data_36062 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; N-terminal Zinc Finger of Synaptotagmin-like Protein 4 ; _BMRB_accession_number 36062 _BMRB_flat_file_name bmr36062.str _Entry_type original _Submission_date 2017-02-23 _Accession_date 2017-10-23 _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 Miyamoto K. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 53 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-02-13 update BMRB 'update entry citation' 2017-10-27 original author 'original release' stop_ _Original_release_date 2017-10-23 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; The unique N-terminal zinc finger of Synaptotagmin-like protein 4 reveals FYVE structure ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28906046 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Miyamoto K. . . 2 Nakatani A. . . 3 Saito K. . . stop_ _Journal_abbreviation 'Protein Sci.' _Journal_volume 26 _Journal_issue 12 _Journal_ASTM PRCIEI _Journal_ISSN 1469-896X _Journal_CSD 0795 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2451 _Page_last 2457 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Synaptotagmin-like protein 4' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 entity_ZN_1 $entity_ZN entity_ZN_2 $entity_ZN stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Synaptotagmin-like protein 4' _Molecular_mass 6040.966 _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 53 _Mol_residue_sequence ; SDRTCARCQESLGRLSPKTN TCRGCNHLVCRDCRIQESNG TWRCKVCAKEIEL ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 SER 2 2 ASP 3 3 ARG 4 4 THR 5 5 CYS 6 6 ALA 7 7 ARG 8 8 CYS 9 9 GLN 10 10 GLU 11 11 SER 12 12 LEU 13 13 GLY 14 14 ARG 15 15 LEU 16 16 SER 17 17 PRO 18 18 LYS 19 19 THR 20 20 ASN 21 21 THR 22 22 CYS 23 23 ARG 24 24 GLY 25 25 CYS 26 26 ASN 27 27 HIS 28 28 LEU 29 29 VAL 30 30 CYS 31 31 ARG 32 32 ASP 33 33 CYS 34 34 ARG 35 35 ILE 36 36 GLN 37 37 GLU 38 38 SER 39 39 ASN 40 40 GLY 41 41 THR 42 42 TRP 43 43 ARG 44 44 CYS 45 45 LYS 46 46 VAL 47 47 CYS 48 48 ALA 49 49 LYS 50 50 GLU 51 51 ILE 52 52 GLU 53 53 LEU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 'ZINC ION' _BMRB_code ZN _PDB_code ZN _Molecular_mass 65.409 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons ZN ZN ZN . 2 . ? 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 $entity_1 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '20 mM d11 Tris-HCl, 50 mM NaCl, 1 mM d10 1,4-DL-dithiothreitol, 50 uM ZnCl2, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' 1,4-DL-dithiothreitol 1 mM [U-2H] NaCl 50 mM 'natural abundance' Tris-HCl 20 mM [U-2H] ZnCl2 50 uM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NMRVIEW _Version . loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 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 'ionic strength' 250 . mM pH 6.9 . pH pressure 1 . atm temperature 293 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 0.000 internal direct . . . 1.0 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '3D NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _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 2 2 ASP HA H 4.334 0.03 1 2 3 3 ARG HA H 4.219 0.03 1 3 4 4 THR HA H 4.63 0.03 1 4 5 5 CYS HA H 4.01 0.03 1 5 6 6 ALA HA H 4.22 0.03 1 6 7 7 ARG HA H 4.34 0.03 1 7 8 8 CYS HA H 4.31 0.03 1 8 9 9 GLN HA H 4.67 0.03 1 9 10 10 GLU HA H 4.78 0.03 1 10 11 11 SER HA H 4.45 0.03 1 11 12 12 LEU HA H 4.201 0.03 1 12 13 13 GLY HA2 H 3.992 0.03 2 13 13 13 GLY HA3 H 3.992 0.03 2 14 14 14 ARG HA H 4.19 0.03 1 15 15 15 LEU HA H 4.211 0.03 1 16 16 16 SER HA H 4.633 0.03 1 17 17 17 PRO HA H 4.19 0.03 1 18 18 18 LYS HA H 4.56 0.03 1 19 19 19 THR HA H 4.89 0.03 1 20 20 20 ASN HA H 4.78 0.03 1 21 21 21 THR HA H 4.45 0.03 1 22 22 22 CYS HA H 4.57 0.03 1 23 23 23 ARG HA H 4.16 0.03 1 24 24 24 GLY HA2 H 3.98 0.03 2 25 24 24 GLY HA3 H 3.98 0.03 2 26 25 25 CYS HA H 4.42 0.03 1 27 26 26 ASN HA H 4.12 0.03 1 28 27 27 HIS HA H 4.75 0.03 1 29 28 28 LEU HA H 4.66 0.03 1 30 29 29 VAL HA H 4.98 0.03 1 31 30 30 CYS HA H 4.02 0.03 1 32 32 32 ASP HA H 4.31 0.03 1 33 33 33 CYS HA H 4.33 0.03 1 34 34 34 ARG HA H 4.42 0.03 1 35 35 35 ILE HA H 4.66 0.03 1 36 36 36 GLN HA H 4.30 0.03 1 37 37 37 GLU HA H 4.56 0.03 1 38 38 38 SER HA H 4.32 0.03 1 39 39 39 ASN HA H 4.211 0.03 1 40 40 40 GLY HA2 H 4.22 0.03 2 41 40 40 GLY HA3 H 4.22 0.03 2 42 41 41 THR HA H 4.35 0.03 1 43 42 42 TRP HA H 4.91 0.03 1 44 43 43 ARG HA H 4.56 0.03 1 45 44 44 CYS HA H 4.82 0.03 1 46 45 45 LYS HA H 3.56 0.03 1 47 46 46 VAL HA H 3.98 0.03 1 48 47 47 CYS HA H 4.16 0.03 1 49 48 48 ALA HA H 4.65 0.03 1 50 49 49 LYS HA H 4.34 0.03 1 51 50 50 GLU HA H 4.10 0.03 1 52 51 51 ILE HA H 3.98 0.03 1 53 52 52 GLU HA H 3.87 0.03 1 stop_ save_