data_25591 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solid-state NMR structure of Vpu ; _BMRB_accession_number 25591 _BMRB_flat_file_name bmr25591.str _Entry_type original _Submission_date 2015-05-01 _Accession_date 2015-05-01 _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 Zhang H. . . 2 Lin E. C. . 3 Tian Y. . . 4 Das B. B. . 5 Opella S. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 112 "15N chemical shifts" 47 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-08-24 update BMRB 'update entry citation' 2015-09-28 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 25592 'Vpu cytoplasmic domain' stop_ _Original_release_date 2015-09-28 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural determination of virus protein U from HIV-1 by NMR in membrane environments ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26362058 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhang H. . . 2 Lin E. C. . 3 Tian Y. . . 4 Das B. B. . 5 Opella S. J. . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_volume 1848 _Journal_issue 11 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3007 _Page_last 3018 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Vpu from HIV-1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'HIV-1 Virus protein U' $HIV-1_Virus_protein_U 4-(TRIFLUOROMETHYL)ANILINE $entity_ANI 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_HIV-1_Virus_protein_U _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common HIV-1_Virus_protein_U _Molecular_mass 9147.735 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 81 _Mol_residue_sequence ; MQPIQIAIVALVVAIIIAIV VWSIVIIEYRKILRQRKIDR LIDRLIERAEDSGNESEGEI SALVELGVELGHHAPWDVDD L ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 MET 2 2 GLN 3 3 PRO 4 4 ILE 5 5 GLN 6 6 ILE 7 7 ALA 8 8 ILE 9 9 VAL 10 10 ALA 11 11 LEU 12 12 VAL 13 13 VAL 14 14 ALA 15 15 ILE 16 16 ILE 17 17 ILE 18 18 ALA 19 19 ILE 20 20 VAL 21 21 VAL 22 22 TRP 23 23 SER 24 24 ILE 25 25 VAL 26 26 ILE 27 27 ILE 28 28 GLU 29 29 TYR 30 30 ARG 31 31 LYS 32 32 ILE 33 33 LEU 34 34 ARG 35 35 GLN 36 36 ARG 37 37 LYS 38 38 ILE 39 39 ASP 40 40 ARG 41 41 LEU 42 42 ILE 43 43 ASP 44 44 ARG 45 45 LEU 46 46 ILE 47 47 GLU 48 48 ARG 49 49 ALA 50 50 GLU 51 51 ASP 52 52 SER 53 53 GLY 54 54 ASN 55 55 GLU 56 56 SER 57 57 GLU 58 58 GLY 59 59 GLU 60 60 ILE 61 61 SER 62 62 ALA 63 63 LEU 64 64 VAL 65 65 GLU 66 66 LEU 67 67 GLY 68 68 VAL 69 69 GLU 70 70 LEU 71 71 GLY 72 72 HIS 73 73 HIS 74 74 ALA 75 75 PRO 76 76 TRP 77 77 ASP 78 78 VAL 79 79 ASP 80 80 ASP 81 81 LEU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_ANI _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 4-(trifluoromethyl)aniline _BMRB_code ANI _PDB_code ANI _Molecular_mass 161.124 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? F1 F1 F . 0 . ? F2 F2 F . 0 . ? F3 F3 F . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H5 H5 H . 0 . ? H6 H6 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 SING N C1 ? ? SING N HN1 ? ? SING N HN2 ? ? DOUB C1 C2 ? ? SING C1 C6 ? ? SING C2 C3 ? ? SING C2 H2 ? ? DOUB C3 C4 ? ? SING C3 H3 ? ? SING C4 C5 ? ? SING C4 C7 ? ? DOUB C5 C6 ? ? SING C5 H5 ? ? SING C6 H6 ? ? SING C7 F1 ? ? SING C7 F2 ? ? SING C7 F3 ? ? 