data_15499 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of human NEMO zinc finger ; _BMRB_accession_number 15499 _BMRB_flat_file_name bmr15499.str _Entry_type new _Submission_date 2007-09-28 _Accession_date 2007-09-28 _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 Cordier Florence . . 2 Vinolo Emilie . . 3 Veron Michel . . 4 Delepierre Muriel . . 5 Agou Fabrice . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 156 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-03 update BMRB 'complete entry citation' 2008-03-13 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 15500 'mutant zinc fingers of the NEMO protein' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution Structure of NEMO Zinc Finger and Impact of an Anhidrotic Ectodermal Dysplasia with Immunodeficiency-related Point Mutation' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18313693 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Cordier Florence . . 2 Vinolo Emilie . . 3 Veron Michel . . 4 Delepierre Muriel . . 5 Agou Fabrice . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 377 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1419 _Page_last 1432 _Year 2008 _Details . loop_ _Keyword NF-kappaB NEMO 'zinc finger' EDA-ID NMR stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name ZF:ZN _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'ZINC ION' $ZN 'NEMO ZF' $NEMO_ZF stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details 'zinc-bound form of NEMO ZF' save_ ######################## # Monomeric polymers # ######################## save_NEMO_ZF _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common NEMO_ZF _Molecular_mass . _Mol_thiol_state 'free and other bound' loop_ _Biological_function 'NEMO is a regulatory protein of the NF-kappaB signaling pathway' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; SSDFCCPKCQYQAPDMDTLQ IHVMECIE ; loop_ _Residue_seq_code _Residue_label 1 SER 2 SER 3 ASP 4 PHE 5 CYS 6 CYS 7 PRO 8 LYS 9 CYS 10 GLN 11 TYR 12 GLN 13 ALA 14 PRO 15 ASP 16 MET 17 ASP 18 THR 19 LEU 20 GLN 21 ILE 22 HIS 23 VAL 24 MET 25 GLU 26 CYS 27 ILE 28 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value UNP Q9Y6K9 NEMO_HUMAN . . . . . stop_ 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 Tue Aug 21 03:50:37 2007 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons ZN ZN ZN N 2 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single coordination 'NEMO ZF' 6 CYS SG 'ZINC ION' . . ZN single coordination 'NEMO ZF' 9 CYS SG 'ZINC ION' . . ZN single coordination 'NEMO ZF' 22 HIS NE2 'ZINC ION' . . ZN single coordination 'NEMO ZF' 26 CYS SG 'ZINC ION' . . ZN stop_ loop_ _Deleted_atom_mol_system_component_name _Deleted_atom_residue_seq_code _Deleted_atom_residue_label _Deleted_atom_name 'ZINC ION' 6 CYS HG 'ZINC ION' 9 CYS HG 'ZINC ION' 22 HIS HE2 'ZINC ION' 26 CYS HG stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $NEMO_ZF 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 _Details $NEMO_ZF 'chemical synthesis' . . . . . 