data_11056 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; KMTM7 a peptide derived from V-ATPase subunit a, putative TM7 ; _BMRB_accession_number 11056 _BMRB_flat_file_name bmr11056.str _Entry_type new _Submission_date 2008-11-07 _Accession_date 2008-11-10 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'KMTM7 a peptide derived from V-ATPase subunit a, putative TM7' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Vermeer Louic S. . 2 Reat Valerie . . 3 Hemminga Marcus A. . 4 Milon Alain . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 spectral_peak_list 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 145 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-05-05 update BMRB 'complete entry citation' 2009-04-17 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural properties of a peptide derived from H(+)-V-ATPase subunit a' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19249284 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Vermeer Louic S. . 2 Reat Valerie . . 3 Hemminga Marcus A. . 4 Milon Alain . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta.' _Journal_volume 1788 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1204 _Page_last 1212 _Year 2009 _Details . loop_ _Keyword 'V-ATPase subunit a' 'circular dichroism' NMR 'peptide conformation' 'histidine titration' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'peptide from V-ATPase' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label KMTM7 $KMTM7 stop_ _System_molecular_weight 2783 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_KMTM7 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common KMTM7 _Molecular_mass 2783 _Mol_thiol_state 'not present' loop_ _Biological_function 'proton translocation' stop_ _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 2015-11-05 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 15025 sMTM7 72.00 25 100.00 100.00 4.09e-02 PDB 2JTW "Solution Structure Of Tm7 Bound To Dpc Micelles" 100.00 25 100.00 100.00 6.27e-06 PDB 2NVJ "Nmr Structures Of Transmembrane Segment From Subunit A From The Yeast Proton V-Atpase" 72.00 25 100.00 100.00 4.09e-02 PDB 2RPW "Structure Of A Peptide Derived From H+-V-Atpase Subunit A" 100.00 25 100.00 100.00 6.27e-06 PDB 3J9T "Yeast V-atpase State 1" 84.00 840 100.00 100.00 9.43e-04 PDB 3J9U "Yeast V-atpase State 2" 84.00 840 100.00 100.00 9.43e-04 PDB 3J9V "Yeast V-atpase State 3" 84.00 840 100.00 100.00 9.43e-04 DBJ BAB62291 "VHA-5 [Caenorhabditis elegans]" 80.00 873 100.00 100.00 9.89e-04 DBJ BAB62292 "VHA-6 [Caenorhabditis elegans]" 80.00 865 100.00 100.00 9.87e-04 DBJ BAB62293 "VHA-7 [Caenorhabditis elegans]" 80.00 966 100.00 100.00 2.48e-03 DBJ GAA25496 "K7_Stv1p [Saccharomyces cerevisiae Kyokai no. 7]" 84.00 890 100.00 100.00 3.91e-04 DBJ GAA26581 "K7_Vph1p [Saccharomyces cerevisiae Kyokai no. 7]" 