data_34309 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Yeast V-ATPase transmembrane helix 7 NMR structure in DPC micelles ; _BMRB_accession_number 34309 _BMRB_flat_file_name bmr34309.str _Entry_type original _Submission_date 2018-08-24 _Accession_date 2018-08-24 _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 Zangger K. . . 2 Hohlweg W. . . 3 Wagner G. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 126 "13C chemical shifts" 4 "15N chemical shifts" 2 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-07-31 update BMRB 'update entry citation' 2018-09-06 original author 'original release' stop_ _Original_release_date 2018-09-04 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; A cation-Pi interaction in a transmembrane helix of vacuolar ATPase keeps the proton transporting arginine in a hydrophobic environment ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30209131 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hohlweg W. . . 2 Wagner-Lichtenegger G. . . 3 Hofbauer H. . . 4 Sarkleti F. . . 5 Setz M. . . 6 Gubensak N. . . 7 Lichtenegger S. . . 8 Falsone F. . . 9 Wolinski H. . . 10 Kosol S. . . 11 Oostenrbink C. . . 12 Kohlwein S. . . 13 Zangger K. . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 293 _Journal_issue 49 _Journal_ISSN 1083-351X _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 18977 _Page_last 18988 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'V-type proton ATPase subunit a, vacuolar isoform' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 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 entity_1 _Molecular_mass 2832.328 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; KKSHTASYLRLWALSLAHAQ LSSKK ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 LYS 3 SER 4 HIS 5 THR 6 ALA 7 SER 8 TYR 9 LEU 10 ARG 11 LEU 12 TRP 13 ALA 14 LEU 15 SER 16 LEU 17 ALA 18 HIS 19 ALA 20 GLN 21 LEU 22 SER 23 SER 24 LYS 25 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Gene_mnemonic $entity_1 "Baker's yeast" 4932 Eukaryota Fungi Saccharomyces cerevisiae 'VPH1, YOR270C' 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 'recombinant technology' . synthetic construct . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelle _Details ; 100 mM [U-99% 2H] Deuterated DPC, 50 mM potassium phosphate, 0.02 % sodium azide, 1 mM 13C and 15N labeled aminoacids 8 and 12 TM7 peptide, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'Deuterated DPC' 100 mM '[U-99% 2H]' 'potassium phosphate' 50 mM none 'sodium azide' 0.02 % none $entity_1 1 mM '13C and 15N labeled aminoacids 8 and 12' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_3D_NOESY-N-HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D NOESY-N-HSQC' _Sample_label $sample_1 save_ save_2D_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HSQC' _Sample_label $sample_1 save_ save_3D_NOESY_C-HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D NOESY C-HSQC' _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' 50 . mM pH 5.0 . pH pressure 1 . atm temperature 298 . 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 '2D NOESY' '2D TOCSY' '3D NOESY-N-HSQC' '2D HSQC' '3D NOESY C-HSQC' 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 1 1 LYS HA H 3.9793 0.0000 1 2 1 1 LYS HB2 H 1.8090 0.0000 2 3 1 1 LYS HB3 H 1.8910 0.0000 2 4 1 1 LYS HG2 H 1.5630 0.0000 2 5 1 1 LYS HE2 H 2.9959 0.0000 2 6 2 2 LYS H H 8.1961 0.0000 1 7 2 2 LYS HA H 4.2590 0.0000 1 8 2 2 LYS HB2 H 1.7160 0.0000 2 9 2 2 LYS HB3 H 1.8780 0.0000 2 10 2 2 LYS HG2 H 1.3676 0.0000 2 11 2 2 LYS HE2 H 2.9039 0.0000 2 12 2 2 LYS HZ H 7.9180 0.0000 1 13 3 3 SER H H 8.4755 0.0000 1 14 3 3 SER HA H 4.3434 0.0000 1 15 3 3 SER HB2 H 3.7776 0.0000 2 16 4 4 HIS H H 8.8208 0.0000 1 17 4 4 HIS HA H 4.6534 0.0000 1 18 4 4 HIS HB2 H 3.1623 0.0000 2 19 4 4 HIS HB3 H 3.2640 0.0000 2 20 4 4 HIS HD2 H 7.1715 