data_30349 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of HIV-1 GP41 Transmembrane Domain in Bicelles ; _BMRB_accession_number 30349 _BMRB_flat_file_name bmr30349.str _Entry_type original _Submission_date 2017-09-24 _Accession_date 2017-09-24 _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 Chiliveri S. C. . 2 Louis J. M. . 3 Ghirlando R. . . 4 Baber J. L. . 5 Bax A. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 38 "13C chemical shifts" 77 "15N chemical shifts" 38 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-01-19 original BMRB . stop_ _Original_release_date 2018-01-17 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Tilted, Uninterrupted, Monomeric HIV-1 gp41 Transmembrane Helix from Residual Dipolar Couplings. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29277995 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chiliveri S. C. . 2 Louis J. M. . 3 Ghirlando R. . . 4 Baber J. L. . 5 Bax A. . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 140 _Journal_issue 1 _Journal_ASTM JACSAT _Journal_ISSN 1520-5126 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 34 _Page_last 37 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'HIV-1 GP41 Transmembrane Domain' _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 4650.604 _Mol_thiol_state 'not present' _Details 'Polypeptide sequence for the solution structure corresponds to GP160 (677-716; HXB2 numbering).' ############################## # Polymer residue sequence # ############################## _Residue_count 40 _Mol_residue_sequence ; NWLWYIRIFIIIVGSLIGLR IVFAVLSLVNRVRQGYSPLS ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 677 ASN 2 678 TRP 3 679 LEU 4 680 TRP 5 681 TYR 6 682 ILE 7 683 ARG 8 684 ILE 9 685 PHE 10 686 ILE 11 687 ILE 12 688 ILE 13 689 VAL 14 690 GLY 15 691 SER 16 692 LEU 17 693 ILE 18 694 GLY 19 695 LEU 20 696 ARG 21 697 ILE 22 698 VAL 23 699 PHE 24 700 ALA 25 701 VAL 26 702 LEU 27 703 SER 28 704 LEU 29 705 VAL 30 706 ASN 31 707 ARG 32 708 VAL 33 709 ARG 34 710 GLN 35 711 GLY 36 712 TYR 37 713 SER 38 714 PRO 39 715 LEU 40 716 SER 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 HIV-1 11676 Viruses . Lentivirus HIV-1 env 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' . . . BL21(DE3) . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type bicelle _Details '500 uM [U-100% 13C; U-100% 15N; U-100% 2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 500 uM '[U-100% 13C; U-100% 15N; U-80% 2H]' 'MES buffer' 25 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type 'gel solid' _Details '100 uM [U-100% 15N; 80%-2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 100 uM '[U-100% 15N; 80%-2H]' 'MES buffer' 25 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type 'gel solid' _Details '100 uM [U-100% 15N; 80%-2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 100 uM '[U-100% 15N; 80%-2H]' 'MES buffer' 25 mM 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type bicelle _Details '40 uM [U-100% 15N; U-80% 2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 40 uM '[U-100% 15N; U-80% 2H]' 'MES buffer' 25 mM 'natural abundance' stop_ save_ save_sample_5 _Saveframe_category sample _Sample_type bicelle _Details '70 uM [U-100% 15N; U-80% 2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 70 uM '[U-100% 15N; U-80% 2H]' 'MES buffer' 25 mM 'natural