data_11059 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Chemical shift assignment of PACAP27 bound to phospholipid membranes by magic angle spinning solid-state NMR ; _BMRB_accession_number 11059 _BMRB_flat_file_name bmr11059.str _Entry_type original _Submission_date 2008-11-25 _Accession_date 2008-11-25 _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 Komi Nobuyasu . . 2 Okawa Kayo . . 3 Tateishi Yukihiro . . 4 Shirakawa Masahiro . . 5 Fujiwara Toshimichi . . 6 Akutsu Hideo . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 131 "15N chemical shifts" 21 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-09-12 update BMRB 'update residue sequence: split 27 LEU_NH2' 2009-03-18 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 11058 'Chemical shift data for PACAP21 which is PACAP27's C-terminal truncated form bound to membranes' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural analysis of pituitary adenylate cyclase-activating polypeptides bound to phospholipid membranes by magic angle spinning solid-state NMR. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17996724 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Komi Nobuyasu . . 2 Okawa Kayo . . 3 Tateishi Yukihiro . . 4 Shirakawa Masahiro . . 5 Fujiwara Toshimichi . . 6 Akutsu Hideo . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_name_full 'Biochimica et Biophysica Acta' _Journal_volume 1768 _Journal_issue 12 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3001 _Page_last 3011 _Year 2007 _Details . loop_ _Keyword 'Extended conformation' Isotope-labeling 'Membrane-bound peptide' 'NMR signal assignment' PACAP27 'Pituitary hormone' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'pituitary adenylate cyclase-activating polypeptide (PACAP)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label PACAP27 $PACAP27 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_PACAP27 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PACAP27 _Molecular_mass 3146.4 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; HSDGIFTDSYSRYRKQMAVK KYLAAVLX ; loop_ _Residue_seq_code _Residue_label 1 HIS 2 SER 3 ASP 4 GLY 5 ILE 6 PHE 7 THR 8 ASP 9 SER 10 TYR 11 SER 12 ARG 13 TYR 14 ARG 15 LYS 16 GLN 17 MET 18 ALA 19 VAL 20 LYS 21 LYS 22 TYR 23 LEU 24 ALA 25 ALA 26 VAL 27 LEU 28 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-02-27 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 11058 PACAP21 71.43 21 100.00 100.00 1.02e-04 PDB 1GEA "Receptor-Bound Conformation Of Pacap21" 71.43 21 100.00 100.00 1.02e-04 PDB 2D2P "The Solution Structure Of Micelle-Bound Peptide" 96.43 39 100.00 100.00 1.54e-09 PDB 2JOD "Pac1-Rshort N-Terminal Ec Domain Pacap(6-38) Complex" 78.57 33 100.00 100.00 3.38e-05 DBJ BAA28355 "PACAP ligand precursor [Mus musculus]" 96.43 175 100.00 100.00 5.87e-09 DBJ BAC21153 "pituitary adenylate cyclase activating polypeptide, partial [Trachurus japonicus]" 96.43 38 100.00 100.00 1.73e-09 DBJ BAC21154 "pituitary adenylate cyclase activating polypeptide [Acipenser schrenckii]" 96.43 38 100.00 100.00 1.68e-09 DBJ BAC21155 "pituitary adenylate cyclase activating polypeptide [Dugesia japonica]" 96.43 38 100.00 100.00 1.97e-09 DBJ BAC21156 "pituitary adenylate cyclase activating polypeptide, partial [Hydra vulgaris]" 96.43 38 100.00 100.00 1.97e-09 EMBL CAA42962 "PACAP precursor [Homo sapiens]" 96.43 