data_15095 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of a Dodecapeptide from Alpha-Synuclein Bound with Synphilin-1 ; _BMRB_accession_number 15095 _BMRB_flat_file_name bmr15095.str _Entry_type new _Submission_date 2007-01-04 _Accession_date 2007-01-04 _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 Zhou Chen-Jie . . 2 Hu Hong-Yu . . 3 Lin Dong-Hai . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 65 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-05-25 update BMRB 'update entity name' 2010-01-26 update BMRB 'complete entry citation' 2009-09-29 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Interaction with synphilin-1 promotes inclusion formation of alpha-synuclein: mechanistic insights and pathological implication.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19762560 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Xie Yuan-Yuan . . 2 Zhou Chen-Jie . . 3 Zhou Zi-Ren . . 4 Hong Jing . . 5 Che Mei-Xia . . 6 Fu Qing-Shan . . 7 Song Ai-Xin . . 8 Lin Dong-Hai . . 9 Hu Hong-Yu . . stop_ _Journal_abbreviation 'FASEB J.' _Journal_name_full 'The FASEB journal : official publication of the Federation of American Societies for Experimental Biology' _Journal_volume 24 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 196 _Page_last 205 _Year 2010 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Alpha-Syn12 bound with Synphilin-1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Alpha-Syn12 $entity Synphilin-1 $Synphilin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic ? _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Alpha-Syn12 _Molecular_mass 1357.708 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence MDVFMKGLSKAK loop_ _Residue_seq_code _Residue_label 1 MET 2 ASP 3 VAL 4 PHE 5 MET 6 LYS 7 GLY 8 LEU 9 SER 10 LYS 11 ALA 12 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_Synphilin _Saveframe_category ligand _Mol_type non-polymer _Name_common "Synphilin (Synphilin-1)" _BMRB_code . _PDB_code Synphilin _Molecular_mass . _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic . _Details . 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 . . ? ? DOUB . . ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $entity . . . . . . 'The N-terminal 12 residues of alpha-synuclein' $Synphilin . . . . . . 'The middle part of Synphilin-1 fused with GB1' 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 _Details $entity 'chemical synthesis' . . . . . 'The N-terminal 12 residues of alpha-synuclein' $Synphilin 'recombinant technology' . . . . . 'The middle part of Synphilin-1 fused with GB1' 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 $entity 1 mM 'natural abundance' 'sodium phosphate' 20 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' $Synphilin 0.1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRDraw _Saveframe_category software _Name NMRDraw _Version 2.3 loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.110 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' 'chemical shift assignment' stop_ _Details . save_ save_ARIA _Saveframe_category software _Name ARIA _Version 2.0 loop_ _Vendor _Address _Electronic_address 'Linge, O'Donoghue and Nilges' . . stop_ loop_ _Task 'data analysis' 'structure solution' refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_nmr_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . 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_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 6.5 . pH 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 H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name Alpha-Syn12 _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 MET HA H 4.064 0.003 . 2 1 1 MET HB2 H 2.112 0.012 . 3 1 1 MET HG2 H 2.571 0.001 . 4 1 1 MET HG3 H 2.564 0.005 . 5 2 2 ASP H H 7.877 0.000 . 6 2 2 ASP HA H 4.700 0.007 . 7 2 2 ASP HB2 H 2.614 0.000 . 8 2 2 ASP HB3 H 2.553 0.010 . 9 3 3 VAL H H 8.209 0.005 . 10 3 3 VAL HA H 4.023 0.004 . 11 3 3 VAL HB H 2.013 0.004 . 12 3 3 VAL HG1 H 0.832 0.005 . 13 4 4 PHE H H 8.307 0.007 . 14 4 4 PHE HA H 4.611 0.004 . 15 4 4 PHE HB2 H 3.118 0.008 . 16 4 4 PHE HB3 H 3.057 0.007 . 17 4 4 PHE HD2 H 7.267 0.008 . 18 4 4 PHE HE2 H 7.348 0.008 . 19 4 4 PHE HZ H 7.298 0.011 . 20 5 5 MET H H 8.181 0.010 . 21 5 5 MET HA H 4.393 0.006 . 22 5 5 MET HB2 H 2.073 0.026 . 23 5 5 MET HB3 H 1.963 0.011 . 24 5 5 MET HG2 H 2.534 0.007 . 25 5 5 MET HG3 H 2.467 0.007 . 26 6 6 LYS H H 8.233 0.005 . 27 6 6 LYS HA H 4.209 0.005 . 28 6 6 LYS HB2 H 1.835 0.005 . 29 6 6 LYS HG2 H 1.467 0.000 . 30 6 6 LYS HD2 H 1.774 0.010 . 31 6 6 LYS HE2 H 2.996 0.000 . 32 6 6 LYS HE3 H 3.001 0.002 . 33 7 7 GLY H H 8.387 0.005 . 34 7 7 GLY HA2 H 3.938 0.006 . 35 7 7 GLY HA3 H 3.860 0.000 . 36 8 8 LEU H H 8.033 0.003 . 37 8 8 LEU HA H 4.385 0.005 . 38 8 8 LEU HB2 H 1.616 0.004 . 39 8 8 LEU HD1 H 0.915 0.007 . 40 8 8 LEU HD2 H 0.870 0.008 . 41 9 9 SER H H 8.294 0.007 . 42 9 9 SER HA H 4.423 0.010 . 43 9 9 SER HB2 H 3.845 0.003 . 44 10 10 LYS H H 8.306 0.006 . 45 10 10 LYS HA H 4.339 0.006 . 46 10 10 LYS HB2 H 1.850 0.009 . 47 10 10 LYS HG2 H 1.434 0.008 . 48 10 10 LYS HG3 H 1.392 0.002 . 49 10 10 LYS HD2 H 1.712 0.008 . 50 10 10 LYS HD3 H 1.696 0.006 . 51 10 10 LYS HE2 H 3.048 0.026 . 52 10 10 LYS HE3 H 2.992 0.003 . 53 11 11 ALA H H 8.301 0.001 . 54 11 11 ALA HA H 4.292 0.007 . 55 11 11 ALA HB H 1.386 0.002 . 56 12 12 LYS H H 7.885 0.005 . 57 12 12 LYS HA H 4.124 0.004 . 58 12 12 LYS HB2 H 1.805 0.007 . 59 12 12 LYS HB3 H 1.808 0.000 . 60 12 12 LYS HG2 H 1.404 0.009 . 61 12 12 LYS HG3 H 1.391 0.004 . 62 12 12 LYS HD2 H 1.702 0.006 . 63 12 12 LYS HD3 H 1.686 0.006 . 64 12 12 LYS HE2 H 3.001 0.002 . 65 12 12 LYS HE3 H 2.985 0.009 . stop_ save_