data_6728 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR STRUCTURAL STUDIES OF A POTASSIUM CHANNEL/CHARYBDOTOXIN COMPLEX ; _BMRB_accession_number 6728 _BMRB_flat_file_name bmr6728.str _Entry_type original _Submission_date 2005-07-08 _Accession_date 2005-07-11 _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 Yu Liping . . 2 Olejniczak Edward T. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 48 "13C chemical shifts" 46 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2006-08-15 original BMRB . stop_ _Original_release_date 2005-07-12 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Nuclear Magnetic Resonance Structural Studies of a Potassium Channel-Charybdotoxin Complex ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16313186 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Yu Liping . . 2 Sun Chaohong . . 3 Song Danying . . 4 Shen Jianwei . . 5 Xu Nan . . 6 Gunasekera Angelo . . 7 Haiduk Philip J. . 8 Olejniczak Edward T. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 44 _Journal_issue 48 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 15834 _Page_last 15841 _Year 2005 _Details . loop_ _Keyword KcsA NMR 'Potassium channel' 'membrane protein' structure stop_ save_ ################################## # Molecular system description # ################################## save_system_KcsA _Saveframe_category molecular_system _Mol_system_name 'potassium channel KcsA' _Abbreviation_common KcsA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'potassium channel KcsA, chain 1' $KcsA 'potassium channel KcsA, chain 2' $KcsA 'potassium channel KcsA, chain 3' $KcsA 'potassium channel KcsA, chain 4' $KcsA Charybdotoxin $Charybdotoxin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state tetramer _System_paramagnetic no _System_thiol_state 'all disulfide bound' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'potassium channel KcsA, chain 1' 1 'potassium channel KcsA, chain 2' 1 'potassium channel KcsA, chain 3' 1 'potassium channel KcsA, chain 4' stop_ loop_ _Biological_function 'potassium channel' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_KcsA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'potassium channel' _Abbreviation_common KcsA _Molecular_mass . _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 129 _Mol_residue_sequence ; MPPMLSGLLARLVKLLLGRH GSALHWRAAGAATVLLVIVL LAGSYLAVLAERGAPGAALI SYPDALWWSVETATTVGYGD LYPVTLWGRCVAVVVMVAGI TSYGLVFAAVATWFVGREQE RRGHFVRHS ; loop_ _Residue_seq_code _Residue_label 1 MET 2 PRO 3 PRO 4 MET 5 LEU 6 SER 7 GLY 8 LEU 9 LEU 10 ALA 11 ARG 12 LEU 13 VAL 14 LYS 15 LEU 16 LEU 17 LEU 18 GLY 19 ARG 20 HIS 21 GLY 22 SER 23 ALA 24 LEU 25 HIS 26 TRP 27 ARG 28 ALA 29 ALA 30 GLY 31 ALA 32 ALA 33 THR 34 VAL 35 LEU 36 LEU 37 VAL 38 ILE 39 VAL 40 LEU 41 LEU 42 ALA 43 GLY 44 SER 45 TYR 46 LEU 47 ALA 48 VAL 49 LEU 50 ALA 51 GLU 52 ARG 53 GLY 54 ALA 55 PRO 56 GLY 57 ALA 58 ALA 59 LEU 60 ILE 61 SER 62 TYR 63 PRO 64 ASP 65 ALA 66 LEU 67 TRP 68 TRP 69 SER 70 VAL 71 GLU 72 THR 73 ALA 74 THR 75 THR 76 VAL 77 GLY 78 TYR 79 GLY 80 ASP 81 LEU 82 TYR 83 PRO 84 VAL 85 THR 86 LEU 87 TRP 88 GLY 89 ARG 90 CYS 91 VAL 92 ALA 93 VAL 94 VAL 95 VAL 96 MET 97 VAL 98 ALA 99 GLY 100 ILE 101 THR 102 SER 103 TYR 104 GLY 105 LEU 106 VAL 107 PHE 108 ALA 109 ALA 110 VAL 111 ALA 112 THR 113 TRP 114 PHE 115 VAL 116 GLY 117 ARG 