'synthetic peptide termini-blocked by N-acetyl and C-amide groups, purchased from a company' 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 $NEMO_ZF 1 mM 'natural abundance' $ZN 2 mM 'natural abundance' TCEP 2 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1C loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 2.2 loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version 5.03 loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'data analysis' 'peak picking' 'chemical shift assignment' stop_ _Details . save_ save_ARIA _Saveframe_category software _Name ARIA _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Linge, O'Donoghue and Nilges' . . stop_ loop_ _Task 'structure solution' refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details 'Spectrometer equipped with a cryoprobe' 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_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_purged-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D purged-COSY' _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 298 . K pH 7.3 . pH pressure 1 . atm 'ionic strength' 0 . M 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D purged-COSY' 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 'NEMO ZF' _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 SER H H 8.130 0.005 1 2 1 1 SER HA H 4.397 0.005 1 3 1 1 SER HB2 H 3.718 0.005 2 4 1 1 SER HB3 H 3.791 0.005 2 5 2 2 SER H H 8.370 0.005 1 6 2 2 SER HA H 4.300 0.005 1 7 2 2 SER HB2 H 3.627 0.005 2 8 2 2 SER HB3 H 3.762 0.005 2 9 3 3 ASP H H 7.946 0.005 1 10 3 3 ASP HA H 4.264 0.005 1 11 3 3 ASP HB2 H 1.958 0.005 2 12 3 3 ASP HB3 H 2.134 0.005 2 13 4 4 PHE H H 8.167 0.005 1 14 4 4 PHE HA H 4.643 0.005 1 15 4 4 PHE HB2 H 2.967 0.005 2 16 4 4 PHE HB3 H 2.967 0.005 2 17 4 4 PHE HD1 H 6.980 0.005 3 18 4 4 PHE HD2 H 6.980 0.005 3 19 4 4 PHE HE1 H 7.263 0.005 3 20 4 4 PHE HE2 H 7.263 0.005 3 21 5 5 CYS H H 7.840 0.005 1 22 5 5 CYS HA H 5.148 0.005 1 23 5 5 CYS HB2 H 2.563 0.005 2 24 5 5 CYS HB3 H 2.616 0.005 2 25 6 6 CYS H H 9.209 0.005 1 26 6 6 CYS HA H 4.512 0.005 1 27 6 6 CYS HB2 H 2.717 0.005 2 28 6 6 CYS HB3 H 3.270 0.005 2 29 7 7 PRO HA H 4.478 0.005 1 30 7 7 PRO HB2 H 2.112 0.005 2 31 7 7 PRO HB3 H 2.363 0.005 2 32 7 7 PRO HD2 H 4.070 0.005 2 33 7 7 PRO HD3 H 4.209 0.005 2 34 7 7 PRO HG2 H 2.008 0.005 2 35 7 7 PRO HG3 H 2.008 0.005 2 36 8 8 LYS H H 9.230 0.005 1 37 8 8 LYS HA H 4.344 0.005 1 38 8 8 LYS HB2 H 1.899 0.005 2 39 8 8 LYS HB3 H 1.977 0.005 2 40 8 8 LYS HD2 H 1.635 0.005 2 41 8 8 LYS HD3 H 1.820 0.005 2 42 8 8 LYS HE2 H 2.921 0.005 2 43 8 8 LYS HE3 H 3.015 0.005 2 44 8 8 LYS HG2 H 1.249 0.005 2 45 8 8 LYS HG3 H 1.357 0.005 2 46 9 9 CYS H H 8.263 0.005 1 47 9 9 CYS HA H 5.016 0.005 1 48 9 9 CYS HB2 H 2.387 0.005 2 49 9 9 CYS HB3 H 3.285 0.005 2 50 10 10 GLN H H 7.988 0.005 1 51 10 10 GLN HA H 4.091 0.005 1 52 10 10 GLN HB2 H 2.235 0.005 2 53 10 10 GLN HB3 H 2.366 0.005 2 54 11 11 TYR H H 8.798 0.005 1 55 11 11 TYR HA H 4.155 0.005 1 56 11 11 TYR HB2 H 1.923 0.005 2 57 11 11 TYR HB3 H 3.089 0.005 2 58 11 11 TYR HD1 H 6.345 0.005 3 59 11 11 TYR HD2 H 6.345 0.005 3 60 11 11 TYR HE1 H 6.444 0.005 3 61 11 11 TYR HE2 H 6.444 0.005 3 62 12 12 GLN H H 7.633 0.005 1 63 12 12 GLN HA H 4.378 0.005 1 64 12 12 GLN HB2 H 1.641 0.005 2 65 12 12 GLN HB3 H 1.718 0.005 