84.00 840 100.00 100.00 9.43e-04 EMBL CAA20334 "V-type proton ATPase subunit a [Caenorhabditis elegans]" 80.00 865 100.00 100.00 9.87e-04 EMBL CAA61776 "vacuolar ATP synthase VPH1 [Saccharomyces cerevisiae]" 84.00 840 100.00 100.00 9.43e-04 EMBL CAA77448 "Probable V-type proton ATPase 116 kDa subunit a [Caenorhabditis elegans]" 80.00 905 100.00 100.00 9.98e-04 EMBL CAA77453 "Probable V-type proton ATPase 116 kDa subunit a [Caenorhabditis elegans]" 80.00 883 100.00 100.00 9.92e-04 EMBL CAA89764 "Stv1p [Saccharomyces cerevisiae]" 84.00 890 100.00 100.00 4.14e-04 GB AAA35211 "vacuolar H+-ATPase subunit [Saccharomyces cerevisiae]" 84.00 840 100.00 100.00 9.43e-04 GB AAD34771 "unknown [Drosophila melanogaster]" 80.00 834 100.00 100.00 9.78e-04 GB AAF28475 "V-ATPase 110 kDa integral membrane subunit [Aedes aegypti]" 80.00 804 100.00 100.00 1.44e-03 GB AAF53116 "vacuolar H[+] ATPase 100kD subunit 5, isoform A [Drosophila melanogaster]" 80.00 814 100.00 100.00 9.71e-04 GB AAF55550 "vacuolar H[+] ATPase 100kD subunit 4 [Drosophila melanogaster]" 80.00 844 100.00 100.00 9.81e-04 REF NP_001023017 "Probable V-type proton ATPase 116 kDa subunit a [Caenorhabditis elegans]" 80.00 905 100.00 100.00 9.98e-04 REF NP_001023018 "Probable V-type proton ATPase 116 kDa subunit a [Caenorhabditis elegans]" 80.00 883 100.00 100.00 9.92e-04 REF NP_001023019 "Probable V-type proton ATPase 116 kDa subunit a [Caenorhabditis elegans]" 80.00 894 100.00 100.00 9.95e-04 REF NP_001023020 "Probable V-type proton ATPase 116 kDa subunit a [Caenorhabditis elegans]" 80.00 899 100.00 100.00 9.97e-04 REF NP_001023021 "Probable V-type proton ATPase 116 kDa subunit a [Caenorhabditis elegans]" 80.00 888 100.00 100.00 9.94e-04 SP P30628 "RecName: Full=Probable V-type proton ATPase 116 kDa subunit a; Short=V-ATPase 116 kDa isoform a; AltName: Full=Uncoordinated pr" 80.00 905 100.00 100.00 9.98e-04 SP P32563 "RecName: Full=V-type proton ATPase subunit a, vacuolar isoform; Short=V-ATPase a 1 subunit; AltName: Full=V-ATPase 95 kDa subun" 84.00 840 100.00 100.00 9.43e-04 SP P37296 "RecName: Full=V-type proton ATPase subunit a, Golgi isoform; Short=V-ATPase a 2 subunit; AltName: Full=Similar to VPH1 protein " 84.00 890 100.00 100.00 4.14e-04 TPG DAA09953 "TPA: H(+)-transporting V0 sector ATPase subunit a [Saccharomyces cerevisiae S288c]" 84.00 890 100.00 100.00 4.14e-04 TPG DAA11036 "TPA: H(+)-transporting V0 sector ATPase subunit a [Saccharomyces cerevisiae S288c]" 84.00 840 100.00 100.00 9.43e-04 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $KMTM7 'baker's yeast' 4932 Eukaryota Fungi Saccharomyces cerevisiae ; A synthesised peptide, derived from Saccheromyces cerevisiae V-ATPase subunit a, transmembrane helix 7 ; 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 $KMTM7 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type 'solution