data_11058 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Chemical shift assignment of PACAP21 bound to phospholipid membranes by magic angle spinning solid-state NMR ; _BMRB_accession_number 11058 _BMRB_flat_file_name bmr11058.str _Entry_type new _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" 104 "15N chemical shifts" 15 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-03-18 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 11059 'Chemical shift data for PACAP27' 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 'Pituitary hormone' PACAP27 'Membrane-bound peptide' Isotope-labeling 'NMR signal assignment' 'Extended conformation' 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 PACAP21 $PACAP21 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_PACAP21 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PACAP21 _Molecular_mass 2522.9 _Mol_thiol_state 'not present' _Details ; PACAP(1-21)NH2 (PACAP21) is PACAP27's C-terminal truncated form bound to membranes. ; ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; HSDGIFTDSYSRYRKQMAVK X ; 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_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 11059 PACAP27 95.24 28 100.00 100.00 7.63e-05 PDB 1GEA "Receptor-Bound Conformation Of Pacap21" 95.24 21 100.00 100.00 1.19e-04 PDB 2D2P "The Solution Structure Of Micelle-Bound Peptide" 95.24 39 100.00 100.00 7.75e-05 PDB 2JOD "Pac1-Rshort N-Terminal Ec Domain Pacap(6-38) Complex" 71.43 33 100.00 100.00 1.01e+00 DBJ BAA28355 "PACAP ligand precursor [Mus musculus]" 95.24 175 100.00 100.00 1.91e-04 DBJ BAC21153 "pituitary adenylate cyclase activating polypeptide, partial [Trachurus japonicus]" 95.24 38 100.00 100.00 9.26e-05 DBJ BAC21154 "pituitary adenylate cyclase activating polypeptide [Acipenser schrenckii]" 95.24 38 100.00 100.00 9.07e-05 DBJ BAC21155 "pituitary adenylate cyclase activating polypeptide [Dugesia japonica]" 95.24 38 100.00 100.00 1.04e-04 DBJ BAC21156 "pituitary adenylate cyclase activating polypeptide, partial [Hydra vulgaris]" 95.24 38 100.00 100.00 1.04e-04 EMBL CAA42962 "PACAP precursor [Homo sapiens]" 95.24 176 100.00 100.00 4.91e-04 EMBL CAA51705 "unnamed protein product [Oncorhynchus nerka]" 95.24 173 100.00 100.00 1.79e-04 EMBL CAA55684 "pituitary adenylate cyclase activating polypeptide [Clarias macrocephalus]" 95.24 195 100.00 100.00 2.03e-04 EMBL CAA56564 "pituitary adenylate cyclase activating polypeptide [Rattus rattus]" 95.24 175 100.00 100.00 1.75e-04 EMBL CAG10213 "unnamed protein product, partial [Tetraodon nigroviridis]" 95.24 173 100.00 100.00 2.17e-04 GB AAA31575 "pituitary adenylate cyclase activating polypeptide precursor [Ovis sp.]" 95.24 176 100.00 100.00 1.67e-04 GB AAA41791 "pituitary adenylate cyclase activating polypeptide precursor protein [Rattus norvegicus]" 95.24 175 100.00 100.00 1.70e-04 GB AAB20402 "pituitary adenylate cyclase-activating polypeptide, PACAP [Rana ridibunda=frogs, Peptide, 38 aa]" 95.24 38 100.00 100.00 8.17e-05 GB AAB21469 "pituitary adenylate cyclase activating polypeptide [Ovis aries]" 95.24 176 100.00 100.00 1.67e-04 GB AAB21470 "pituitary adenylate cyclase activating polypeptide [Homo sapiens]" 95.24 176 100.00 100.00 4.91e-04 PRF 2107317A "PACAP/somatoliberin-like peptide" 95.24 195 100.00 100.00 2.03e-04 REF NP_001001544 "pituitary adenylate cyclase-activating polypeptide precursor [Sus scrofa]" 95.24 176 100.00 100.00 1.90e-04 REF NP_001009776 "pituitary adenylate cyclase-activating polypeptide precursor [Ovis aries]" 95.24 176 100.00 100.00 1.67e-04 