176 100.00 100.00 3.01e-09 EMBL CAA51705 "unnamed protein product [Oncorhynchus nerka]" 96.43 173 100.00 100.00 6.31e-09 EMBL CAA55684 "pituitary adenylate cyclase activating polypeptide [Clarias macrocephalus]" 96.43 195 100.00 100.00 4.23e-09 EMBL CAA56564 "pituitary adenylate cyclase activating polypeptide [Rattus rattus]" 96.43 175 100.00 100.00 6.17e-09 EMBL CAG10213 "unnamed protein product, partial [Tetraodon nigroviridis]" 96.43 173 100.00 100.00 6.69e-09 GB AAA31575 "pituitary adenylate cyclase activating polypeptide precursor [Ovis sp.]" 96.43 176 100.00 100.00 4.79e-09 GB AAA41791 "pituitary adenylate cyclase activating polypeptide precursor protein [Rattus norvegicus]" 96.43 175 100.00 100.00 5.93e-09 GB AAB20402 "pituitary adenylate cyclase-activating polypeptide, PACAP [Rana ridibunda=frogs, Peptide, 38 aa]" 96.43 38 100.00 100.00 1.59e-09 GB AAB21469 "pituitary adenylate cyclase activating polypeptide [Ovis aries]" 96.43 176 100.00 100.00 4.79e-09 GB AAB21470 "pituitary adenylate cyclase activating polypeptide [Homo sapiens]" 96.43 176 100.00 100.00 3.01e-09 PRF 2107317A "PACAP/somatoliberin-like peptide" 96.43 195 100.00 100.00 4.23e-09 REF NP_001001544 "pituitary adenylate cyclase-activating polypeptide precursor [Sus scrofa]" 96.43 176 100.00 100.00 5.72e-09 REF NP_001009776 "pituitary adenylate cyclase-activating polypeptide precursor [Ovis aries]" 96.43 176 100.00 100.00 4.79e-09 REF NP_001040020 "pituitary adenylate cyclase-activating polypeptide precursor [Bos taurus]" 96.43 176 100.00 100.00 5.45e-09 REF NP_001081947 "adenylate cyclase activating polypeptide 1 (pituitary) precursor [Xenopus laevis]" 96.43 171 100.00 100.00 5.91e-09 REF NP_001093203 "pituitary adenylate cyclase-activating polypeptide preproprotein [Homo sapiens]" 96.43 176 100.00 100.00 3.29e-09 SP O70176 "RecName: Full=Pituitary adenylate cyclase-activating polypeptide; Short=PACAP; Contains: RecName: Full=PACAP-related peptide; A" 96.43 175 100.00 100.00 5.87e-09 SP P0DJ95 "RecName: Full=Pituitary adenylate cyclase-activating polypeptide; Short=PACAP; Contains: RecName: Full=PACAP-related peptide; A" 96.43 56 100.00 100.00 2.26e-09 SP P13589 "RecName: Full=Pituitary adenylate cyclase-activating polypeptide; Short=PACAP; Contains: RecName: Full=PACAP-related peptide; A" 96.43 175 100.00 100.00 5.93e-09 SP P16613 "RecName: Full=Pituitary adenylate cyclase-activating polypeptide; Short=PACAP; Contains: RecName: Full=PACAP-related peptide; A" 96.43 176 100.00 100.00 4.79e-09 SP P18509 "RecName: Full=Pituitary adenylate cyclase-activating polypeptide; Short=PACAP; Contains: RecName: Full=PACAP-related peptide; A" 96.43 176 100.00 100.00 3.29e-09 TPG DAA15829 "TPA: pituitary adenylate cyclase-activating polypeptide [Bos taurus]" 96.43 176 100.00 100.00 5.45e-09 stop_ 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 $PACAP27 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 $PACAP27 'recombinant technology' . Escherichia coli BL21(DE3) pET21b stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type membrane _Details ; PACAP27 binded to DMPC bilayers that were used as membranes. The liposome with peptide was once dried and then hydorolyzed under 32% relative humidity. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $PACAP27 4 mg '[U-13C; U-15N]' DMPC 25.4 uM '[U-98% 2H]' stop_ save_ ############################ # Computer software used # ############################ save_Felix _Saveframe_category software _Name FELIX _Version 2002 loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Infinity-plus _Field_strength 500 _Details ; Static magnetic field was 11.74 T. Broadband double and triple resonance MAS probes for the sample rotors with 3.2 and 4 mm diameters were used. ; save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Infinity-plus _Field_strength 600 _Details ; Static magnetic field was 14.09 T. Broadband double and triple resonance MAS probes for the sample rotors with 3.2 and 4 mm diameters were used. ; save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Infinity-plus _Field_strength 700 _Details ; Static magnetic field was 16.44 T. Broadband double and triple resonance MAS probes for the sample rotors with 3.2 and 4 mm diameters were used. ; save_ ############################# # NMR applied experiments # ############################# save_2D_13C-13C_DARR_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR' _Sample_label $sample_1 save_ save_2D_13C-13C_RFDR_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C RFDR' _Sample_label $sample_1 save_ save_2D_13C-13C_SPC-5_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C SPC-5' _Sample_label $sample_1 save_ save_2D_15N-13C_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C' _Sample_label $sample_1 save_ save_2D_15N-13C_RFDR_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C RFDR' _Sample_label $sample_1 save_ save_2D_CA-CA_DARR_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D CA-CA DARR' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_233K _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pressure 1 . atm temperature 233 . K stop_ save_ save_sample_conditions_273K _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pressure 1 . atm temperature 273 . K stop_ save_ save_sample_conditions_213K _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pressure 1 . atm temperature 213 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_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 0.00 . indirect . . . 0.251449530 DSS N 15 'methyl protons' ppm 0.00 . 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 13C-13C DARR' '2D 13C-13C RFDR' '2D 13C-13C SPC-5' '2D 15N-13C' '2D 15N-13C RFDR' '2D CA-CA DARR' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_273K _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name PACAP27 _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 HIS C C 174 2 1 2 1 1 HIS CA C 55.6 1.5 1 3 1 1 HIS CB C 30 1 1 4 1 1 HIS CG C 130 1 1 5 1 1 HIS N N 38 1 1 6 2 2 SER C C 173 1.5 5 7 2 2 SER CA C 56 1.5 5 8 2 2 SER CB C 66 2 5 9 3 3 ASP C C 174 2 1 10 3 3 ASP CA C 53 1.5 1 11 3 3 ASP CB C 46 2 1 12 3 3 ASP CG C 178 2 5 13 3 3 ASP N N 122 1 1 14 4 4 GLY C C 171 1 1 15 4 4 GLY CA C 46 1.5 1 16 4 4 GLY N N 105 1 1 17 5 5 ILE C C 175 1.7 1 18 5 5 ILE CA C 59.5 1 1 19 5 5 ILE CB C 42 2 1 20 5 5 ILE CD1 C 15 1 1 21 5 5 ILE CG1 C 28 1 1 22 5 5 ILE CG2 C 18 1 1 23 5 5 ILE N N 124 2 1 24 6 6 PHE C C 174 2 1 25 6 6 PHE CA C 56 2.5 1 26 6 6 PHE CB C 43 1.5 1 27 6 6 PHE CD1 C 132 2 3 28 6 6 PHE CD2 C 132 2 3 29 6 6 PHE CG C 133 1 1 30 6 6 PHE CZ C 130 1 1 31 7 7 THR C C 170 1 1 32 7 7 THR CA C 59.5 1 1 33 7 7 THR CB C 72 1 1 34 7 7 THR CG2 C 19.5 1 1 35 7 7 THR N N 112 1 1 36 8 8 ASP