2 66 12 12 GLN HG2 H 2.127 0.005 2 67 12 12 GLN HG3 H 2.207 0.005 2 68 13 13 ALA H H 8.275 0.005 1 69 13 13 ALA HA H 4.338 0.005 1 70 13 13 ALA HB H 1.442 0.005 1 71 14 14 PRO HA H 4.420 0.005 1 72 14 14 PRO HB2 H 2.087 0.005 2 73 14 14 PRO HB3 H 2.239 0.005 2 74 14 14 PRO HD2 H 3.636 0.005 2 75 14 14 PRO HD3 H 3.724 0.005 2 76 14 14 PRO HG2 H 1.963 0.005 2 77 14 14 PRO HG3 H 1.963 0.005 2 78 15 15 ASP H H 6.948 0.005 1 79 15 15 ASP HA H 3.673 0.005 1 80 15 15 ASP HB2 H 2.732 0.005 2 81 15 15 ASP HB3 H 2.732 0.005 2 82 16 16 MET H H 8.139 0.005 1 83 16 16 MET HA H 3.906 0.005 1 84 16 16 MET HB2 H 1.912 0.005 2 85 16 16 MET HB3 H 1.912 0.005 2 86 16 16 MET HE H 2.117 0.005 1 87 16 16 MET HG2 H 2.532 0.005 2 88 16 16 MET HG3 H 2.532 0.005 2 89 17 17 ASP H H 8.227 0.005 1 90 17 17 ASP HA H 4.271 0.005 1 91 17 17 ASP HB2 H 2.534 0.005 2 92 17 17 ASP HB3 H 2.534 0.005 2 93 18 18 THR H H 8.645 0.005 1 94 18 18 THR HA H 3.913 0.005 1 95 18 18 THR HB H 3.944 0.005 1 96 18 18 THR HG2 H 1.403 0.005 1 97 19 19 LEU H H 7.795 0.005 1 98 19 19 LEU HA H 4.100 0.005 1 99 19 19 LEU HB2 H 1.443 0.005 2 100 19 19 LEU HB3 H 2.239 0.005 2 101 19 19 LEU HD1 H 0.874 0.005 4 102 19 19 LEU HD2 H 0.978 0.005 4 103 19 19 LEU HG H 1.715 0.005 1 104 20 20 GLN H H 8.305 0.005 1 105 20 20 GLN HA H 4.020 0.005 1 106 20 20 GLN HB2 H 2.138 0.005 2 107 20 20 GLN HB3 H 2.209 0.005 2 108 20 20 GLN HG2 H 2.494 0.005 2 109 20 20 GLN HG3 H 2.494 0.005 2 110 21 21 ILE H H 7.342 0.005 1 111 21 21 ILE HA H 3.754 0.005 1 112 21 21 ILE HB H 1.890 0.005 1 113 21 21 ILE HD1 H 0.817 0.005 1 114 21 21 ILE HG12 H 1.194 0.005 4 115 21 21 ILE HG13 H 1.688 0.005 4 116 21 21 ILE HG2 H 0.899 0.005 4 117 22 22 HIS H H 7.905 0.005 1 118 22 22 HIS HA H 4.094 0.005 1 119 22 22 HIS HB2 H 3.072 0.005 2 120 22 22 HIS HB3 H 3.635 0.005 2 121 22 22 HIS HD2 H 6.963 0.005 1 122 22 22 HIS HE1 H 7.538 0.005 1 123 23 23 VAL H H 9.191 0.005 1 124 23 23 VAL HA H 3.627 0.005 1 125 23 23 VAL HB H 2.247 0.005 1 126 23 23 VAL HG1 H 1.174 0.005 4 127 23 23 VAL HG2 H 1.348 0.005 4 128 24 24 MET H H 7.399 0.005 1 129 24 24 MET HA H 4.155 0.005 1 130 24 24 MET HB2 H 2.142 0.005 2 131 24 24 MET HB3 H 2.142 0.005 2 132 24 24 MET HG2 H 2.622 0.005 2 133 24 24 MET HG3 H 2.743 0.005 2 134 25 25 GLU H H 7.023 0.005 1 135 25 25 GLU HA H 4.263 0.005 1 136 25 25 GLU HB2 H 1.836 0.005 2 137 25 25 GLU HB3 H 1.936 0.005 2 138 25 25 GLU HG2 H 2.112 0.005 2 139 25 25 GLU HG3 H 2.182 0.005 2 140 26 26 CYS H H 7.757 0.005 1 141 26 26 CYS HA H 3.783 0.005 1 142 26 26 CYS HB2 H 2.026 0.005 2 143 26 26 CYS HB3 H 2.512 0.005 2 144 27 27 ILE H H 8.239 0.005 1 145 27 27 ILE HA H 4.142 0.005 1 146 27 27 ILE HB H 1.975 0.005 1 147 27 27 ILE HD1 H 0.863 0.005 1 148 27 27 ILE HG12 H 1.133 0.005 4 149 27 27 ILE HG13 H 1.455 0.005 4 150 27 27 ILE HG2 H 0.863 0.005 4 151 28 28 GLU H H 7.868 0.005 1 152 28 28 GLU HA H 4.143 0.005 1 153 28 28 GLU HB2 H 1.902 0.005 2 154 28 28 GLU HB3 H 2.056 0.005 2 155 28 28 GLU HG2 H 2.244 0.005 2 156 28 28 GLU HG3 H 2.244 0.005 2 stop_ loop_ _Atom_shift_assign_ID_ambiguity 101 '101,101,102,102,102' '114,115,116,116,116' '126,126,126,127,127,127' '148,149,150,150,150' stop_ save_