REF NP_001040020 "pituitary adenylate cyclase-activating polypeptide precursor [Bos taurus]" 95.24 176 100.00 100.00 2.02e-04 REF NP_001081947 "adenylate cyclase activating polypeptide 1 (pituitary) precursor [Xenopus laevis]" 95.24 171 100.00 100.00 2.49e-03 REF NP_001093203 "pituitary adenylate cyclase-activating polypeptide preproprotein [Homo sapiens]" 95.24 176 100.00 100.00 5.94e-04 SP O70176 "RecName: Full=Pituitary adenylate cyclase-activating polypeptide; Short=PACAP; Contains: RecName: Full=PACAP-related peptide; A" 95.24 175 100.00 100.00 1.91e-04 SP P0DJ95 "RecName: Full=Pituitary adenylate cyclase-activating polypeptide; Short=PACAP; Contains: RecName: Full=PACAP-related peptide; A" 95.24 56 100.00 100.00 8.26e-05 SP P13589 "RecName: Full=Pituitary adenylate cyclase-activating polypeptide; Short=PACAP; Contains: RecName: Full=PACAP-related peptide; A" 95.24 175 100.00 100.00 1.70e-04 SP P16613 "RecName: Full=Pituitary adenylate cyclase-activating polypeptide; Short=PACAP; Contains: RecName: Full=PACAP-related peptide; A" 95.24 176 100.00 100.00 1.67e-04 SP P18509 "RecName: Full=Pituitary adenylate cyclase-activating polypeptide; Short=PACAP; Contains: RecName: Full=PACAP-related peptide; A" 95.24 176 100.00 100.00 5.94e-04 TPG DAA15829 "TPA: pituitary adenylate cyclase-activating polypeptide [Bos taurus]" 95.24 176 100.00 100.00 2.02e-04 stop_ save_ ###################### # Polymer residues # ###################### save_LYS_NH2 _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common L-LYSINAMIDE _Abbreviation_common LYS-NH2 _BMRB_code LYS_NH2 _PDB_code . _Standard_residue_derivative LYS loop_ _Mol_label _Residue_seq_code $PACAP21 21 stop_ _Molecular_mass . _Mol_paramagnetic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N . N . 0 . ? NT . N . 0 . ? CA . C . 0 . ? C . C . 0 . ? O . O . 0 . ? CB . C . 0 . ? CG . C . 0 . ? CD . C . 0 . ? CE . C . 0 . ? NZ . N . 1 . ? H . H . 0 . ? HA . H . 0 . ? HB2 . H . 0 . ? HB3 . H . 0 . ? HG2 . H . 0 . ? HG3 . H . 0 . ? HD2 . H . 0 . ? HD3 . H . 0 . ? HE2 . H . 0 . ? HE3 . H . 0 . ? HZ1 . H . 0 . ? HZ2 . H . 0 . ? HZ3 . H . 0 . ? HT1 . H . 0 . ? HT2 . 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 H . . SING CA C . . SING CA CB . . SING CA HA . . DOUB C O . . SING CB CG . . SING CB HB2 . . SING CB HB3 . . SING CG CD . . SING CG HG2 . . SING CG HG3 . . SING CD CE . . SING CD HD2 . . SING CD HD3 . . SING CE NZ . . SING CE HE2 . . SING CE HE3 . . SING NZ HZ1 . . SING NZ HZ2 . . SING NZ HZ3 . . SING NT C . . SING NT HT1 . . SING NT HT2 . . stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $PACAP21 . . . . . . 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 $PACAP21 '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 ; PACAP21 binded to DPPC/DPPG 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 $PACAP21 3.8 mg '[U-13C; U-15N]' DPPC 43.2 uM '[U-98% 2H]' DPPG 10.8 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_15N-13C_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C' _Sample_label $sample_1 save_ save_2D_15N-13C_DARR_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C DARR' _Sample_label $sample_1 save_ save_2D_(CACB)-CA_DARR_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D (CACB)-CA DARR' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_213K _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 213 . K pressure 1 . atm stop_ save_ save_sample_conditions_223K _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 223 . K pressure 1 . atm 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 n/a indirect . . . 