data_5837 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of a peptide derived from the voltage gated Na+ channel and its selective interaction with local anesthetic as determined by NMR spectroscopy ; _BMRB_accession_number 5837 _BMRB_flat_file_name bmr5837.str _Entry_type original _Submission_date 2003-06-18 _Accession_date 2003-06-18 _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 Fraceto Leonardo F. . 2 Nakaie Clovis R. . 3 Spisni Alberto . . 4 'de Paula' Eneida . . 5 Pertinhez Thelma A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 129 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-27 update BMRB 'update entry citation' 2006-01-23 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Interaction of local anesthetics with a peptide encompassing the IV/S4-S5 linker of the Na+ channel. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16687202 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Fraceto Leonardo F. . 2 Oyama Sergio . Jr. 3 Nakaie Clovis R. . 4 Spisni Alberto . . 5 'de Paula' Eneida . . 6 Pertinhez Thelma A. . stop_ _Journal_abbreviation 'Biophys. Chem.' _Journal_volume 123 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 29 _Page_last 39 _Year 2006 _Details . loop_ _Keyword 'local anesthetic' 'Na+ channel' NMR interaction stop_ save_ ################################## # Molecular system description # ################################## save_system_Na+_Sodium_Channel _Saveframe_category molecular_system _Mol_system_name 'Sodium Channel' _Abbreviation_common 'Na+ Sodium Channel' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Sodium channel subunit 4' $Chan stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Chan _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Sodium Channel' _Abbreviation_common Chan _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; KGIRTLLFALMMSLPALFNI G ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 GLY 3 ILE 4 ARG 5 THR 6 LEU 7 LEU 8 PHE 9 ALA 10 LEU 11 MET 12 MET 13 SER 14 LEU 15 PRO 16 ALA 17 LEU 18 PHE 19 ASN 20 ILE 21 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-28 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 DBJ BAA07195 "sodium channel alpha subunit, partial [Takifugu rubripes]" 76.19 1717 100.00 100.00 3.48e+00 DBJ BAA78033 "sodium channel [Homo sapiens]" 100.00 1980 100.00 100.00 1.03e-03 DBJ BAA90445 "voltage-gated sodium channel alpha subunit [Homo sapiens]" 100.00 364 100.00 100.00 1.46e-03 DBJ BAA90446 "voltage-gated sodium channel alpha subunit [Pan troglodytes]" 100.00 364 100.00 100.00 1.46e-03 DBJ BAA90447 "voltage-gated sodium channel alpha subunit [Gorilla gorilla]" 100.00 364 100.00 100.00 1.46e-03 EMBL CAA25587 "unnamed protein product [Electrophorus electricus]" 100.00 1820 100.00 100.00 1.65e-03 EMBL CAA27286 "unnamed protein product [Rattus norvegicus]" 100.00 2009 100.00 100.00 9.99e-04 EMBL CAA27287 "unnamed protein product [Rattus norvegicus]" 100.00 2005 100.00 100.00 1.03e-03 