data_30076 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Domain 4 Segment 6 of voltage-gated sodium channel Nav1.4 ; _BMRB_accession_number 30076 _BMRB_flat_file_name bmr30076.str _Entry_type original _Submission_date 2016-05-05 _Accession_date 2016-05-05 _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 Niitsu Ai . . 2 Egawa Ayako . . 3 Ikeda Keisuke . . 4 Tachibana Kazuo . . 5 Fujiwara Toshimichi . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 111 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-07-19 update BMRB 'update entry citation' 2017-05-15 original author 'original release' stop_ _Original_release_date 2016-05-26 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Veratridine binding to a transmembrane helix of sodium channel Na ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30389410 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Niitsu Ai . . 2 Egawa Ayako . . 3 Ikeda Keisuke . . 4 Tachibana Kazuo . . 5 Fujiwara Toshimichi . . stop_ _Journal_abbreviation 'Bioorg. Med. Chem.' _Journal_name_full 'Bioorganic & medicinal chemistry' _Journal_volume 26 _Journal_issue 21 _Journal_ISSN 1464-3391 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5644 _Page_last 5653 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Sodium channel protein type 4 subunit alpha' _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 'Sodium channel protein type 4 subunit alpha' _Molecular_mass 4033.070 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 35 _Mol_residue_sequence ; KKKGICFFCSYIIISFLIVV NMYIAIILENFKKKX ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 LYS 2 2 LYS 3 3 LYS 4 4 GLY 5 5 ILE 6 6 CYS 7 7 PHE 8 8 PHE 9 9 CYS 10 10 SER 11 11 TYR 12 12 ILE 13 13 ILE 14 14 ILE 15 15 SER 16 16 PHE 17 17 LEU 18 18 ILE 19 19 VAL 20 20 VAL 21 21 ASN 22 22 MET 23 23 TYR 24 24 ILE 25 25 ALA 26 26 ILE 27 27 ILE 28 28 LEU 29 29 GLU 30 30 ASN 31 31 PHE 32 32 LYS 33 33 LYS 34 34 LYS 35 35 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _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 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 HN1 ? ? SING N HN2 ? ? 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 Rat 10116 Eukaryota Metazoa Rattus . 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 liposome _Details '16 % U-13C I23, L17, V20 peptide, 69 % d-54 DMPC, water' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling DMPC 69 % d-54 $entity_1 16 % 'U-13C I23, L17, V20' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type liposome _Details '16 % U-13C G, I, F, L, V, A peptide, 69 % d-54 DMPC, water' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling DMPC 69 % d-54 $entity_1 16 % 'U-13C G, I, F, L, V, A' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CHARMM _Version . loop_ _Vendor _Address _Electronic_address 'M. KARPLUS ET AL, HARVARD UNIVERSITY' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name DELTA _Version . loop_ _Task 'structure solution' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name FELIX _Version . loop_ _Task 'structure solution' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name SPARKY _Version . loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Infinity Plus 700' _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_13C-13C_dipolar-assisted_rotational_resonance_1 _Saveframe_category NMR_applied_experiment _Experiment_name '13C-13C dipolar-assisted rotational resonance' _Sample_label $sample_1 save_ save_13C-13C_dipolar-assisted_rotational_resonance_2 _Saveframe_category NMR_applied_experiment _Experiment_name '13C-13C dipolar-assisted rotational resonance' _Sample_label $sample_2 save_ save_13C_observation_of_2H-selective_1H-depolarization_3 _Saveframe_category NMR_applied_experiment _Experiment_name '13C observation of 2H-selective 1H-depolarization' _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 . mM pH 7.4 . pH pressure 1 . atm temperature 213 . 