in SDS (micelles)' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $KMTM7 1 mM 'natural abundance' SDS 250 mM '[U-100% 2H]' 'sodium phosphate' 10 mM 'natural abundance' DSS 0.3 mM 'natural abundance' H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_ARIA _Saveframe_category software _Name ARIA _Version 2.2 loop_ _Vendor _Address _Electronic_address 'Linge, O'Donoghue and Nilges' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_AQUA _Saveframe_category software _Name AQUA _Version 3.2 loop_ _Vendor _Address _Electronic_address 'Rullmann, Doreleijers and Kaptein' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' 'chemical shift assignment' stop_ _Details . save_ save_ProcheckNMR _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . 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 Avance _Field_strength 600 _Details cryoprobe 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 5.0 . 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 KMTM7 _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 LYS H H 8.578 0.025 1 2 2 2 LYS HA H 4.397 0.003 1 3 2 2 LYS HB2 H 1.823 0.016 1 4 2 2 LYS HB3 H 1.823 0.016 1 5 2 2 LYS HD2 H 1.721 0.000 1 6 2 2 LYS HD3 H 1.721 0.000 1 7 2 2 LYS HE2 H 3.027 0.009 1 8 2 2 LYS HE3 H 3.027 0.009 1 9 2 2 LYS HG2 H 1.462 0.000 1 10 2 2 LYS HG3 H 1.462 0.000 1 11 3 3 SER H H 8.183 0.043 1 12 3 3 SER HA H 4.424 0.004 1 13 3 3 SER HB2 H 3.816 0.015 1 14 3 3 SER HB3 H 3.816 0.015 1 15 4 4 HIS H H 8.342 0.025 1 16 4 4 HIS HA H 4.869 0.004 1 17 4 4 HIS HB2 H 3.265 0.057 1 18 4 4 HIS HB3 H 3.265 0.057 1 19 4 4 HIS HD2 H 7.379 0.005 1 20 4 4 HIS HE1 H 8.633 0.000 1 21 5 5 THR H H 8.108 0.031 1 22 5 5 THR HA H 4.274 0.005 1 23 5 5 THR HB H 4.220 0.001 1 24 5 5 THR HG2 H 1.215 0.005 1 25 6 6 ALA H H 8.305 0.042 1 26 6 6 ALA HA H 4.315 0.010 1 27 6 6 ALA HB H 1.401 0.003 1 28 7 7 SER H H 8.026 0.038 1 29 7 7 SER HA H 4.290 0.004 1 30 7 7 SER HB2 H 3.906 0.009 1 31 7 7 SER HB3 H 3.906 0.009 1 32 8 8 TYR H H 7.951 0.038 1 33 8 8 TYR HA H 4.265 0.010 1 34 8 8 TYR HB2 H 2.954 0.051 1 35 8 8 TYR HB3 H 2.954 0.051 1 36 8 8 TYR HD1 H 7.089 0.005 1 37 8 8 TYR HD2 H 7.089 0.005 1 38 8 8 TYR HE1 H 6.784 0.007 1 39 8 8 TYR HE2 H 6.784 0.007 1 40 9 9 LEU H H 7.868 0.101 1 41 9 9 LEU HA H 4.194 0.009 1 42 9 9 LEU HB2 H 1.791 0.055 1 43 9 9 LEU HB3 H 1.791 0.055 1 44 9 9 LEU HD1 H 0.938 0.036 1 45 9 9 LEU HD2 H 0.938 0.036 1 46 9 9 LEU HG H 1.601 0.089 1 47 10 10 ARG H H 7.942 0.036 1 48 10 10 ARG HA H 3.937 0.005 1 49 10 10 ARG HB2 H 1.876 0.094 1 50 10 10 ARG HB3 H 1.876 0.094 1 51 10 10 ARG HD2 H 3.234 0.002 1 52 10 10 ARG HD3 H 3.234 0.002 1 53 10 10 ARG HE H 7.176 0.015 1 54 10 10 ARG HG2 H 1.643 0.040 1 55 10 10 ARG HG3 H 1.643 0.040 1 56 11 11 LEU H H 7.660 0.040 1 57 11 11 LEU HA H 4.089 0.003 1 58 11 11 LEU HB2 H 1.778 0.046 1 59 11 11 LEU HB3 H 1.778 0.046 1 60 