abundance' stop_ save_ save_sample_6 _Saveframe_category sample _Sample_type bicelle _Details '300 uM [U-100% 15N; U-80% 2H] HIV-1 GP41 Transmembrane domain, 93% H2O/7% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 300 uM '[U-100% 15N; U-80% 2H]' 'MES buffer' 25 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CcpNMR _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceII _Field_strength 900 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_HNCO_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $sample_1 save_ save_3D_HNCA_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label $sample_1 save_ save_3D_1H-15N_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_1 save_ save_2D_TROSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TROSY' _Sample_label $sample_1 save_ save_2D_ARTSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ARTSY' _Sample_label $sample_1 save_ save_2D_ARTSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ARTSY' _Sample_label $sample_2 save_ save_2D_ARTSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ARTSY' _Sample_label $sample_3 save_ save_2D_ARTSY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ARTSY' _Sample_label $sample_4 save_ save_2D_ARTSY_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ARTSY' _Sample_label $sample_5 save_ save_2D_TROSY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TROSY' _Sample_label $sample_6 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' 25 . mM pH 6.5 . pH pressure 1 . bar temperature 318 . 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 C 13 'methyl protons' ppm 0.000 internal indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.000 internal indirect . . . 0.10132912 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 HNCO' '3D HNCA' '3D 1H-15N NOESY' '2D TROSY' '2D ARTSY' stop_ loop_ _Sample_label $sample_1 $sample_2 $sample_3 $sample_4 $sample_5 $sample_6 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 1 677 1 ASN C C 175.96 0.2 1 2 678 2 TRP H H 8.27 0.01 1 3 678 2 TRP C C 177.69 0.2 1 4 678 2 TRP CA C 59.89 0.2 1 5 678 2 TRP N N 120.22 0.05 1 6 679 3 LEU H H 7.75 0.01 1 7 679 3 LEU C C 178.76 0.2 1 8 679 3 LEU CA C 58.05 0.2 1 9 679 3 LEU N N 120.02 0.05 1 10 680 4 TRP H H 7.76 0.01 1 11 680 4 TRP C C 177.92 0.2 1 12 680 4 TRP CA C 61.47 0.2 1 13 680 4 TRP N N 120.29 0.05 1 14 681 5 TYR H H 7.55 0.01 1 15 681 5 TYR C C 178.12 0.2 1 16 681 5 TYR CA C 61.21 0.2 1 17 681 5 TYR N N 115.45 0.05 1 18 682 6 ILE H H 8.03 0.01 1 19 682 6 ILE C C 177.29 0.2 1 20 682 6 ILE CA C 64.84 0.2 1 21 682 6 ILE N N 118.14 0.05 1 22 683 7 ARG H H 8.09 0.01 1 23 683 7 ARG C C 177.81 0.2 1 24 683 7 ARG CA C 60.64 0.2 1 25 683 7 ARG N N 119.99 0.05 1 26 684 8 ILE H H 7.78 0.01 1 27 684 8 ILE C C 177.4 0.2 1 28 684 8 ILE CA C 64.16 0.2 1 29 684 8 ILE N N 117.01 0.05 1 30 685 9 PHE H H 8.21 0.01 1 31 685 9 PHE C C 176.73 0.2 1 32 685 9 PHE CA C 62.01 0.2 1 33 685 9 PHE N N 120.36 0.05 1 34 686 10 ILE H H 8.39 0.01 1 35 686 10 ILE C C 177.79 0.2 1 36 686 10 ILE CA C 65.22 0.2 1 37 686 10 ILE N N 118.03 0.05 1 38 687 11 ILE H H 8.06 0.01 1 39 687 11 ILE C C 178.82 0.2 1 40 687 11 ILE CA C 65.70 0.2 1 41 687 11 ILE N N 120.18 0.05 1 42 688 12 ILE H H 8.45 0.01 1 43 688 12 ILE C C 177.29 0.2 1 44 688 12 ILE CA C 66.15 0.2 1 45 688 12 ILE N N 121.86 0.05 1 46 689 13 VAL H H 8.37 0.01 1 47 689 13 VAL C C 