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 C 13 'methyl protons' ppm 0.000 external indirect . . . 0.25144953 acetate C 13 'methylene protons' ppm 38.5 external direct . . . 0.25144953 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_ _Software_label $software_1 stop_ loop_ _Experiment_label '13C-13C dipolar-assisted rotational resonance' stop_ loop_ _Sample_label $sample_1 $sample_2 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 4 4 GLY C C 173.8 0.3 1 2 4 4 GLY CA C 43.4 0.3 1 3 5 5 ILE C C 177.2 0.3 5 4 5 5 ILE CA C 59.9 0.3 1 5 5 5 ILE CB C 39.0 0.3 1 6 5 5 ILE CG1 C 28.1 0.3 1 7 5 5 ILE CG2 C 20.7 0.3 1 8 5 5 ILE CD1 C 16.4 0.3 1 9 7 7 PHE C C 175.8 0.3 5 10 7 7 PHE CA C 61.0 0.3 5 11 7 7 PHE CB C 39.4 0.3 5 12 7 7 PHE CG C 139.3 0.3 5 13 7 7 PHE CD1 C 131.1 0.3 . 14 7 7 PHE CD2 C 131.1 0.3 . 15 7 7 PHE CE1 C 131.1 0.3 . 16 7 7 PHE CE2 C 131.1 0.3 . 17 7 7 PHE CZ C 131.1 0.3 5 18 8 8 PHE C C 175.8 0.3 5 19 8 8 PHE CA C 61.0 0.3 5 20 8 8 PHE CB C 39.4 0.3 5 21 8 8 PHE CG C 139.3 0.3 5 22 8 8 PHE CD1 C 131.1 0.3 . 23 8 8 PHE CD2 C 131.1 0.3 . 24 8 8 PHE CE1 C 131.1 0.3 . 25 8 8 PHE CE2 C 131.1 0.3 . 26 8 8 PHE CZ C 131.1 0.3 5 27 12 12 ILE C C 177.7 0.3 1 28 12 12 ILE CA C 66.2 0.3 1 29 12 12 ILE CB C 36.1 0.3 1 30 12 12 ILE CG1 C 30.2 0.3 1 31 12 12 ILE CG2 C 18.7 0.3 1 32 12 12 ILE CD1 C 15.2 0.3 1 33 13 13 ILE C C 177.2 0.3 5 34 13 13 ILE CA C 65.9 0.3 5 35 13 13 ILE CB C 37.9 0.3 5 36 13 13 ILE CG1 C 29.8 0.3 5 37 13 13 ILE CG2 C 17.4 0.3 5 38 13 13 ILE CD1 C 14.5 0.3 5 39 14 14 ILE C C 177.2 0.3 5 40 14 14 ILE CA C 65.9 0.3 5 41 14 14 ILE CB C 37.9 0.3 5 42 14 14 ILE CG1 C 29.8 0.3 5 43 14 14 ILE CG2 C 17.4 0.3 5 44 14 14 ILE CD1 C 14.5 0.3 5 45 16 16 PHE C C 173.4 0.3 1 46 16 16 PHE CA C 61.0 0.3 1 47 16 16 PHE CB C 39.4 0.3 5 48 16 16 PHE CG C 139.3 0.3 5 49 16 16 PHE CD1 C 131.1 0.3 . 50 16 16 PHE CD2 C 131.1 0.3 . 51 16 16 PHE CE1 C 131.1 0.3 . 52 16 16 PHE CE2 C 131.1 0.3 . 53 16 16 PHE CZ C 131.1 0.3 5 54 17 17 LEU C C 178.9 0.3 1 55 17 17 LEU CA C 58.1 0.3 1 56 17 17 LEU CB C 42.2 0.3 1 57 17 17 LEU CG C 26.8 0.3 1 58 17 17 LEU CD1 C 22.1 0.3 . 59 17 17 LEU CD2 C 22.1 0.3 . 60 18 18 ILE C C 177.2 0.3 5 61 18 18 ILE CA C 66.1 0.3 1 62 18 18 ILE CB C 38.0 0.3 1 63 18 18 ILE CG1 C 29.9 0.3 5 64 18 18 ILE CG2 C 17.4 0.3 5 65 18 18 ILE CD1 C 14.6 0.3 5 66 19 19 VAL C C 176.9 0.3 1 67 19 19 VAL CA C 66.9 0.3 1 68 19 19 VAL CB C 31.7 0.3 1 69 19 19 VAL CG1 C 22.8 0.3 . 70 19 19 VAL CG2 C 22.8 0.3 . 71 20 20 VAL C C 178.5 0.3 1 72 20 20 VAL CA C 67.7 0.3 1 73 20 20 VAL CB C 31.3 0.3 1 74 20 20 VAL CG1 C 23.2 0.3 . 75 20 20 VAL CG2 C 23.2 0.3 . 76 24 24 ILE C C 177.2 0.3 5 77 24 24 ILE CA C 62.1 0.3 5 78 24 24 ILE CB C 39.0 0.3 5 79 24 24 ILE CG1 C 29.3 0.3 5 80 24 24 ILE CG2 C 17.4 0.3 5 81 24 24 ILE CD1 C 14.5 0.3 5 82 25 25 ALA C C 180.1 0.3 1 83 25 25 ALA CA C 55.7 0.3 1 84 25 25 ALA CB C 18.1 0.3 1 85 26 26 ILE C C 177.2 0.3 5 86 26 26 ILE CA C 65.6 0.3 1 87 26 26 ILE CB C 37.9 0.3 5 88 26 26 ILE CG1 C 29.9 0.3 5 89 26 26 ILE CG2 C 17.4 0.3 5 90 26 26 ILE CD1 C 14.6 0.3 1 91 27 27 ILE C C 177.2 0.3 5 92 27 27 ILE CA C 60.8 0.3 1 93 27 27 ILE CB C 35.0 0.3 1 94 27 27 ILE CG1 C 30.4 0.3 5 95 27 27 ILE CG2 C 18.7 0.3 1 96 27 27 ILE CD1 C 14.6 0.3 5 97 28 28 LEU C C 177.9 0.3 1 98 28 28 LEU CA C 58.3 0.3 1 99 28 28 LEU CB C 40.9 0.3 1 100 28 28 LEU CG C 27.0 0.3 1 101 28 28 LEU CD1 C 23.4 0.3 . 102 28 28 LEU CD2 C 23.4 0.3 . 103 31 31 PHE C C 175.8 0.3 5 104 31 31 PHE CA C 61.0 0.3 5 105 31 31 PHE CB C 39.4 0.3 5 106 31 31 PHE CG C 139.3 0.3 5 107 31 31 PHE CD1 C 131.1 0.3 . 108 31 31 PHE CD2 C 131.1 0.3 . 109 31 31 PHE CE1 C 131.1 0.3 . 110 31 31 PHE CE2 C 131.1 0.3 . 111 31 31 PHE CZ C 131.1 0.3 5 stop_ save_