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 $HIV-1_Virus_protein_U 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 $HIV-1_Virus_protein_U 'recombinant technology' . Escherichia coli C41 pET31b+ stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details 'DMPC proteoliposomes' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HIV-1_Virus_protein_U 8.5 mM '[U-100% 13C; U-100% 15N]' H20 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger A. T. et.al.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_13C/13C_PDSD_1 _Saveframe_category NMR_applied_experiment _Experiment_name 2D_13C/13C_PDSD _Sample_label $sample save_ save_2D_13C/15N_HETCOR_2 _Saveframe_category NMR_applied_experiment _Experiment_name 2D_13C/15N_HETCOR _Sample_label $sample save_ save_2D_13C/13C_TOBSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name 2D_13C/13C_TOBSY _Sample_label $sample save_ save_2D_13C-1H_DC/13C_SLF_4 _Saveframe_category NMR_applied_experiment _Experiment_name 2D_13C-1H_DC/13C_SLF _Sample_label $sample save_ save_2D_15N-1H_DC/13C_SLF_5 _Saveframe_category NMR_applied_experiment _Experiment_name 2D_15N-1H_DC/13C_SLF _Sample_label $sample save_ save_3D_15N/13CA/13C_6 _Saveframe_category NMR_applied_experiment _Experiment_name 3D_15N/13CA/13C _Sample_label $sample save_ save_3D_15N/13C'/13C_7 _Saveframe_category NMR_applied_experiment _Experiment_name 3D_15N/13C'/13C _Sample_label $sample save_ save_3D_1H-15N_DC/15N/13CA_SLF_8 _Saveframe_category NMR_applied_experiment _Experiment_name 3D_1H-15N_DC/15N/13CA_SLF _Sample_label $sample save_ save_3D_1H-13C_DC/15N/13CA_SLF_9 _Saveframe_category NMR_applied_experiment _Experiment_name 3D_1H-13C_DC/15N/13CA_SLF _Sample_label $sample 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' 20 . mM pH 7.3 . pH pressure 1 . atm temperature 298 . K 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 adamantane C 13 'methyl carbons' ppm 40.5 external direct . . . 1 water H 1 protons ppm 4.7 external direct . . . 1 TMS N 15 nitrogen ppm 26.8 external direct . . . 1 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_13C/13C_PDSD 2D_13C/15N_HETCOR 2D_13C/13C_TOBSY 3D_15N/13CA/13C 3D_15N/13C'/13C stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'HIV-1 Virus protein U' _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 3 3 PRO CB C 30.902 . . 2 3 3 PRO CG C 26.399 . . 3 3 3 PRO CD C 49.527 . . 4 8 8 ILE C C 175.900 . . 5 8 8 ILE CA C 65.300 . . 6 8 8 ILE N N 119.520 . . 7 9 9 VAL C C 176.692 . . 8 9 9 VAL CA C 66.804 . . 9 9 9 VAL N N 119.926 . . 10 10 10 ALA C C 175.619 . . 11 10 10 ALA CA C 55.394 . . 12 10 10 ALA N N 116.535 . . 13 11 11 LEU C C 176.154 . . 14 11 11 LEU CA C 58.530 . . 15 11 11 LEU N N 119.255 . . 16 12 12 VAL C C 175.682 . . 17 12 12 VAL CA C 66.768 . . 18 12 12 VAL N N 119.700 . . 19 13 13 VAL C C 175.573 . . 20 13 13 VAL CA C 66.658 . . 21 13 13 VAL N N 120.637 . . 22 14 14 ALA C C 176.031 . . 23 14 14 ALA CA C 54.521 . . 24 14 14 ALA N N 121.480 . . 25 15 15 ILE C C 177.003 . . 26 15 15 ILE CA C 64.645 . . 27 15 15 ILE N N 115.912 . . 28 16 16 ILE C C 176.090 . . 29 16 16 ILE CA C 65.285 . . 30 16 16 ILE N N 122.123 . . 31 17 17 ILE C C 176.144 . . 32 17 17 ILE CA C 65.051 . . 33 17 17 ILE N N 121.840 . . 34 18 18 ALA C C 177.067 . . 35 18 18 ALA CA C 54.311 . . 36 18 18 ALA N N 121.435 . . 37 19 19 ILE C C 177.118 . . 38 19 19 ILE CA C 64.605 . . 39 19 19 ILE N N 121.083 . . 40 20 20 VAL C C 175.871 . . 41 20 20 VAL CA C 66.736 . . 42 20 20 VAL N N 122.700 . . 43 21 21 VAL C C 175.668 . . 44 21 21 VAL CA C 66.559 . . 