data_10001 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; A high resolution structure of mastoparan-X strongly bound to lipid-bilayer membrane determined by solid-state NMR ; _BMRB_accession_number 10001 _BMRB_flat_file_name bmr10001.str _Entry_type original _Submission_date 2005-07-31 _Accession_date 2005-08-01 _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 Akutsu Hideo . . 2 Fujiwara Toshimichi . . 3 Todokoro Yasuto . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 73 "15N chemical shifts" 20 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-07-15 update BMRB 'C-terminal a.a. is LEUCINE AMIDE' 2007-11-14 update BMRB 'complete entry citation' 2006-06-28 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 6214 'Mastopran X in the other condition' stop_ _Original_release_date 2015-09-03 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure of Tightly Membrane-Bound Mastoparan-X, a G-protein-Activating Peptide, Determined by Solid-State NMR ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16714348 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Todokoro Yasuto . . 2 Yumen Ikuko . . 3 Fukushima Kei . . 4 Kang S.-W. . . 5 Park J.-S. . . 6 Kohno Toshiyuki . . 7 Wakamatsu Kaori . . 8 Akutsu Hideo . . 9 Fujiwara Toshimichi . . stop_ _Journal_abbreviation 'Biophys. J.' _Journal_name_full 'Biophys. Journal' _Journal_volume 91 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1368 _Page_last 1379 _Year 2006 _Details . loop_ _Keyword 3D-structure Amidation 'MASTOPARAN X' MP-X 'Mast cell degranulation' Venom 'membrane bound' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_citation_2 _Saveframe_category citation _Citation_full . _Citation_title ; Chemical shift referencing in MAS solid state NMR. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 12810033 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Corey Morcombe R. . 2 Kurt Zilm W. . stop_ _Journal_abbreviation 'J. Magn. Reson.' _Journal_name_full 'Journal of Magnetic Resonance' _Journal_volume 162 _Journal_issue 2 _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 479 _Page_last 486 _Year 2003 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name mastoparan-X _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label MP-X $MP-X stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_MP-X _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common MP-X _Molecular_mass 1556 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence ; INWKGIAAMAKKLX ; loop_ _Residue_seq_code _Residue_label 1 ILE 2 ASN 3 TRP 4 LYS 5 GLY 6 ILE 7 ALA 8 ALA 9 MET 10 ALA 11 LYS 12 LYS 13 LEU 14 NLW stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_NLW _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common L-leucinamide _BMRB_code NLW _PDB_code NLW _Standard_residue_derivative . _Molecular_mass 130.188 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CD2 CD2 C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? CB CB C . 0 . ? CA CA C . 0 . ? N N N . 0 . ? C C C . 0 . ? O O O . 0 . ? NH2 NH2 N . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H8 H8 H . 0 . ? H9 H9 H . 0 . ? H10 H10 H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H14 H14 H . 