11 11 LEU HD1 H 0.887 0.002 1 61 11 11 LEU HD2 H 0.887 0.002 1 62 11 11 LEU HG H 1.620 0.005 1 63 12 12 TRP H H 8.351 0.030 1 64 12 12 TRP HA H 4.351 0.010 1 65 12 12 TRP HB2 H 3.347 0.080 1 66 12 12 TRP HB3 H 3.347 0.080 1 67 12 12 TRP HD1 H 7.233 0.034 1 68 12 12 TRP HE1 H 9.872 0.035 1 69 12 12 TRP HE3 H 7.522 0.007 1 70 12 12 TRP HH2 H 7.080 0.169 1 71 12 12 TRP HZ2 H 7.375 0.003 1 72 12 12 TRP HZ3 H 6.928 0.003 1 73 13 13 ALA H H 8.591 0.053 1 74 13 13 ALA HA H 3.702 0.023 1 75 13 13 ALA HB H 1.487 0.005 1 76 14 14 LEU H H 8.120 0.045 1 77 14 14 LEU HA H 4.032 0.051 1 78 14 14 LEU HB2 H 1.837 0.036 1 79 14 14 LEU HB3 H 1.837 0.036 1 80 14 14 LEU HD1 H 0.908 0.018 1 81 14 14 LEU HD2 H 0.908 0.018 1 82 14 14 LEU HG H 1.583 0.043 1 83 15 15 SER H H 7.969 0.013 1 84 15 15 SER HA H 4.272 0.005 1 85 15 15 SER HB2 H 4.023 0.026 1 86 15 15 SER HB3 H 4.023 0.026 1 87 16 16 LEU H H 7.919 0.010 1 88 16 16 LEU HA H 4.101 0.002 1 89 16 16 LEU HD1 H 0.943 0.033 1 90 16 16 LEU HD2 H 0.943 0.033 1 91 16 16 LEU HG H 1.481 0.002 1 92 17 17 ALA H H 8.241 0.047 1 93 17 17 ALA HA H 3.973 0.012 1 94 17 17 ALA HB H 1.410 0.002 1 95 18 18 HIS H H 8.286 0.047 1 96 18 18 HIS HA H 4.421 0.012 1 97 18 18 HIS HB2 H 3.342 0.028 1 98 18 18 HIS HB3 H 3.342 0.028 1 99 18 18 HIS HD2 H 7.347 0.010 1 100 18 18 HIS HE1 H 8.646 0.008 1 101 19 19 ALA H H 8.032 0.031 1 102 19 19 ALA HA H 4.192 0.005 1 103 19 19 ALA HB H 1.543 0.005 1 104 20 20 GLN H H 8.144 0.025 1 105 20 20 GLN HA H 4.221 0.018 1 106 20 20 GLN HB2 H 2.108 0.061 1 107 20 20 GLN HB3 H 2.108 0.061 1 108 20 20 GLN HE21 H 7.182 0.026 2 109 20 20 GLN HE22 H 6.674 0.030 2 110 20 20 GLN HG2 H 2.368 0.093 1 111 20 20 GLN HG3 H 2.368 0.093 1 112 21 21 LEU H H 8.215 0.000 1 113 21 21 LEU HA H 4.140 0.113 1 114 21 21 LEU HB2 H 1.630 0.356 1 115 21 21 LEU HB3 H 1.630 0.356 1 116 21 21 LEU HD1 H 0.916 0.000 2 117 21 21 LEU HG H 1.614 0.009 1 118 22 22 SER H H 7.945 0.032 1 119 22 22 SER HA H 4.320 0.010 1 120 22 22 SER HB2 H 3.909 0.022 1 121 22 22 SER HB3 H 3.909 0.022 1 122 23 23 SER H H 7.807 0.010 1 123 23 23 SER HA H 4.448 0.005 1 124 23 23 SER HB2 H 3.962 0.021 1 125 23 23 SER HB3 H 3.962 0.021 1 126 24 24 LYS H H 7.819 0.051 1 127 24 24 LYS HA H 4.377 0.005 1 128 24 24 LYS HB2 H 1.908 0.074 1 129 24 24 LYS HB3 H 1.908 0.074 1 130 24 24 LYS HD2 H 1.700 0.007 1 131 24 24 LYS HD3 H 1.700 0.007 1 132 24 24 LYS HE2 H 3.012 0.000 1 133 24 24 LYS HE3 H 3.012 0.000 1 134 24 24 LYS HG2 H 1.504 0.001 1 135 24 24 LYS HG3 H 1.504 0.001 1 136 25 25 LYS H H 7.631 0.025 1 137 25 25 LYS HA H 4.185 0.009 1 138 25 25 LYS HB2 H 2.143 0.839 1 139 25 25 LYS HB3 H 2.143 0.839 1 140 25 25 LYS HD2 H 1.695 0.006 1 141 25 25 LYS HD3 H 1.695 0.006 1 142 25 25 LYS HE2 H 3.008 0.000 1 143 25 25 LYS HE3 H 3.008 0.000 1 144 25 25 LYS HG2 H 1.444 0.013 1 145 25 25 LYS HG3 H 1.444 0.013 1 stop_ save_