0.251449530 DSS N 15 'methyl protons' ppm 0.00 n/a 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 15N-13C' '2D 15N-13C DARR' '2D (CACB)-CA DARR' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_213K _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name PACAP21 _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 1 1 3 1 1 HIS CB C 32 1.3 1 4 1 1 HIS CG C 131 1 1 5 1 1 HIS N N 32 1 1 6 2 2 SER C C 173 1.5 5 7 2 2 SER CA C 56 2 5 8 2 2 SER CB C 66 1.5 5 9 2 2 SER N N 112 2 5 10 3 3 ASP C C 174 2 1 11 3 3 ASP CA C 53 2.5 1 12 3 3 ASP CB C 45 2 1 13 3 3 ASP CG C 178 2 5 14 4 4 GLY C C 171 2 1 15 4 4 GLY CA C 45 1 1 16 4 4 GLY N N 108 1 1 17 5 5 ILE C C 174 2 1 18 5 5 ILE CA C 59 1.5 1 19 5 5 ILE CB C 42 1 1 20 5 5 ILE CD1 C 14 1 1 21 5 5 ILE CG1 C 29 1 1 22 5 5 ILE CG2 C 18 1 1 23 5 5 ILE N N 120 1 1 24 6 6 PHE C C 174 2 1 25 6 6 PHE CA C 56 2 1 26 6 6 PHE CB C 44 2 1 27 6 6 PHE CD1 C 133 2 3 28 6 6 PHE CD2 C 133 2 3 29 6 6 PHE CG C 133 1 1 30 6 6 PHE CZ C 128 1 1 31 6 6 PHE N N 126 1 1 32 7 7 THR C C 174 2 1 33 7 7 THR CA C 59.6 1.5 1 34 7 7 THR CB C 71 1.5 1 35 7 7 THR CG2 C 22 1 1 36 8 8 ASP C C 174 2 1 37 8 8 ASP CA C 53 2 1 38 8 8 ASP CB C 45 2 1 39 8 8 ASP CG C 178 2 5 40 8 8 ASP N N 122 1 1 41 9 9 SER C C 173 1.5 5 42 9 9 SER CA C 56 2 5 43 9 9 SER CB C 66 1.5 5 44 9 9 SER N N 112 2 5 45 10 10 TYR C C 174 2 1 46 10 10 TYR CA C 55 2.5 1 47 10 10 TYR CB C 44 2 5 48 10 10 TYR CD1 C 133 2 3 49 10 10 TYR CD2 C 133 2 3 50 10 10 TYR CE1 C 118 2 5 51 10 10 TYR CE2 C 118 2 5 52 10 10 TYR CG C 129 2 5 53 10 10 TYR CZ C 158 2 5 54 11 11 SER C C 173 1.5 5 55 11 11 SER CA C 56 2 5 56 11 11 SER CB C 66 1.5 5 57 11 11 SER N N 112 2 5 58 12 12 ARG C C 174 2 1 59 12 12 ARG CA C 54 1.5 1 60 12 12 ARG CB C 34 1.5 5 61 12 12 ARG CD C 44 2 5 62 12 12 ARG CG C 28 2 5 63 12 12 ARG CZ C 160 2 5 64 12 12 ARG NE N 82 2 5 65 13 13 TYR C C 174 2 1 66 13 13 TYR CA C 55 2.5 1 67 13 13 TYR CB C 44 2 5 68 13 13 TYR CD1 C 133 2 3 69 13 13 TYR CD2 C 133 2 3 70 13 13 TYR CE1 C 118 2 5 71 13 13 TYR CE2 C 118 2 5 72 13 13 TYR CG C 129 2 5 73 13 13 TYR CZ C 158 2 5 74 14 14 ARG C C 174 2 1 75 14 14 ARG CA C 54 1.5 1 76 14 14 ARG CB C 35 1.5 5 77 14 14 ARG CD C 44 2 5 78 14 14 ARG CG C 28 2 5 79 14 14 ARG CZ C 160 2 5 80 14 14 ARG NE N 82 1 5 81 15 15 LYS C C 174 2 1 82 15 15 LYS CA C 54 1.5 1 83 15 15 LYS CB C 36 1.5 1 84 15 15 LYS CD C 29 2 5 85 15 15 LYS CE C 42 2 5 86 15 15 LYS CG C 26 2 5 87 15 15 LYS NZ N 30 2 5 88 16 16 GLN C C 174 2 1 89 16 16 GLN CA C 54 1.5 1 90 16 16 GLN CB C 30 2 1 91 16 16 GLN CD C 179 1 1 92 16 16 GLN CG C 35 1 1 93 17 17 MET C C 174 2 1 94 17 17 MET CA C 54 1 1 95 17 17 MET CB C 35 4 1 96 18 18 ALA C C 175 1 1 97 18 18 ALA CA C 51 1.3 1 98 18 18 ALA CB C 23 1.5 1 99 19 19 VAL C C 174 2 1 100 19 19 VAL CA C 60.4 1.5 1 101 19 19 VAL CB C 35 2 1 102 19 19 VAL CG1 C 22 1 2 103 19 19 VAL CG2 C 22 1 2 104 19 19 VAL N N 122 1 1 105 20 20 LYS C C 174 2 1 106 20 20 LYS CA C 54 1.5 1 107 20 20 LYS CB C 36 1.5 1 108 20 20 LYS CD C 28 2 5 109 20 20 LYS CE C 42 2 5 110 20 20 LYS CG C 26 2 5 111 20 20 LYS N N 126 1 1 112 20 20 LYS NZ N 30 2 5 113 21 21 LYS_NH2 C C 180 2 1 114 21 21 LYS_NH2 CA C 53 1.5 1 115 21 21 LYS_NH2 CB C 36 1.5 1 116 21 21 LYS_NH2 CD C 28 2 5 117 21 21 LYS_NH2 CE C 42 2 5 118 21 21 LYS_NH2 CG C 26 2 5 119 21 21 LYS_NH2 NZ N 30 2 5 stop_ loop_ _Atom_shift_assign_ID_ambiguity 6 '41,54' '7,42,55' '8,43,56' '9,44,57' '13,39' '47,67' '52,72' '50,51,70,71' '53,73' '60,76' '62,78' '61,77' '63,79' '64,80' '86,110,118' '84,108,116' '85,109,117' '87,112,119' stop_ save_