178.05 0.2 1 48 689 13 VAL CA C 67.36 0.2 1 49 689 13 VAL N N 118.46 0.05 1 50 690 14 GLY H H 8.83 0.01 1 51 690 14 GLY C C 175.19 0.2 1 52 690 14 GLY CA C 47.47 0.2 1 53 690 14 GLY N N 106.66 0.05 1 54 691 15 SER H H 8.13 0.01 1 55 691 15 SER C C 175.42 0.2 1 56 691 15 SER CA C 63.60 0.2 1 57 691 15 SER N N 117.99 0.05 1 58 692 16 LEU H H 7.89 0.01 1 59 692 16 LEU C C 178.82 0.2 1 60 692 16 LEU CA C 58.31 0.2 1 61 692 16 LEU N N 121.8 0.05 1 62 693 17 ILE H H 8.12 0.01 1 63 693 17 ILE C C 178.09 0.2 1 64 693 17 ILE CA C 65.19 0.2 1 65 693 17 ILE N N 118.34 0.05 1 66 694 18 GLY H H 8.58 0.01 1 67 694 18 GLY C C 174.88 0.2 1 68 694 18 GLY CA C 47.67 0.2 1 69 694 18 GLY N N 107.13 0.05 1 70 695 19 LEU H H 8.46 0.01 1 71 695 19 LEU C C 178.15 0.2 1 72 695 19 LEU CA C 58.14 0.2 1 73 695 19 LEU N N 121.25 0.05 1 74 696 20 ARG H H 7.97 0.01 1 75 696 20 ARG C C 179.52 0.2 1 76 696 20 ARG CA C 59.08 0.2 1 77 696 20 ARG N N 118.79 0.05 1 78 697 21 ILE H H 8.2 0.01 1 79 697 21 ILE C C 177.37 0.2 1 80 697 21 ILE CA C 65.59 0.2 1 81 697 21 ILE N N 120.05 0.05 1 82 698 22 VAL H H 8.31 0.01 1 83 698 22 VAL C C 177.72 0.2 1 84 698 22 VAL CA C 67.73 0.2 1 85 698 22 VAL N N 120.06 0.05 1 86 699 23 PHE H H 8.46 0.01 1 87 699 23 PHE C C 178.1 0.2 1 88 699 23 PHE CA C 61.82 0.2 1 89 699 23 PHE N N 117.86 0.05 1 90 700 24 ALA H H 8.11 0.01 1 91 700 24 ALA C C 180.47 0.2 1 92 700 24 ALA CA C 55.30 0.2 1 93 700 24 ALA N N 123.09 0.05 1 94 701 25 VAL H H 8.36 0.01 1 95 701 25 VAL C C 177.69 0.2 1 96 701 25 VAL CA C 66.95 0.2 1 97 701 25 VAL N N 118.55 0.05 1 98 702 26 LEU H H 8.39 0.01 1 99 702 26 LEU C C 178.88 0.2 1 100 702 26 LEU CA C 58.27 0.2 1 101 702 26 LEU N N 119.5 0.05 1 102 703 27 SER H H 8.07 0.01 1 103 703 27 SER C C 176.78 0.2 1 104 703 27 SER CA C 61.82 0.2 1 105 703 27 SER N N 114.14 0.05 1 106 704 28 LEU H H 7.7 0.01 1 107 704 28 LEU C C 178.59 0.2 1 108 704 28 LEU CA C 58.21 0.2 1 109 704 28 LEU N N 122.76 0.05 1 110 705 29 VAL H H 8.26 0.01 1 111 705 29 VAL C C 177.44 0.2 1 112 705 29 VAL CA C 66.56 0.2 1 113 705 29 VAL N N 118.05 0.05 1 114 706 30 ASN H H 8.12 0.01 1 115 706 30 ASN C C 177.02 0.2 1 116 706 30 ASN CA C 56.20 0.2 1 117 706 30 ASN N N 117.45 0.05 1 118 707 31 ARG H H 7.86 0.01 1 119 707 31 ARG C C 178.85 0.2 1 120 707 31 ARG CA C 58.94 0.2 1 121 707 31 ARG N N 119.2 0.05 1 122 708 32 VAL H H 8.04 0.01 1 123 708 32 VAL C C 178.26 0.2 1 124 708 32 VAL CA C 65.17 0.2 1 125 708 32 VAL N N 118.88 0.05 1 126 709 33 ARG H H 8.14 0.01 1 127 709 33 ARG C C 177.35 0.2 1 128 709 33 ARG CA C 58.41 0.2 1 129 709 33 ARG N N 120.12 0.05 1 130 710 34 GLN H H 7.79 0.01 1 131 710 34 GLN C C 176.71 0.2 1 132 710 34 GLN CA C 56.84 0.2 1 133 710 34 GLN N N 117.49 0.05 1 134 711 35 GLY H H 7.88 0.01 1 135 711 35 GLY C C 173.79 0.2 1 136 711 35 GLY CA C 45.49 0.2 1 137 711 35 GLY N N 107.51 0.05 1 138 712 36 TYR H H 7.83 0.01 1 139 712 36 TYR C C 175.17 0.2 1 140 712 36 TYR CA C 57.93 0.2 1 141 712 36 TYR N N 120.26 0.05 1 142 713 37 SER H H 7.97 0.01 1 143 713 37 SER CA C 55.83 0.2 1 144 713 37 SER N N 118.35 0.05 1 145 714 38 PRO C C 176.4 0.2 1 146 714 38 PRO CA C 63.61 0.2 1 147 715 39 LEU H H 8.03 0.01 1 148 715 39 LEU C C 176.34 0.2 1 149 715 39 LEU CA C 55.11 0.2 1 150 715 39 LEU N N 120.58 0.05 1 151 716 40 SER H H 7.58 0.01 1 152 716 40 SER CA C 60.06 0.2 1 153 716 40 SER N N 121.28 0.05 1 stop_ save_