0.0000 1 21 4 4 HIS HE1 H 8.4620 0.0000 1 22 5 5 THR H H 8.2186 0.0000 1 23 5 5 THR HA H 4.0196 0.0000 1 24 5 5 THR HB H 4.0963 0.0000 1 25 5 5 THR HG1 H 1.2190 0.0000 1 26 5 5 THR HG2 H 1.1394 0.0000 1 27 6 6 ALA H H 8.7756 0.0000 1 28 6 6 ALA HA H 4.0251 0.0000 1 29 6 6 ALA HB H 1.3929 0.0000 1 30 7 7 SER H H 8.1539 0.0000 1 31 7 7 SER HA H 4.1734 0.0000 1 32 7 7 SER HB2 H 4.9602 0.0000 2 33 8 8 TYR H H 8.1234 0.0000 1 34 8 8 TYR HA H 4.1916 0.0000 1 35 8 8 TYR HB2 H 2.9750 0.0000 2 36 8 8 TYR HB3 H 3.0970 0.0000 2 37 8 8 TYR HD1 H 7.0530 0.0000 3 38 8 8 TYR HD2 H 6.9734 0.0000 3 39 8 8 TYR HE1 H 6.6795 0.0000 3 40 9 9 LEU H H 8.0694 0.0000 1 41 9 9 LEU HA H 4.0852 0.0000 1 42 9 9 LEU HB2 H 1.7665 0.0000 2 43 9 9 LEU HG H 1.4966 0.0000 1 44 9 9 LEU HD1 H 0.9450 0.0000 2 45 9 9 LEU HD2 H 0.8805 0.0000 2 46 10 10 ARG H H 8.0288 0.0000 1 47 10 10 ARG HA H 3.8473 0.0000 1 48 10 10 ARG HB2 H 1.8760 0.0000 2 49 10 10 ARG HB3 H 2.0180 0.0000 2 50 10 10 ARG HG2 H 1.5388 0.0000 2 51 10 10 ARG HD2 H 3.1794 0.0000 2 52 10 10 ARG HE H 7.5575 0.0000 1 53 10 10 ARG HH11 H 7.0244 0.0000 9 54 10 10 ARG CA C 55.5081 0.0000 1 55 10 10 ARG CB C 33.6787 0.0000 1 56 10 10 ARG CG C 31.5635 0.0000 1 57 10 10 ARG CD C 42.7307 0.0000 1 58 10 10 ARG N N 119.3146 0.0000 1 59 10 10 ARG NE N 84.1312 0.0000 1 60 11 11 LEU H H 7.7240 0.0000 1 61 11 11 LEU HA H 3.9794 0.0000 1 62 11 11 LEU HB2 H 1.6337 0.0000 2 63 11 11 LEU HB3 H 1.8370 0.0000 2 64 11 11 LEU HG H 1.6545 0.0000 1 65 11 11 LEU HD1 H 0.9011 0.0000 2 66 11 11 LEU HD2 H 0.8186 0.0000 2 67 12 12 TRP H H 8.3308 0.0000 1 68 12 12 TRP HA H 4.1949 0.0000 1 69 12 12 TRP HB2 H 3.2183 0.0000 2 70 12 12 TRP HB3 H 3.3950 0.0000 2 71 12 12 TRP HD1 H 7.0915 0.0000 1 72 12 12 TRP HE1 H 10.3796 0.0000 1 73 12 12 TRP HE3 H 7.4391 0.0000 1 74 12 12 TRP HZ2 H 7.3242 0.0000 1 75 12 12 TRP HZ3 H 6.8697 0.0000 1 76 12 12 TRP HH2 H 6.9454 0.0000 1 77 13 13 ALA H H 8.5351 0.0000 1 78 13 13 ALA HA H 3.6027 0.0000 1 79 13 13 ALA HB H 1.4229 0.0000 1 80 14 14 LEU H H 8.1422 0.0000 1 81 14 14 LEU HB2 H 1.3430 0.0000 2 82 14 14 LEU HD1 H 0.9045 0.0000 2 83 14 14 LEU HD2 H 0.8199 0.0000 2 84 15 15 SER H H 7.9157 0.0000 1 85 15 15 SER HA H 4.2009 0.0000 1 86 15 15 SER HB2 H 3.8981 0.0000 2 87 16 16 LEU H H 7.8207 0.0000 1 88 16 16 LEU HA H 3.9810 0.0000 1 89 16 16 LEU HB2 H 1.4014 0.0000 2 90 16 16 LEU HD1 H 0.6778 0.0000 2 91 16 16 LEU HD2 H 0.6117 0.0000 2 92 17 17 ALA H H 8.0104 0.0000 1 93 17 17 ALA HA H 3.9081 0.0000 1 94 17 17 ALA HB H 1.3141 0.0000 1 95 18 18 HIS H H 8.1489 0.0000 1 96 18 18 HIS HA H 4.3427 0.0000 1 97 18 18 HIS HB2 H 3.2453 0.0000 2 98 18 18 HIS HB3 H 3.3210 0.0000 2 99 18 18 HIS HD2 H 7.2138 0.0000 1 100 18 18 HIS HE1 H 8.5293 0.0000 1 101 19 19 ALA H H 7.9077 0.0000 1 102 19 19 ALA HA H 4.1466 0.0000 1 103 19 19 ALA HB H 1.4302 0.0000 1 104 20 20 GLN H H 8.0446 0.0000 1 105 20 20 GLN HA H 4.1514 0.0000 1 106 20 20 GLN HB2 H 2.0139 0.0000 2 107 20 20 GLN HB3 H 2.0826 0.0000 2 108 20 20 GLN HG2 H 2.2406 0.0000 2 109 20 20 GLN HG3 H 2.2790 0.0000 2 110 20 20 GLN HE21 H 7.1121 0.0000 2 111 20 20 GLN HE22 H 6.8370 0.0000 2 112 21 21 LEU H H 7.9881 0.0000 1 113 21 21 LEU HA H 4.2628 0.0000 1 114 21 21 LEU HG H 0.8132 0.0000 1 115 21 21 LEU HD1 H 0.8986 0.0000 2 116 21 21 LEU HD2 H 0.8127 0.0000 2 117 22 22 SER H H 8.1675 0.0000 1 118 22 22 SER HA H 4.3617 0.0000 1 119 22 22 SER HB2 H 3.8117 0.0000 2 120 23 23 SER H H 7.8525 0.0000 1 121 23 23 SER HA H 4.3604 0.0000 1 122 23 23 SER HB2 H 3.7602 0.0000 2 123 24 24 LYS H H 7.9972 0.0000 1 124 24 24 LYS HA H 4.2618 0.0000 1 125 24 24 LYS HB2 H 1.6282 0.0000 2 126 24 24 LYS HG2 H 1.5151 0.0000 2 127 25 25 LYS H H 7.9398 0.0000 1 128 25 25 LYS HA H 4.0725 0.0000 1 129 25 25 LYS HB2 H 1.6757 0.0000 2 130 25 25 LYS HB3 H 1.8120 0.0000 2 131 25 25 LYS HG2 H 1.3819 0.0000 2 132 25 25 LYS HE2 H 2.9091 0.0000 2 stop_ save_