0 . ? H15 H15 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 CD1 CG ? ? SING CG CD2 ? ? SING CG CB ? ? SING CB CA ? ? SING N CA ? ? SING CA C ? ? SING C NH2 ? ? DOUB C O ? ? SING CD2 H1 ? ? SING CD2 H2 ? ? SING CD2 H3 ? ? SING CG H4 ? ? SING CD1 H5 ? ? SING CD1 H6 ? ? SING CD1 H7 ? ? SING CB H8 ? ? SING CB H9 ? ? SING CA H10 ? ? SING N H11 ? ? SING N H12 ? ? SING NH2 H14 ? ? SING NH2 H15 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $MP-X wasps 7448 Eukaryota Metazoa Vespa simillima 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_name _Details $MP-X 'recombinant technology' . Escherichia coli 'BL21 Star (DE3)' PLASMID pUBK19 ; MP-X was overexpressed as a recombinant fusion protein with Saccharomyces cerevisiae ubiquitin. ; stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solid _Details 'Mastoparan-X was bound with liposome (DPPC:DPPG=4:1).' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MP-X 5 mg '[U-95% 13C; U-95% 15N]' liposome 50 mg . stop_ save_ ############################ # Computer software used # ############################ save_Felix2000 _Saveframe_category software _Name Felix2000 _Version 2000 loop_ _Vendor _Address _Electronic_address 'Accelrys Inc.' . . stop_ loop_ _Task assignment stop_ _Details . save_ save_spinsight _Saveframe_category software _Name spinsight _Version 4.3.2 loop_ _Vendor _Address _Electronic_address VARIAN . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_CMX600infinity _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model CMX _Field_strength 600 _Details . save_ save_CMX500infinity _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model CMX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_N-CA-CO_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D N-CA-CO' _Sample_label $sample_1 save_ save_3D_Ni-COi+1-CAi+1_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D Ni-COi+1-CAi+1' _Sample_label $sample_1 save_ save_2D_RFDR_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D RFDR' _Sample_label $sample_1 save_ save_2D_SPCz5_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D SPCz5' _Sample_label $sample_1 save_ save_2D_(CACB)i+1-(COCA)i_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D (CACB)i+1-(COCA)i' _Sample_label $sample_1 save_ save_2D_Ni-(COCA)i+1_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D Ni-(COCA)i+1' _Sample_label $sample_1 save_ save_2D_N-CA_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D N-CA' _Sample_label $sample_1 save_ save_2D_Ni-(COCACB)i+1_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D Ni-(COCACB)i+1' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.4 0.1 pH temperature 253 0.1 K stop_ save_ save_condition_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.4 0.1 pH temperature 283 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_ref_1 _Saveframe_category chemical_shift_reference _Details ; The 13C chemical shift was referenced to the methyl signal of hexamethyl benzene resonating at 19.2 ppm which gives chemical shift relative to DSS (2, 2- dimethylsilapentane-5-sulfonic acid) (Morcombe and Zilm, 2003). The 15N chemical shift reference was computed from the ratios of resonance frequencies in the IUPAC recommendations. ; 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 0.00 na indirect . . . 