118 GLU 119 GLN 120 GLU 121 ARG 122 ARG 123 GLY 124 HIS 125 PHE 126 VAL 127 ARG 128 HIS 129 SER stop_ _Sequence_homology_query_date 2008-08-19 _Sequence_homology_query_revised_last_date 2008-08-19 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 PDB 2A9H 'Nmr Structural Studies Of A Potassium Channel Charybdotoxin Complex' 100.00 155 100.00 100.00 1.65e-65 stop_ save_ save_Charybdotoxin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Charybdotoxin _Abbreviation_common Charybdotoxin _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . _Residue_count 37 _Mol_residue_sequence ; XFTNVSCTTSKECWSVCQRL HNTSRGKCMNKKCRCYS ; loop_ _Residue_seq_code _Residue_label 1 PCA 2 PHE 3 THR 4 ASN 5 VAL 6 SER 7 CYS 8 THR 9 THR 10 SER 11 LYS 12 GLU 13 CYS 14 TRP 15 SER 16 VAL 17 CYS 18 GLN 19 ARG 20 LEU 21 HIS 22 ASN 23 THR 24 SER 25 ARG 26 GLY 27 LYS 28 CYS 29 MET 30 ASN 31 LYS 32 LYS 33 CYS 34 ARG 35 CYS 36 TYR 37 SER stop_ _Sequence_homology_query_date 2008-08-19 _Sequence_homology_query_revised_last_date 2008-08-19 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 BMRB 114 charybdotoxin 97.30 36 100.00 100.00 4.81e-12 PDB 2A9H 'Nmr Structural Studies Of A Potassium Channel Charybdotoxin Complex' 97.30 37 100.00 100.00 4.81e-12 PDB 2CRD 'Analysis Of Side-Chain Organization On A Refined Model Of Charybdotoxin: Structural And Functional Implications' 97.30 37 100.00 100.00 4.81e-12 GenBank AAA73014 charybdotoxin 97.30 45 100.00 100.00 2.71e-12 SWISS-PROT P13487 'Potassium channel toxin alpha-KTx 1.1 precursor (Charybdotoxin) (ChTX) (ChTX-Lq1) (ChTx-a)' 97.30 59 100.00 100.00 1.07e-12 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_PCA _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 'PYROGLUTAMIC ACID' _BMRB_code PCA _PDB_code PCA _Standard_residue_derivative . _Molecular_mass 129.114 _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 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? OE OE O . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HXT HXT 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 CA ? ? SING N CD ? ? SING N H ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? DOUB CD OE ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $KcsA 'Streptomyces lividans' 1916 Bacteria . Streptomyces lividans $Charybdotoxin Scorpion 72113 Eukaryota Metazoa Scorpaena . 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 $KcsA 'recombinant technology' . . . . . . $Charybdotoxin 'purchased from vendor' . . . . . 'Scorpion Toxin purchased from Bachem.' 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $KcsA . mM 0.030 1.0 . $Charybdotoxin . mM . . . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 800 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_13C-edited_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '13C-edited NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_experimental_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.5 0.2 pH temperature 315 0.5 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details ; Chemical shift reference for carbon based on Tsp (0ppm). JMR 67(1986),565-569. Chemical shift reference for 1H based on water resonance at experimental temperature. ; 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 TSP C 13 'methyl protons' ppm . . . . . . 