C C 174 2 1 37 8 8 ASP CA C 53 1.5 1 38 8 8 ASP CB C 16 2 1 39 8 8 ASP CG C 178 1 5 40 9 9 SER C C 173 1.5 5 41 9 9 SER CA C 56 1.5 5 42 9 9 SER CB C 66 2 5 43 10 10 TYR C C 174 2 1 44 10 10 TYR CA C 56 1.5 5 45 10 10 TYR CB C 43 2 5 46 10 10 TYR CD1 C 132 2 3 47 10 10 TYR CD2 C 132 2 3 48 10 10 TYR CE1 C 117 2 5 49 10 10 TYR CE2 C 117 2 5 50 10 10 TYR CG C 129 2 5 51 10 10 TYR CZ C 158 2 5 52 10 10 TYR N N 122 2 1 53 11 11 SER C C 173 1.5 5 54 11 11 SER CA C 56 1.5 5 55 11 11 SER CB C 66 2 5 56 12 12 ARG C C 174 2 1 57 12 12 ARG CA C 55 1.5 1 58 12 12 ARG CB C 34 2 5 59 12 12 ARG CD C 43.5 2 5 60 12 12 ARG CG C 29.5 2 5 61 12 12 ARG CZ C 160 2 5 62 12 12 ARG N N 122 2 1 63 12 12 ARG NE N 85 2 5 64 13 13 TYR C C 174 2 1 65 13 13 TYR CA C 53 1.5 1 66 13 13 TYR CB C 41 1.5 1 67 13 13 TYR CD1 C 132 2 3 68 13 13 TYR CD2 C 132 2 3 69 13 13 TYR CE1 C 117 2 5 70 13 13 TYR CE2 C 117 2 5 71 13 13 TYR CG C 129 2 5 72 13 13 TYR CZ C 158 2 5 73 14 14 ARG C C 174 2 1 74 14 14 ARG CA C 55 1.5 1 75 14 14 ARG CB C 34 2 5 76 14 14 ARG CD C 43.5 2 5 77 14 14 ARG CG C 29.5 2 5 78 14 14 ARG CZ C 160 2 5 79 14 14 ARG NE N 85 2 5 80 15 15 LYS C C 174 2 1 81 15 15 LYS CA C 55 1.5 1 82 15 15 LYS CB C 36 2 5 83 15 15 LYS CD C 30 2 5 84 15 15 LYS CE C 42 2 5 85 15 15 LYS CG C 27 2 5 86 15 15 LYS NZ N 32 2 5 87 16 16 GLN C C 174 2 1 88 16 16 GLN CA C 55 1.3 1 89 16 16 GLN CB C 29 2 1 90 16 16 GLN CD C 179 1 1 91 16 16 GLN CG C 35 1 1 92 17 17 MET C C 174 2 1 93 17 17 MET CA C 54 1.5 1 94 18 18 ALA C C 175.6 1 5 95 18 18 ALA CA C 51 1.5 1 96 18 18 ALA CB C 24 1.5 5 97 18 18 ALA N N 122 1 1 98 19 19 VAL C C 175 1.7 1 99 19 19 VAL CA C 59.5 1 1 100 19 19 VAL CB C 35 1.5 5 101 19 19 VAL CG1 C 21 1 2 102 19 19 VAL CG2 C 21 1 2 103 19 19 VAL N N 120 2 1 104 20 20 LYS C C 174 2 1 105 20 20 LYS CA C 54.5 2 1 106 20 20 LYS CB C 37 1 1 107 20 20 LYS CD C 30 2 5 108 20 20 LYS CE C 42 2 5 109 20 20 LYS CG C 27 2 5 110 20 20 LYS N N 125 2 1 111 20 20 LYS NZ N 32 2 5 112 21 21 LYS C C 174 2 1 113 21 21 LYS CA C 55 2 1 114 21 21 LYS CB C 36 2 5 115 21 21 LYS CD C 30 2 5 116 21 21 LYS CE C 42 2 5 117 21 21 LYS CG C 27 2 5 118 21 21 LYS N N 125 2 1 119 21 21 LYS NZ N 32 2 5 120 22 22 TYR C C 174 2 1 121 22 22 TYR CA C 56 1.5 5 122 22 22 TYR CB C 43 2 5 123 22 22 TYR CD1 C 132 2 3 124 22 22 TYR CD2 C 132 2 3 125 22 22 TYR CE1 C 117 2 5 126 22 22 TYR CE2 C 117 2 5 127 22 22 TYR CG C 129 2 5 128 22 22 TYR CZ C 158 2 5 129 23 23 LEU C C 174 2 1 130 23 23 LEU CA C 53 2 1 131 23 23 LEU CB C 46 2 1 132 23 23 LEU CG C 28 1 1 133 24 24 ALA C C 175.6 1 5 134 24 24 ALA CA C 51 1.5 1 135 24 24 ALA CB C 23 1.5 1 136 24 24 ALA N N 122 1 1 137 25 25 ALA C C 175.6 1 5 138 25 25 ALA CA C 50 1.5 1 139 25 25 ALA CB C 24 1.5 5 140 25 25 ALA N N 125 1 1 141 26 26 VAL C C 175 1.7 1 142 26 26 VAL CA C 60 1 1 143 26 26 VAL CB C 35 1.5 5 144 26 26 VAL CG1 C 21 1 2 145 26 26 VAL CG2 C 21 1 2 146 26 26 VAL N N 120 2 1 147 27 27 LEU C C 181 2 1 148 27 27 LEU CA C 55 2 1 149 27 27 LEU CB C 41 1.5 1 150 27 27 LEU CG C 28 1 1 151 27 27 LEU N N 125 2 1 152 27 28 NH2 N N 107 1 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity 6 '40,53' '7,41,54' '8,42,55' '12,39' '44,121' '45,122' '50,71,127' '48,49,69,70,125,126' '51,72,128' '58,75' '60,77' '59,76' '61,78' '63,79' '82,114' '85,109,117' '83,107,115' '84,108,116' '86,111,119' '94,133,137' '96,139' '100,143' stop_ save_