 40 14 13 CYS CA C 58.350 0.310 1 41 14 13 CYS CB C 33.083 0.310 1 42 14 13 CYS N N 120.732 0.140 1 43 15 14 SER H H 9.482 0.015 1 44 15 14 SER C C 173.824 0.080 1 45 15 14 SER CA C 59.818 0.310 1 46 15 14 SER CB C 64.577 0.310 1 47 15 14 SER N N 115.924 0.140 1 48 16 15 SER H H 7.506 0.015 1 49 16 15 SER C C 174.093 0.080 1 50 16 15 SER CA C 57.034 0.310 1 51 16 15 SER CB C 66.805 0.310 1 52 16 15 SER N N 111.965 0.140 1 53 17 16 LEU H H 9.171 0.015 1 54 17 16 LEU C C 178.588 0.080 1 55 17 16 LEU CA C 58.553 0.310 1 56 17 16 LEU CB C 41.690 0.310 1 57 17 16 LEU N N 124.125 0.140 1 58 18 17 PHE H H 8.392 0.015 1 59 18 17 PHE C C 177.883 0.080 1 60 18 17 PHE CA C 61.236 0.310 1 61 18 17 PHE CB C 39.412 0.310 1 62 18 17 PHE N N 119.742 0.140 1 63 19 18 ASP H H 8.091 0.015 1 64 19 18 ASP C C 178.655 0.080 1 65 19 18 ASP CA C 57.693 0.310 1 66 19 18 ASP CB C 41.488 0.310 1 67 19 18 ASP N N 119.601 0.140 1 68 20 19 LEU H H 8.223 0.015 1 69 20 19 LEU C C 178.118 0.080 1 70 20 19 LEU CA C 58.705 0.310 1 71 20 19 LEU CB C 41.994 0.310 1 72 20 19 LEU N N 122.853 0.140 1 73 21 20 GLN H H 8.482 0.015 1 74 21 20 GLN C C 177.246 0.080 1 75 21 20 GLN CA C 60.629 0.310 1 76 21 20 GLN CB C 28.323 0.310 1 77 21 20 GLN N N 118.611 0.140 1 78 22 21 ARG H H 7.867 0.015 1 79 22 21 ARG C C 178.152 0.080 1 80 22 21 ARG CA C 59.616 0.310 1 81 22 21 ARG CB C 30.045 0.310 1 82 22 21 ARG N N 118.045 0.140 1 83 23 22 HIS H H 8.375 0.015 1 84 23 22 HIS C C 176.810 0.080 1 85 23 22 HIS CA C 58.958 0.310 1 86 23 22 HIS CB C 29.083 0.310 1 87 23 22 HIS N N 119.318 0.140 1 88 24 23 LEU H H 8.650 0.015 1 89 24 23 LEU C C 178.722 0.080 1 90 24 23 LEU CA C 58.958 0.310 1 91 24 23 LEU CB C 42.602 0.310 1 92 24 23 LEU N N 119.176 0.140 1 93 25 24 LEU H H 7.715 0.015 1 94 25 24 LEU C C 177.850 0.080 1 95 25 24 LEU CA C 57.895 0.310 1 96 25 24 LEU CB C 41.944 0.310 1 97 25 24 LEU N N 116.914 0.140 1 98 26 25 LYS H H 8.287 0.015 1 99 26 25 LYS C C 177.715 0.080 1 100 26 25 LYS CA C 58.300 0.310 1 101 26 25 LYS CB C 33.640 0.310 1 102 26 25 LYS N N 117.762 0.140 1 103 27 26 ASP H H 8.074 0.015 1 104 27 26 ASP CA C 55.869 0.310 1 105 27 26 ASP CB C 40.779 0.310 1 106 27 26 ASP N N 114.793 0.140 1 107 31 30 GLN C C 176.072 0.080 1 108 31 30 GLN CA C 56.375 0.310 1 109 31 30 GLN CB C 29.842 0.310 1 110 32 31 ASP H H 8.299 0.015 1 111 32 31 ASP C C 176.072 0.080 1 112 32 31 ASP CA C 55.261 0.310 1 113 32 31 ASP CB C 41.387 0.310 1 114 32 31 ASP N N 120.025 0.140 1 115 33 32 PHE H H 7.937 0.015 1 116 33 32 PHE C C 175.200 0.080 1 117 33 32 PHE CA C 57.743 0.310 1 118 33 32 PHE CB C 39.614 0.310 1 119 33 32 PHE N N 119.569 0.140 1 120 34 33 LYS H H 7.948 0.015 1 121 34 33 LYS C C 175.770 0.080 1 122 34 33 LYS CA C 56.426 0.310 1 123 34 33 LYS CB C 33.285 0.310 1 124 34 33 LYS N N 122.004 0.140 1 125 35 34 HIS H H 8.402 0.015 1 126 35 34 HIS CA C 54.654 0.310 1 127 35 34 HIS CB C 30.551 0.310 1 128 35 34 HIS N N 122.004 0.140 1 129 36 35 PRO C C 176.877 0.080 1 130 36 35 PRO CA C 63.650 0.310 1 131 36 35 PRO CB C 32.500 0.310 1 132 37 36 MET H H 8.781 0.015 1 133 37 36 MET C C 174.764 0.080 1 134 37 36 MET CA C 55.603 0.310 1 135 37 36 MET CB C 33.187 0.310 1 136 37 36 MET N N 120.314 0.140 1 137 38 37 GLU H H 7.928 0.015 1 138 38 37 GLU C C 175.133 0.080 1 139 38 37 GLU CA C 54.046 0.310 1 140 38 37 GLU CB C 32.272 0.310 1 141 38 37 GLU N N 121.015 0.140 1 stop_ save_