data_25022 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Polyglutamine binding peptide 1 (QBP1) ; _BMRB_accession_number 25022 _BMRB_flat_file_name bmr25022.str _Entry_type original _Submission_date 2014-06-16 _Accession_date 2014-06-16 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Chemical Shift data for QBP1 and a scrambled variant' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Laurents Douglas V. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 69 "13C chemical shifts" 44 "15N chemical shifts" 11 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-09-18 original author . stop_ _Original_release_date 2014-09-18 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR spectroscopy reveals a preferred conformation with a defined hydrophobic cluster for polyglutamine binding peptide 1.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25009140 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ramos-Martin Francisco . . 2 Hervas Ruben . . 3 Carrion-Vazquez Mariano . . 4 Laurents Douglas V. . stop_ _Journal_abbreviation 'Arch. Biochem. Biophys.' _Journal_name_full 'Archives of biochemistry and biophysics' _Journal_volume 558 _Journal_issue . _Journal_ISSN 1096-0384 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 104 _Page_last 110 _Year 2014 _Details . loop_ _Keyword 'Protein misfolding & aggregation' 'CAG-expansion diseasees' NMR 'Amyloid Inhibitor' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Polyglutamine binding peptide 1 (QBP1)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Polyglutamine binding peptide 1 (QBP1)' $Polyglutamine_binding_peptide_1 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_Polyglutamine_binding_peptide_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Polyglutamine_binding_peptide_1 _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function 'IN VIVO AND IN VITRO INHIBITOR OF POLYGLUTAMINE AGGREGATION AND TOXICITY' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence XWKWWPGIFX loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 0 ACE 2 1 TRP 3 2 LYS 4 3 TRP 5 4 TRP 6 5 PRO 7 6 GLY 8 7 ILE 9 8 PHE 10 9 AMD stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ACE _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'ACETYL GROUP' _BMRB_code ACE _PDB_code ACE _Standard_residue_derivative . _Molecular_mass 44.053 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? O O O . 0 . ? CH3 CH3 C . 0 . ? H H H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 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 DOUB C O ? ? SING C CH3 ? ? SING C H ? ? SING CH3 H1 ? ? SING CH3 H2 ? ? SING CH3 H3 ? ? stop_ save_ save_chem_comp_AMD _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common ASPARTYL-2'-DEOXY-ADENOSINE-5'-MONOPHOSPHATE _BMRB_code AMD _PDB_code AMD _Standard_residue_derivative . _Molecular_mass 446.309 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? O1P O1P O . 0 . ? O2P O2P O . 0 . ? O3P O3P O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C4 C4 C . 0 . ? N3 N3 N . 0 . ? C2 C2 C . 0 . ? N1 N1 N . 0 . ? C6 C6 C . 0 . ? N6 N6 N . 0 . ? C5 C5 C . 0 . ? N7 N7 N . 