EMBL CAA46439 "sodium channel [Homo sapiens]" 100.00 423 100.00 100.00 1.94e-03 EMBL CAA58042 "sodium channel alpha subunit [Homo sapiens]" 100.00 1977 100.00 100.00 1.02e-03 GB AAA18895 "voltage-gated sodium channel [Homo sapiens]" 100.00 2005 100.00 100.00 1.09e-03 GB AAA41682 "voltage-sensitive sodium channel alpha subunit [Rattus norvegicus]" 100.00 1840 100.00 100.00 1.01e-03 GB AAA42114 "sodium channel alpha-subunit [Rattus norvegicus]" 100.00 2019 100.00 100.00 1.34e-03 GB AAA58644 "sodium channel alpha subunit [Homo sapiens]" 100.00 2016 100.00 100.00 1.34e-03 GB AAA60554 "sodium channel alpha subunit [Homo sapiens]" 100.00 1836 100.00 100.00 1.33e-03 PRF 1012288A "protein,Na channel" 100.00 1820 100.00 100.00 1.65e-03 PRF 1204264A "Na channel I protein" 100.00 2009 100.00 100.00 9.99e-04 PRF 1204264B "Na channel II protein" 100.00 2005 100.00 100.00 1.03e-03 PRF 2117364A "voltage-gated Na channel NaCh6" 100.00 1976 100.00 100.00 8.33e-04 PRF 2203417A "voltage gated Na channel Scn8a" 100.00 1732 100.00 100.00 2.16e-03 REF NP_000325 "sodium channel protein type 4 subunit alpha [Homo sapiens]" 100.00 1836 100.00 100.00 1.35e-03 REF NP_000326 "sodium channel protein type 5 subunit alpha isoform b [Homo sapiens]" 100.00 2015 100.00 100.00 1.37e-03 REF NP_001002994 "sodium channel protein type 5 subunit alpha [Canis lupus familiaris]" 100.00 2013 100.00 100.00 1.34e-03 REF NP_001003203 "sodium channel protein type 10 subunit alpha [Canis lupus familiaris]" 100.00 1962 100.00 100.00 1.09e-03 REF NP_001034914 "sodium channel protein type 4 subunit alpha A [Danio rerio]" 100.00 1829 100.00 100.00 2.58e-03 SP O08562 "RecName: Full=Sodium channel protein type 9 subunit alpha; AltName: Full=Peripheral sodium channel 1; Short=PN1; AltName: Full=" 100.00 1984 100.00 100.00 1.01e-03 SP O46669 "RecName: Full=Sodium channel protein type 10 subunit alpha; AltName: Full=NaNG; AltName: Full=Sodium channel protein type X sub" 100.00 1962 100.00 100.00 1.09e-03 SP O88420 "RecName: Full=Sodium channel protein type 8 subunit alpha; AltName: Full=Peripheral nerve protein type 4; Short=PN4; AltName: F" 100.00 1978 100.00 100.00 1.14e-03 SP P02719 "RecName: Full=Sodium channel protein; AltName: Full=Na(+) channel [Electrophorus electricus]" 100.00 1820 100.00 100.00 1.65e-03 SP P04774 "RecName: Full=Sodium channel protein type 1 subunit alpha; AltName: Full=Sodium channel protein brain I subunit alpha; AltName:" 100.00 2009 100.00 100.00 9.99e-04 TPG DAA17127 "TPA: voltage-gated sodium channel type V alpha [Bos taurus]" 100.00 2022 100.00 100.00 1.37e-03 TPG DAA17236 "TPA: tetrodotoxin-resistant voltage-gated sodium channel-like [Bos taurus]" 100.00 1973 100.00 100.00 2.57e-03 TPG DAA30006 "TPA: sodium channel, voltage gated, type VIII, alpha subunit [Bos taurus]" 100.00 1980 100.00 100.00 1.06e-03 TPG DAA32687 "TPA: sodium channel, voltage-gated, type IX, alpha subunit [Bos taurus]" 100.00 1987 100.00 100.00 1.03e-03 TPG DAA32692 "TPA: sodium channel, voltage-gated, type II, alpha subunit [Bos taurus]" 100.00 2006 100.00 100.00 1.04e-03 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Chan 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 $Chan 'chemical synthesis' . . . . . 