0.251449530 DSS N 15 'methyl protons' ppm 0.00 na 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_mpx_assign _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $spinsight stop_ loop_ _Experiment_label '3D N-CA-CO' '3D Ni-COi+1-CAi+1' '2D RFDR' '2D SPCz5' '2D (CACB)i+1-(COCA)i' '2D Ni-(COCA)i+1' '2D N-CA' '2D Ni-(COCACB)i+1' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $ref_1 _Mol_system_component_name MP-X _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 ILE C C 172.8 0.5 1 2 1 1 ILE CA C 59.2 0.6 1 3 1 1 ILE CB C 37.5 0.6 1 4 1 1 ILE CD1 C 12.9 0.4 5 5 1 1 ILE CG1 C 27.5 0.5 1 6 1 1 ILE CG2 C 15.7 0.4 1 7 1 1 ILE N N 36.9 0.5 1 8 2 2 ASN C C 175.1 0.4 1 9 2 2 ASN CA C 50.6 0.4 1 10 2 2 ASN CB C 37.1 0.5 1 11 2 2 ASN CG C 178.5 0.5 1 12 2 2 ASN N N 126.5 0.9 1 13 2 2 ASN ND2 N 111.6 2.0 1 14 3 3 TRP C C 178.1 0.5 1 15 3 3 TRP CA C 59.5 0.6 1 16 3 3 TRP CB C 31.9 0.6 1 17 3 3 TRP CD1 C 128.2 0.7 1 18 3 3 TRP CD2 C 128.8 0.6 1 19 3 3 TRP CE2 C 140.2 0.4 1 20 3 3 TRP CE3 C 120.2 0.9 1 21 3 3 TRP CG C 109.4 0.6 1 22 3 3 TRP CH2 C 123.4 0.6 1 23 3 3 TRP CZ2 C 114.1 0.6 1 24 3 3 TRP CZ3 C 120.9 0.7 1 25 3 3 TRP N N 125.6 0.7 1 26 3 3 TRP NE1 N 131.9 0.8 1 27 4 4 LYS C C 178.9 0.5 1 28 4 4 LYS CA C 59.9 0.6 1 29 4 4 LYS CB C 32.4 0.6 1 30 4 4 LYS CD C 30.4 1.2 1 31 4 4 LYS CE C 41.8 0.5 5 32 4 4 LYS CG C 27.5 0.4 1 33 4 4 LYS N N 116.7 0.8 1 34 4 4 LYS NZ N 31.7 0.8 5 35 5 5 GLY C C 174.9 0.4 1 36 5 5 GLY CA C 47.2 0.4 1 37 5 5 GLY N N 107.2 0.9 1 38 6 6 ILE C C 178.7 0.3 1 39 6 6 ILE CA C 65.5 0.4 1 40 6 6 ILE CB C 37.2 0.4 1 41 6 6 ILE CD1 C 12.9 0.4 5 42 6 6 ILE CG1 C 27.2 0.5 1 43 6 6 ILE CG2 C 17.9 0.3 1 44 6 6 ILE N N 122.1 0.6 1 45 7 7 ALA C C 178.1 0.6 1 46 7 7 ALA CA C 54.9 0.7 1 47 7 7 ALA CB C 18.1 0.6 1 48 7 7 ALA N N 122.1 0.8 1 49 8 8 ALA C C 180.2 0.5 1 50 8 8 ALA CA C 54.7 0.6 1 51 8 8 ALA CB C 17.9 0.7 1 52 8 8 ALA N N 121.0 0.6 1 53 9 9 MET C C 177.4 0.5 1 54 9 9 MET CA C 59.4 0.7 1 55 9 9 MET CB C 33.5 0.6 1 56 9 9 MET CE C 15.8 0.4 9 57 9 9 MET CG C 35.3 0.7 1 58 9 9 MET N N 118.1 0.7 1 59 10 10 ALA C C 179.1 0.4 1 60 10 10 ALA CA C 55.1 0.5 1 61 10 10 ALA CB C 18.0 0.5 1 62 10 10 ALA N N 121.2 0.6 1 63 11 11 LYS C C 178.1 0.5 1 64 11 11 LYS CA C 59.6 0.6 1 65 11 11 LYS CB C 31.6 0.5 1 66 11 11 LYS CD C 30.4 1.2 1 67 11 11 LYS CE C 41.8 0.5 5 68 11 11 LYS CG C 27.0 0.4 1 69 11 11 LYS N N 117.4 0.6 1 70 11 11 LYS NZ N 31.7 0.8 5 71 12 12 LYS C C 176.9 0.4 1 72 12 12 LYS CA C 56.9 0.7 1 73 12 12 LYS CB C 31.7 0.4 1 74 12 12 LYS CD C 30.4 1.2 1 75 12 12 LYS CE C 41.8 0.5 5 76 12 12 LYS CG C 27.0 0.4 1 77 12 12 LYS N N 117.8 0.8 1 78 12 12 LYS NZ N 31.7 0.8 5 79 13 13 LEU C C 176.2 0.6 1 80 13 13 LEU CA C 56.8 0.6 1 81 13 13 LEU CB C 43.6 0.5 1 82 13 13 LEU CD1 C 24.3 0.7 5 83 13 13 LEU CD2 C 23.3 0.7 5 84 13 13 LEU CG C 27.5 0.5 1 85 13 13 LEU N N 116.1 0.8 1 86 14 14 NLW C C 182.4 0.5 1 87 14 14 NLW CA C 55.9 0.6 1 88 14 14 NLW CB C 44.5 0.5 1 89 14 14 NLW CD1 C 24.3 0.7 5 90 14 14 NLW CD2 C 23.3 0.7 5 91 14 14 NLW CG C 27.1 0.5 1 92 14 14 NLW N N 115.0 1.0 1 93 14 14 NLW N2 N 106.0 1.0 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity 4,41 31,67,75 34,70,78 82,89 83,90 stop_ save_