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 ; 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_ _BMRB_accession_number 10001 _BMRB_flat_file_name bmr10001.str _Entry_type new _Submission_date 2005-07-31 _Accession_date 2005-08-01 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . 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_ 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 'MASTOPARAN X' MP-X 'membrane bound' 'Mast cell degranulation' Venom Amidation 3D-structure 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 CLE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_CLE _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common 'LEUCINE AMIDE' _BMRB_code . _PDB_code CLE _Standard_residue_derivative . _Molecular_mass 130.188 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 13:29:12 2009 ; 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 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? C C C . 0 . ? O O O . 0 . ? N2 N2 N . 0 . ? H2 H2 H . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG HG H . 0 . ? HD11 HD11 H . 0 . ? HD12 HD12 H . 0 . ? HD13 HD13 H . 0 . ? HD21 HD21 H . 0 . ? HD22 HD22 H . 0 . ? HD23 HD23 H . 0 . ? HN21 HN21 H . 0 . ? HN22 HN22 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 N CA SING N H2 N H2 SING N H N H SING CA CB CA CB SING CA C CA C SING CA HA CA HA SING CB CG CB CG SING CB HB2 CB HB2 SING CB HB3 CB HB3 SING CG CD1 CG CD1 SING CG CD2 CG CD2 SING CG HG CG HG SING CD1 HD11 CD1 HD11 SING CD1 HD12 CD1 HD12 SING CD1 HD13 CD1 HD13 SING CD2 HD21 CD2 HD21 SING CD2 HD22 CD2 HD22 SING CD2 HD23 CD2 HD23 DOUB C O C O SING C N2 C N2 SING N2 HN21 N2 HN21 SING N2 HN22 N2 HN22 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 6 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 CLE C C 182.4 0.5 1 87 14 14 CLE CA C 55.9 0.6 1 88 14 14 CLE CB C 44.5 0.5 1 89 14 14 CLE CD1 C 24.3 0.7 5 90 14 14 CLE CD2 C 23.3 0.7 5 91 14 14 CLE CG C 27.1 0.5 1 92 14 14 CLE N N 115.0 1.0 1 93 14 14 CLE 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_