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 $Chan 1.0 mM . trifluethanol 30 % . stop_ save_ ############################ # Computer software used # ############################ save_Felix _Saveframe_category software _Name Felix _Version 2000 _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _Sample_label . save_ save_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label . save_ save_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label . save_ save_ROESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name ROESY _Sample_label . save_ save_15N-HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name 15N-HSQC _Sample_label . save_ save_DOSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name DOSY _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _BMRB_pulse_sequence_accession_number . _Details 'triple-resonance probe' save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _BMRB_pulse_sequence_accession_number . _Details 'triple-resonance probe' save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details 'triple-resonance probe' save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name ROESY _BMRB_pulse_sequence_accession_number . _Details 'triple-resonance probe' save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name 15N-HSQC _BMRB_pulse_sequence_accession_number . _Details 'triple-resonance probe' save_ save_NMR_spec_expt__0_6 _Saveframe_category NMR_applied_experiment _Experiment_name DOSY _BMRB_pulse_sequence_accession_number . _Details 'triple-resonance probe' save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.1 0.1 pH temperature 293 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 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_chemical_shift_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'Sodium channel subunit 4' _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 LYS HA H 4.13 0.01 1 2 . 1 LYS HB2 H 1.96 0.01 1 3 . 1 LYS HB3 H 1.96 0.01 1 4 . 1 LYS HG2 H 1.54 0.01 1 5 . 1 LYS HG3 H 1.26 0.01 1 6 . 1 LYS HD2 H 1.77 0.01 1 7 . 1 LYS HD3 H 1.77 0.01 1 8 . 1 LYS HE2 H 3.05 0.01 1 9 . 1 LYS HE3 H 3.05 0.01 1 10 . 2 GLY H H 8.17 0.01 1 11 . 2 GLY HA2 H 4.30 0.01 1 12 . 2 GLY HA3 H 4.01 0.01 1 13 . 3 ILE H H 8.36 0.01 1 14 . 3 ILE HA H 4.13 0.01 1 15 . 3 ILE HB H 1.96 0.01 1 16 . 3 ILE HG12 H 1.55 0.01 1 17 . 3 ILE HG13 H 1.55 0.01 1 18 . 3 ILE HG2 H 1.02 0.01 1 19 . 3 ILE HD1 H 1.37 0.01 1 20 . 4 ARG H H 8.34 0.01 1 21 . 4 ARG HA H 4.05 0.01 1 22 . 4 ARG HB2 H 1.93 0.01 1 23 . 4 ARG HB3 H 1.80 0.01 1 24 . 4 ARG HG2 H 1.66 0.01 1 25 . 4 ARG HG3 H 1.66 0.01 1 26 . 4 ARG HD2 H 3.23 0.01 1 27 . 4 ARG HD3 H 3.23 0.01 1 28 . 4 ARG HH11 H 7.18 0.01 2 29 . 4 ARG HH21 H 7.18 0.01 2 30 . 