0 . ? C8 C8 C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? OD1 OD1 O . 0 . ? OD2 OD2 O . 0 . ? C C C . 0 . ? O O O . 0 . ? HOP2 HOP2 H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? H4' H4' H . 0 . ? H1' H1' H . 0 . ? H2 H2 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H8 H8 H . 0 . ? H2'1 H2'1 H . 0 . ? H2'2 H2'2 H . 0 . ? H3' H3' H . 0 . ? HO'3 HO'3 H . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HD2 HD2 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 DOUB P O1P ? ? SING P O2P ? ? SING P O3P ? ? SING P O5' ? ? SING O2P HOP2 ? ? SING O3P C ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C1' N9 ? ? SING C1' C2' ? ? SING C1' H1' ? ? SING N9 C4 ? ? SING N9 C8 ? ? SING C4 N3 ? ? DOUB C4 C5 ? ? DOUB N3 C2 ? ? SING C2 N1 ? ? SING C2 H2 ? ? DOUB N1 C6 ? ? SING C6 N6 ? ? SING C6 C5 ? ? SING N6 H61 ? ? SING N6 H62 ? ? SING C5 N7 ? ? DOUB N7 C8 ? ? SING C8 H8 ? ? SING C2' C3' ? ? SING C2' H2'1 ? ? SING C2' H2'2 ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING O3' HO'3 ? ? SING N CA ? ? SING N H ? ? SING N HN2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB1 ? ? SING CB HB2 ? ? DOUB CG OD1 ? ? SING CG OD2 ? ? SING OD2 HD2 ? ? DOUB C O ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Polyglutamine_binding_peptide_1 . . . . . . 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 $Polyglutamine_binding_peptide_1 'chemical synthesis' . . . . . 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 _Isotopic_labeling $Polyglutamine_binding_peptide_1 0.75 mM 'natural abundance' DSS 0.05 mM 'natural abundance' 'potassium dihydrogen phosphate' 10 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'QBP1 in D2O for 13C NMR spectra' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Polyglutamine_binding_peptide_1 0.75 mM 'natural abundance' DSS 0.05 mM 'natural abundance' 'potassium dihydrogen phosphate' 10 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details 'equipped with cyroprobe and z-gradients' save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details 'equipped with cyroprobe and z-gradients' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_aliphatic_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_aromatic_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 278 . K pH 6.9 0.05 pH pressure 1 . atm 'ionic strength' 0.02 . M stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 278 . K pH 6.9 0.05 pH pressure 1 . atm 'ionic strength' 0.02 . M 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 H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-15N HSQC' '2D 1H-13C HSQC aliphatic' '2D 1H-13C HSQC aromatic' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Polyglutamine binding peptide 1 (QBP1)' _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 0 1 ACE H H 1.98 0.01 1 2 0 1 ACE CM C 24.2 0.1 1 3 1 2 TRP H H 8.31 0.01 1 4 1 2 TRP HA H 4.46 0.01 1 5 1 2 TRP HB2 H 3.13 0.01 1 6 1 2 TRP HB3 H 3.13 0.01 1 7 1 2 TRP HD1 H 7.09 0.01 1 8 1 2 TRP HE1 H 10.06 0.01 1 9 1 2 TRP HE3 H 7.54 0.01 1 10 1 2 TRP HZ2 H 7.44 0.01 1 11 1 2 TRP HZ3 H 7.11 0.01 1 12 1 2 TRP HH2 H 7.22 0.01 1 13 1 2 TRP CA C 57.8 0.1 1 14 1 2 TRP CB C 29.4 0.1 1 15 1 