45 21 21 VAL N N 120.200 . . 46 22 22 TRP C C 177.266 . . 47 22 22 TRP CA C 56.538 . . 48 22 22 TRP N N 121.450 . . 49 23 23 SER C C 177.2 . . 50 23 23 SER CA C 58.188 . . 51 23 23 SER CB C 61.7 . . 52 23 23 SER N N 118.800 . . 53 24 24 ILE C C 176.090 . . 54 24 24 ILE CA C 64.400 . . 55 24 24 ILE N N 121.100 . . 56 25 25 VAL C C 176.590 . . 57 25 25 VAL CA C 66.956 . . 58 25 25 VAL N N 121.100 . . 59 26 26 ILE C C 176.027 . . 60 26 26 ILE CA C 64.538 . . 61 26 26 ILE N N 120.787 . . 62 27 27 ILE C C 175.745 . . 63 27 27 ILE CA C 66.557 . . 64 27 27 ILE N N 122.037 . . 65 29 29 TYR CA C 58.112 . . 66 29 29 TYR CB C 38.239 . . 67 35 35 GLN C C 174.683 . . 68 35 35 GLN CA C 60.808 . . 69 35 35 GLN N N 120.836 . . 70 36 36 ARG C C 177.826 . . 71 36 36 ARG CA C 60.340 . . 72 36 36 ARG N N 116.758 . . 73 37 37 LYS C C 174.027 . . 74 37 37 LYS CA C 60.808 . . 75 37 37 LYS N N 120.935 . . 76 38 38 ILE C C 176.314 . . 77 38 38 ILE CA C 63.387 . . 78 38 38 ILE N N 118.101 . . 79 39 39 ASP C C 176.811 . . 80 39 39 ASP CA C 56.438 . . 81 39 39 ASP N N 119.195 . . 82 40 40 ARG C C 177.050 . . 83 40 40 ARG CA C 54.797 . . 84 40 40 ARG N N 121.631 . . 85 41 41 LEU C C 177.620 . . 86 41 41 LEU CA C 58.250 . . 87 41 41 LEU N N 118.817 . . 88 42 42 ILE C C 176.632 . . 89 42 42 ILE CA C 63.420 . . 90 42 42 ILE N N 118.200 . . 91 43 43 ASP C C 176.545 . . 92 43 43 ASP CA C 56.964 . . 93 43 43 ASP N N 119.593 . . 94 44 44 ARG C C 176.968 . . 95 44 44 ARG CA C 57.078 . . 96 44 44 ARG N N 121.763 . . 97 45 45 LEU C C 175.880 . . 98 45 45 LEU CA C 57.781 . . 99 45 45 LEU N N 120.347 . . 100 46 46 ILE C C 175.966 . . 101 46 46 ILE CA C 65.047 . . 102 46 46 ILE N N 119.068 . . 103 47 47 GLU C C 177.285 . . 104 47 47 GLU CA C 60.116 . . 105 47 47 GLU N N 122.353 . . 106 48 48 ARG C C 176.833 . . 107 48 48 ARG CA C 56.980 . . 108 48 48 ARG N N 122.479 . . 109 49 49 ALA C C 176.568 . . 110 49 49 ALA CA C 51.013 . . 111 49 49 ALA N N 122.914 . . 112 54 54 ASN CA C 53.717 . . 113 54 54 ASN CB C 40.329 . . 114 59 59 GLU C C 177.278 . . 115 59 59 GLU CA C 58.989 . . 116 59 59 GLU N N 117.568 . . 117 60 60 ILE C C 176.013 . . 118 60 60 ILE CA C 65.552 . . 119 60 60 ILE N N 119.074 . . 120 61 61 SER C C 175.872 . . 121 61 61 SER CA C 58.051 . . 122 61 61 SER N N 117.317 . . 123 62 62 ALA C C 175.952 . . 124 62 62 ALA CA C 53.832 . . 125 62 62 ALA N N 120.229 . . 126 63 63 LEU C C 176.977 . . 127 63 63 LEU CA C 56.645 . . 128 63 63 LEU N N 115.860 . . 129 64 64 VAL C C 176.856 . . 130 64 64 VAL CA C 66.957 . . 131 64 64 VAL N N 119.727 . . 132 65 65 GLU C C 176.495 . . 133 65 65 GLU CA C 58.284 . . 134 65 65 GLU N N 118.472 . . 135 66 66 LEU C C 175.973 . . 136 66 66 LEU CA C 58.050 . . 137 66 66 LEU N N 115.810 . . 138 67 67 GLY C C 173.834 . . 139 67 67 GLY CA C 46.512 . . 140 67 67 GLY N N 103.047 . . 141 68 68 VAL C C 175.661 . . 142 68 68 VAL CA C 66.439 . . 143 68 68 VAL N N 115.548 . . 144 69 69 GLU C C 176.010 . . 145 69 69 GLU CA C 59.421 . . 146 69 69 GLU N N 120.236 . . 147 70 70 LEU C C 174.019 . . 148 70 70 LEU CA C 60.036 . . 149 70 70 LEU N N 125.548 . . 150 76 76 TRP CA C 56.523 . . 151 76 76 TRP CB C 31.759 . . 152 76 76 TRP CE3 C 119.152 . . 153 78 78 VAL CA C 62.478 . . 154 78 78 VAL CB C 31.056 . . 155 81 81 LEU CA C 55.522 . . 156 81 81 LEU CB C 41.619 . . 157 81 81 LEU CG C 26.022 . . 158 81 81 LEU CD1 C 23.819 . . 159 81 81 LEU CD2 C 22.684 . . stop_ save_