5 THR H H 7.53 0.01 1 31 . 5 THR HA H 4.07 0.01 1 32 . 5 THR HB H 4.26 0.01 1 33 . 5 THR HG2 H 1.33 0.01 1 34 . 6 LEU H H 7.48 0.01 1 35 . 6 LEU HA H 4.20 0.01 1 36 . 6 LEU HB2 H 1.89 0.01 1 37 . 6 LEU HB3 H 1.89 0.01 1 38 . 6 LEU HG H 1.68 0.01 1 39 . 6 LEU HD1 H 0.95 0.01 1 40 . 6 LEU HD2 H 0.95 0.01 1 41 . 7 LEU H H 8.21 0.01 1 42 . 7 LEU HA H 4.09 0.01 1 43 . 7 LEU HB2 H 1.82 0.01 1 44 . 7 LEU HB3 H 1.82 0.01 1 45 . 7 LEU HG H 1.59 0.01 1 46 . 7 LEU HD1 H 0.93 0.01 1 47 . 7 LEU HD2 H 0.93 0.01 1 48 . 8 PHE H H 8.03 0.01 1 49 . 8 PHE HA H 4.25 0.01 1 50 . 8 PHE HB2 H 3.24 0.01 1 51 . 8 PHE HB3 H 3.24 0.01 1 52 . 8 PHE HD1 H 7.22 0.01 1 53 . 8 PHE HD2 H 7.22 0.01 1 54 . 8 PHE HE1 H 7.28 0.01 1 55 . 8 PHE HE2 H 7.28 0.01 1 56 . 9 ALA H H 8.12 0.01 1 57 . 9 ALA HA H 3.96 0.01 1 58 . 9 ALA HB H 1.58 0.01 1 59 . 10 LEU H H 8.50 0.01 1 60 . 10 LEU HA H 4.05 0.01 1 61 . 10 LEU HB2 H 1.93 0.01 1 62 . 10 LEU HB3 H 1.81 0.01 1 63 . 10 LEU HG H 1.67 0.01 1 64 . 10 LEU HD1 H 0.87 0.01 1 65 . 10 LEU HD2 H 0.87 0.01 1 66 . 11 MET H H 8.46 0.01 1 67 . 11 MET HA H 4.04 0.01 1 68 . 11 MET HB2 H 2.66 0.01 1 69 . 11 MET HB3 H 2.41 0.01 1 70 . 11 MET HG2 H 2.16 0.01 1 71 . 11 MET HG3 H 1.99 0.01 1 72 . 12 MET H H 7.99 0.01 1 73 . 12 MET HA H 4.37 0.01 1 74 . 12 MET HB2 H 2.25 0.01 1 75 . 12 MET HB3 H 2.15 0.01 1 76 . 12 MET HG2 H 1.99 0.01 1 77 . 12 MET HG3 H 1.99 0.01 1 78 . 13 SER H H 7.81 0.01 1 79 . 13 SER HA H 4.52 0.01 1 80 . 13 SER HB2 H 4.04 0.01 1 81 . 13 SER HB3 H 3.96 0.01 1 82 . 14 LEU H H 7.92 0.01 1 83 . 14 LEU HA H 4.42 0.01 1 84 . 14 LEU HB2 H 1.92 0.01 1 85 . 14 LEU HB3 H 1.92 0.01 1 86 . 14 LEU HG H 1.53 0.01 1 87 . 14 LEU HD1 H 0.97 0.01 1 88 . 14 LEU HD2 H 0.89 0.01 1 89 . 15 PRO HA H 4.31 0.01 1 90 . 15 PRO HB2 H 2.35 0.01 1 91 . 15 PRO HB3 H 2.13 0.01 1 92 . 15 PRO HG2 H 1.96 0.01 1 93 . 15 PRO HG3 H 1.88 0.01 1 94 . 15 PRO HD2 H 3.72 0.01 1 95 . 15 PRO HD3 H 3.57 0.01 1 96 . 16 ALA H H 7.60 0.01 1 97 . 16 ALA HA H 4.25 0.01 1 98 . 16 ALA HB H 1.49 0.01 1 99 . 17 LEU H H 7.89 0.01 1 100 . 17 LEU HA H 4.13 0.01 1 101 . 17 LEU HB2 H 1.68 0.01 1 102 . 17 LEU HB3 H 1.60 0.01 1 103 . 17 LEU HG H 1.43 0.01 1 104 . 17 LEU HD1 H 0.87 0.01 1 105 . 17 LEU HD2 H 0.80 0.01 1 106 . 18 PHE H H 7.99 0.01 1 107 . 18 PHE HA H 4.50 0.01 1 108 . 18 PHE HB2 H 3.27 0.01 1 109 . 18 PHE HB3 H 3.01 0.01 1 110 . 18 PHE HD1 H 7.26 0.01 1 111 . 18 PHE HD2 H 7.26 0.01 1 112 . 18 PHE HE1 H 7.20 0.01 1 113 . 18 PHE HE2 H 7.20 0.01 1 114 . 19 ASN H H 7.92 0.01 1 115 . 19 ASN HA H 4.72 0.01 1 116 . 19 ASN HB2 H 2.96 0.01 1 117 . 19 ASN HB3 H 2.82 0.01 1 118 . 19 ASN HD21 H 7.55 0.01 1 119 . 19 ASN HD22 H 6.77 0.01 1 120 . 20 ILE H H 7.96 0.01 1 121 . 20 ILE HA H 4.14 0.01 1 122 . 20 ILE HB H 1.98 0.01 1 123 . 20 ILE HG12 H 1.60 0.01 1 124 . 20 ILE HG13 H 1.28 0.01 1 125 . 20 ILE HG2 H 0.97 0.01 1 126 . 20 ILE HD1 H 1.28 0.01 1 127 . 21 GLY H H 8.28 0.01 1 128 . 21 GLY HA2 H 3.91 0.01 1 129 . 21 GLY HA3 H 3.91 0.01 1 stop_ save_