2 TRP CD1 C 126.9 0.1 1 16 1 2 TRP CE3 C 120.9 0.1 1 17 1 2 TRP CZ2 C 114.4 0.1 1 18 1 2 TRP CZ3 C 121.9 0.1 1 19 1 2 TRP CH2 C 124.5 0.1 1 20 1 2 TRP N N 127.4 0.2 1 21 1 2 TRP NE1 N 129.0 0.2 1 22 2 3 LYS H H 7.97 0.01 1 23 2 3 LYS HA H 4.06 0.01 1 24 2 3 LYS HB2 H 1.44 0.01 2 25 2 3 LYS HB3 H 1.37 0.01 2 26 2 3 LYS HG2 H 1.02 0.01 2 27 2 3 LYS HG3 H 1.02 0.01 2 28 2 3 LYS HD2 H 1.47 0.01 2 29 2 3 LYS HD3 H 1.47 0.01 2 30 2 3 LYS HE2 H 2.73 0.01 2 31 2 3 LYS HE3 H 2.73 0.01 2 32 2 3 LYS CA C 55.6 0.1 1 33 2 3 LYS CB C 33.4 0.1 1 34 2 3 LYS CG C 24.3 0.1 1 35 2 3 LYS CD C 28.9 0.1 1 36 2 3 LYS CE C 41.7 0.1 1 37 2 3 LYS N N 123.4 0.2 1 38 3 4 TRP H H 7.87 0.01 1 39 3 4 TRP HA H 4.30 0.01 1 40 3 4 TRP HB2 H 3.06 0.01 1 41 3 4 TRP HB3 H 3.06 0.01 1 42 3 4 TRP HD1 H 7.19 0.01 1 43 3 4 TRP HE1 H 10.25 0.01 1 44 3 4 TRP HE3 H 7.54 0.01 1 45 3 4 TRP HZ2 H 7.44 0.01 1 46 3 4 TRP HZ3 H 7.11 0.01 1 47 3 4 TRP HH2 H 7.22 0.01 1 48 3 4 TRP CA C 55.6 0.1 1 49 3 4 TRP CB C 29.5 0.1 1 50 3 4 TRP CD1 C 127.0 0.1 1 51 3 4 TRP CE3 C 120.9 0.1 1 52 3 4 TRP CZ2 C 114.1 0.1 1 53 3 4 TRP CZ3 C 121.9 0.1 1 54 3 4 TRP CH2 C 124.5 0.1 1 55 3 4 TRP N N 121.5 0.2 1 56 3 4 TRP NE1 N 129.6 0.2 1 57 4 5 TRP H H 7.47 0.01 1 58 4 5 TRP HA H 4.66 0.01 1 59 4 5 TRP HB2 H 3.14 0.01 2 60 4 5 TRP HB3 H 2.97 0.01 2 61 4 5 TRP HD1 H 7.08 0.01 1 62 4 5 TRP HE1 H 10.22 0.01 1 63 4 5 TRP HE3 H 7.47 0.01 1 64 4 5 TRP HZ2 H 7.41 0.01 1 65 4 5 TRP HZ3 H 7.06 0.01 1 66 4 5 TRP HH2 H 7.18 0.01 1 67 4 5 TRP CA C 54.4 0.1 1 68 4 5 TRP CB C 29.0 0.1 1 69 4 5 TRP CD1 C 127.3 0.1 1 70 4 5 TRP CE3 C 120.7 0.1 1 71 4 5 TRP CZ2 C 114.5 0.1 1 72 4 5 TRP CZ3 C 121.1 0.1 1 73 4 5 TRP CH2 C 124.6 0.1 1 74 4 5 TRP N N 124.6 0.2 1 75 4 5 TRP NE1 N 124.6 0.2 1 76 5 6 PRO HA H 4.07 0.01 1 77 5 6 PRO HB2 H 2.20 0.01 2 78 5 6 PRO HB3 H 1.85 0.01 2 79 5 6 PRO HG2 H 1.91 0.01 1 80 5 6 PRO HG3 H 1.91 0.01 1 81 5 6 PRO HD2 H 3.46 0.01 1 82 5 6 PRO HD3 H 3.46 0.01 1 83 5 6 PRO CA C 63.4 0.1 1 84 5 6 PRO CB C 31.8 0.1 1 85 5 6 PRO CG C 27.2 0.1 1 86 5 6 PRO CD C 50.5 0.1 1 87 6 7 GLY H H 7.63 0.01 1 88 6 7 GLY HA2 H 3.72 0.01 2 89 6 7 GLY HA3 H 3.59 0.01 2 90 6 7 GLY CA C 44.7 0.1 1 91 6 7 GLY N N 107.6 0.2 1 92 7 8 ILE H H 7.74 0.01 1 93 7 8 ILE HA H 3.90 0.01 1 94 7 8 ILE HB H 1.47 0.01 1 95 7 8 ILE HG12 H 1.13 0.01 2 96 7 8 ILE HG13 H 0.94 0.01 2 97 7 8 ILE HG2 H 0.60 0.01 1 98 7 8 ILE HD1 H 0.66 0.01 1 99 7 8 ILE CA C 61.6 0.1 1 100 7 8 ILE CB C 38.3 0.1 1 101 7 8 ILE CG1 C 27.2 0.1 1 102 7 8 ILE CG2 C 16.8 0.1 1 103 7 8 ILE CD1 C 13.0 0.1 1 104 7 8 ILE N N 119.7 0.2 1 105 8 9 PHE H H 8.31 0.01 1 106 8 9 PHE HA H 4.60 0.01 1 107 8 9 PHE HB2 H 3.19 0.01 2 108 8 9 PHE HB3 H 2.94 0.01 2 109 8 9 PHE HD1 H 7.24 0.01 3 110 8 9 PHE HD2 H 7.24 0.01 3 111 8 9 PHE HE1 H 7.32 0.01 3 112 8 9 PHE HE2 H 7.32 0.01 3 113 8 9 PHE HZ H 7.27 0.01 1 114 8 9 PHE CA C 57.3 0.1 1 115 8 9 PHE CB C 39.3 0.1 1 116 8 9 PHE CD1 C 131.7 0.1 3 117 8 9 PHE CD2 C 131.7 0.1 3 118 8 9 PHE CE1 C 131.4 0.1 3 119 8 9 PHE CE2 C 131.4 0.1 3 120 8 9 PHE CZ C 129.8 0.1 1 121 8 9 PHE N N 123.4 0.2 1 122 9 10 AMD H H 7.43 0.01 2 123 9 10 AMD HN2 H 7.20 0.01 2 124 9 10 AMD N N 108.8 0.2 1 stop_ save_