0.25144954 H2O H 1 protons ppm 4.76 internal direct spherical internal parallel 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_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $experimental_conditions _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'potassium channel KcsA, chain 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 . 24 LEU HD1 H 1.0180 0.02 2 2 . 24 LEU HD2 H 0.5250 0.02 2 3 . 24 LEU CD1 C 22.8870 0.20 1 4 . 24 LEU CD2 C 25.5340 0.20 1 5 . 28 ALA HB H 1.6900 0.02 1 6 . 28 ALA CB C 19.1800 0.20 1 7 . 29 ALA HB H 1.6900 0.02 1 8 . 32 ALA HB H 1.6280 0.02 1 9 . 32 ALA CB C 18.2980 0.20 1 10 . 36 LEU HD1 H 1.0230 0.02 2 11 . 36 LEU HD2 H 0.9850 0.02 2 12 . 36 LEU CD1 C 25.3580 0.20 1 13 . 36 LEU CD2 C 24.2990 0.20 1 14 . 38 ILE HD1 H 0.9770 0.02 1 15 . 38 ILE CD1 C 13.1800 0.20 1 16 . 40 LEU HD1 H 0.7590 0.02 2 17 . 40 LEU HD2 H 0.8200 0.02 2 18 . 40 LEU CD1 C 22.5200 0.20 1 19 . 40 LEU CD2 C 25.8000 0.20 1 20 . 41 LEU HD1 H 1.0490 0.02 2 21 . 41 LEU CD1 C 22.7090 0.20 1 22 . 47 ALA HB H 1.4410 0.02 1 23 . 47 ALA CB C 18.1220 0.20 1 24 . 48 VAL HG1 H 0.8680 0.02 2 25 . 48 VAL HG2 H 0.7500 0.02 2 26 . 48 VAL CG1 C 23.0500 0.20 1 27 . 48 VAL CG2 C 21.4650 0.20 1 28 . 57 ALA HB H 1.3480 0.02 1 29 . 57 ALA CB C 17.9450 0.20 1 30 . 58 ALA HB H 1.4500 0.02 1 31 . 58 ALA CB C 21.6510 0.20 1 32 . 59 LEU HD1 H -0.4720 0.02 2 33 . 59 LEU HD2 H 0.2780 0.02 2 34 . 59 LEU CD1 C 23.2330 0.20 1 35 . 59 LEU CD2 C 24.2990 0.20 1 36 . 60 ILE HD1 H 0.9020 0.02 1 37 . 60 ILE CD1 C 13.0030 0.20 1 38 . 65 ALA HB H 1.6980 0.02 1 39 . 65 ALA CB C 19.7100 0.20 1 40 . 66 LEU HD1 H 0.8230 0.02 2 41 . 66 LEU HD2 H 1.0690 0.02 2 42 . 66 LEU CD1 C 25.0050 0.20 1 43 . 66 LEU CD2 C 25.7110 0.20 1 44 . 70 VAL HG1 H 1.2200 0.02 2 45 . 70 VAL CG1 C 23.2390 0.20 1 46 . 73 ALA HB H 1.6250 0.02 1 47 . 73 ALA CB C 18.2800 0.20 1 48 . 76 VAL HG1 H 0.0790 0.02 2 49 . 76 VAL HG2 H 0.8970 0.02 2 50 . 76 VAL CG1 C 20.5500 0.20 1 51 . 76 VAL CG2 C 23.2400 0.20 1 52 . 81 LEU HG H 1.6450 0.02 1 53 . 81 LEU HD1 H 0.9200 0.02 2 54 . 81 LEU HD2 H 1.1980 0.02 2 55 . 81 LEU CD1 C 24.8280 0.20 1 56 . 81 LEU CD2 C 27.9900 0.20 1 57 . 84 VAL HG1 H 0.9100 0.02 2 58 . 84 VAL CG1 C 18.2980 0.20 1 59 . 86 LEU HD1 H 0.4550 0.02 2 60 . 86 LEU HD2 H 0.7900 0.02 2 61 . 86 LEU CD1 C 24.9400 0.20 1 62 . 86 LEU CD2 C 24.1400 0.20 1 63 . 91 VAL HG1 H 1.3450 0.02 2 64 . 91 VAL HG2 H 1.2750 0.02 2 65 . 91 VAL CG1 C 22.3700 0.20 1 66 . 91 VAL CG2 C 23.7690 0.20 1 67 . 92 ALA HB H 2.5300 0.02 1 68 . 92 ALA CB C 20.4600 0.20 1 69 . 93 VAL HG1 H 1.6540 0.02 2 70 . 93 VAL HG2 H 1.1000 0.02 2 71 . 93 VAL CG1 C 23.4160 0.20 1 72 . 93 VAL CG2 C 22.0040 0.20 1 73 . 95 VAL HG1 H 1.0700 0.02 2 74 . 95 VAL HG2 H 0.7720 0.02 2 75 . 95 VAL CG1 C 21.6510 0.20 1 76 . 95 VAL CG2 C 23.2390 0.20 1 77 . 96 MET CE C 17.9450 0.20 1 78 . 96 MET HE H 2.1150 0.02 1 79 . 100 ILE HD1 H 0.9700 0.02 1 80 . 100 ILE CD1 C 13.4800 0.20 1 81 . 105 LEU HD1 H 1.3280 0.02 2 82 . 105 LEU HD2 H 1.1500 0.02 2 83 . 105 LEU CD1 C 24.2990 0.20 1 84 . 105 LEU CD2 C 26.9460 0.20 1 85 . 108 ALA HB H 1.7170 0.02 1 86 . 108 ALA CB C 18.2980 0.20 1 87 . 109 ALA HB H 1.2630 0.02 1 88 . 109 ALA CB C 18.2980 0.20 1 89 . 110 VAL HG1 H 1.0530 0.02 2 90 . 110 VAL HG2 H 0.5960 0.02 2 91 . 110 VAL CG1 C 23.0630 0.20 1 92 . 110 VAL CG2 C 21.8280 0.20 1 93 . 111 ALA HB H 1.5070 0.02 1 94 . 111 ALA CB C 16.3570 0.20 1 stop_ save_