data_30090 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the transmembrane domain of HIV-1 gp41 in bicelle ; _BMRB_accession_number 30090 _BMRB_flat_file_name bmr30090.str _Entry_type original _Submission_date 2016-05-14 _Accession_date 2016-05-14 _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 Dev J. . . 2 Fu Q. . . 3 Park D. . . 4 Chen B. . . 5 Chou J. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 37 "13C chemical shifts" 75 "15N chemical shifts" 37 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-06-24 original BMRB . stop_ _Original_release_date 2016-06-24 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural Basis for Membrane Anchoring of HIV-1 Envelope Spike ; _Citation_status . _Citation_type . _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dev J. . . 2 Park D. . . 3 Fu Q. . . 4 Chen J. . . 5 Ha H. H. . 6 Ghantous F. . . 7 Herrmann T. . . 8 Chang W. . . 9 Liu Z. . . 10 Frey G. . . 11 Seaman M. S. . 12 Chen B. . . 13 Chou J. J. . stop_ _Journal_abbreviation 'To be published' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Envelope glycoprotein gp160' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, chain 1' $entity_1 'entity_1, chain 2' $entity_1 'entity_1, chain 3' $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 'Envelope glycoprotein gp160' _Molecular_mass 4650.604 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 40 _Mol_residue_sequence ; NWLWYIRIFIIIVGSLIGLR IVFAVLSLVNRVRQGYSPLS ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 678 ASN 2 679 TRP 3 680 LEU 4 681 TRP 5 682 TYR 6 683 ILE 7 684 ARG 8 685 ILE 9 686 PHE 10 687 ILE 11 688 ILE 12 689 ILE 13 690 VAL 14 691 GLY 15 692 SER 16 693 LEU 17 694 ILE 18 695 GLY 19 696 LEU 20 697 ARG 21 698 ILE 22 699 VAL 23 700 PHE 24 701 ALA 25 702 VAL 26 703 LEU 27 704 SER 28 705 LEU 29 706 VAL 30 707 ASN 31 708 ARG 32 709 VAL 33 710 ARG 34 711 GLN 35 712 GLY 36 713 TYR 37 714 SER 38 715 PRO 39 716 LEU 40 717 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 viruses 11676 Viruses . Lentivirus . 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' . Escherichia coli 'BL21 (DE3)' pMM-LR6 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type bicelle _Details ; 0.8 mM [U-13C; U-15N; 85%-2H] HIV-1 gp41 Transmembrane Domain, 60 mM regular 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM regular 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling '1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)' 120 mM 'natural abundance' '1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)' 60 mM 'natural abundance' $entity_1 0.8 mM '[U-13C; U-15N; 85%-2H]' MES 25 mM 'natural abundance' NaN3 0.1 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type bicelle _Details ; 0.8 mM [U-13C; U-15N] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling '1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)' 120 mM 'acyl chains 2H labeled' '1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)' 60 mM 'acyl chains 2H labeled' $entity_1 0.8 mM '[U-13C; U-15N]' MES 25 mM 'natural abundance' NaN3 0.1 % 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type bicelle _Details ; 0.4 mM [U-15N; U-2H] HIV-1 gp41 Transmembrane Domain, 0.4 mM [15% 13C] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling '1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)' 120 mM 'acyl chains 2H labeled' '1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)' 60 mM 'acyl chains 2H labeled' $entity_1 0.4 mM '[U-15N; U-2H]' $entity_1 0.4 mM '[15% 13C]' MES 25 mM 'natural abundance' NaN3 0.1 % 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type bicelle _Details ; 0.8 mM [U-15N] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling '1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)' 120 mM 'acyl chains 2H labeled' '1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)' 60 mM 'acyl chains 2H labeled' $entity_1 0.8 mM [U-15N] MES 25 mM 'natural abundance' NaN3 0.1 % '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 NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_5 _Saveframe_category software _Name XPLOR-NIH _Version 2.42 loop_ _Vendor _Address _Electronic_address 'G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandra' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceII _Field_strength 600 _Details 'cryogenic probe' save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceII _Field_strength 750 _Details 'cryogenic probe' save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 900 _Details 'cryogenic probe' save_ ############################# # NMR applied experiments # ############################# save_3D_TROSY_HNCA_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D TROSY HNCA' _Sample_label $sample_1 save_ save_3D_TROSY_HNCOCA_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D TROSY HNCOCA' _Sample_label $sample_1 save_ save_3D_TROSY_HNCACO_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D TROSY HNCACO' _Sample_label $sample_1 save_ save_3D_TROSY_HNCO_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D TROSY HNCO' _Sample_label $sample_1 save_ save_3D_15N_NOESY-TROSY-HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N NOESY-TROSY-HSQC' _Sample_label $sample_2 save_ save_3D_13C_NOESY-HSQC_(Methyls)_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 13C NOESY-HSQC (Methyls)' _Sample_label $sample_2 save_ save_3D_15N_NOESY-TROSY-HSQC_(long_mixing_time)_7 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N NOESY-TROSY-HSQC (long mixing time)' _Sample_label $sample_3 save_ save_2D_15N_TROSY-HSQC_for_GdDOTA_titration_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N TROSY-HSQC for GdDOTA titration' _Sample_label $sample_1 save_ save_3D_15N_NOESY-TROSY-HSQC_(short_mixing_time)_9 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N NOESY-TROSY-HSQC (short mixing time)' _Sample_label $sample_4 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 10 mM pH 6.7 0.1 pH pressure 1 . atm temperature 303 0.1 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_ _Software_label $software_1 stop_ loop_ _Experiment_label '3D TROSY HNCA' '3D TROSY HNCOCA' '3D TROSY HNCACO' '3D TROSY HNCO' '3D 15N NOESY-TROSY-HSQC' '3D 15N NOESY-TROSY-HSQC (short mixing time)' stop_ loop_ _Sample_label $sample_1 $sample_2 $sample_4 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, chain 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 1 678 2 TRP C C 177.26 0.001 1 2 678 2 TRP CA C 59.49 0.002 1 3 679 3 LEU H H 7.81 0.002 1 4 679 3 LEU C C 178.38 0.001 1 5 679 3 LEU CA C 57.07 0.002 1 6 679 3 LEU N N 119.64 0.010 1 7 680 4 TRP H H 7.82 0.002 1 8 680 4 TRP C C 175.25 0.001 1 9 680 4 TRP CA C 60.46 0.002 1 10 680 4 TRP N N 120.61 0.010 1 11 681 5 TYR H H 7.82 0.002 1 12 681 5 TYR C C 177.63 0.001 1 13 681 5 TYR CA C 60.27 0.002 1 14 681 5 TYR N N 116.01 0.010 1 15 682 6 ILE H H 8.15 0.002 1 16 682 6 ILE C C 176.82 0.001 1 17 682 6 ILE CA C 63.89 0.002 1 18 682 6 ILE N N 118.31 0.010 1 19 683 7 ARG H H 8.10 0.002 1 20 683 7 ARG C C 177.34 0.001 1 21 683 7 ARG CA C 59.69 0.002 1 22 683 7 ARG N N 120.08 0.010 1 23 684 8 ILE H H 7.86 0.002 1 24 684 8 ILE C C 176.90 0.001 1 25 684 8 ILE CA C 63.22 0.002 1 26 684 8 ILE N N 117.25 0.010 1 27 685 9 PHE H H 8.25 0.002 1 28 685 9 PHE C C 176.16 0.001 1 29 685 9 PHE CA C 61.14 0.002 1 30 685 9 PHE N N 120.44 0.010 1 31 686 10 ILE H H 8.42 0.002 1 32 686 10 ILE C C 177.33 0.001 1 33 686 10 ILE CA C 64.24 0.002 1 34 686 10 ILE N N 118.22 0.010 1 35 687 11 ILE H H 8.12 0.002 1 36 687 11 ILE C C 178.40 0.001 1 37 687 11 ILE CA C 64.67 0.002 1 38 687 11 ILE N N 120.08 0.010 1 39 688 12 ILE H H 8.54 0.002 1 40 688 12 ILE C C 176.78 0.001 1 41 688 12 ILE CA C 65.29 0.002 1 42 688 12 ILE N N 122.03 0.010 1 43 689 13 VAL H H 8.40 0.002 1 44 689 13 VAL C C 177.59 0.001 1 45 689 13 VAL CA C 66.32 0.002 1 46 689 13 VAL N N 118.58 0.010 1 47 690 14 GLY H H 8.87 0.002 1 48 690 14 GLY C C 174.80 0.001 1 49 690 14 GLY CA C 46.62 0.002 1 50 690 14 GLY N N 107.06 0.010 1 51 691 15 SER H H 8.16 0.002 1 52 691 15 SER C C 174.98 0.001 1 53 691 15 SER CA C 62.73 0.002 1 54 691 15 SER N N 118.22 0.010 1 55 692 16 LEU H H 7.93 0.002 1 56 692 16 LEU C C 178.33 0.001 1 57 692 16 LEU CA C 57.31 0.002 1 58 692 16 LEU N N 121.77 0.010 1 59 693 17 ILE H H 8.15 0.002 1 60 693 17 ILE C C 177.65 0.001 1 61 693 17 ILE CA C 64.08 0.002 1 62 693 17 ILE N N 118.58 0.010 1 63 694 18 GLY H H 8.61 0.002 1 64 694 18 GLY C C 174.51 0.001 1 65 694 18 GLY CA C 46.84 0.002 1 66 694 18 GLY N N 107.59 0.010 1 67 695 19 LEU H H 8.51 0.002 1 68 695 19 LEU C C 177.60 0.001 1 69 695 19 LEU CA C 57.10 0.002 1 70 695 19 LEU N N 121.24 0.010 1 71 696 20 ARG H H 8.01 0.002 1 72 696 20 ARG C C 179.05 0.001 1 73 696 20 ARG CA C 58.14 0.002 1 74 696 20 ARG N N 119.11 0.010 1 75 697 21 ILE H H 8.26 0.002 1 76 697 21 ILE C C 176.85 0.001 1 77 697 21 ILE CA C 64.67 0.002 1 78 697 21 ILE N N 120.26 0.010 1 79 698 22 VAL H H 8.35 0.002 1 80 698 22 VAL C C 177.25 0.001 1 81 698 22 VAL CA C 66.63 0.002 1 82 698 22 VAL N N 120.08 0.010 1 83 699 23 PHE H H 8.52 0.002 1 84 699 23 PHE C C 177.60 0.001 1 85 699 23 PHE CA C 60.94 0.002 1 86 699 23 PHE N N 117.96 0.010 1 87 700 24 ALA H H 8.15 0.002 1 88 700 24 ALA C C 180.08 0.001 1 89 700 24 ALA CA C 54.29 0.002 1 90 700 24 ALA N N 123.10 0.010 1 91 701 25 VAL H H 8.42 0.002 1 92 701 25 VAL C C 177.13 0.001 1 93 701 25 VAL CA C 65.90 0.002 1 94 701 25 VAL N N 118.84 0.010 1 95 702 26 LEU H H 8.45 0.002 1 96 702 26 LEU C C 178.37 0.001 1 97 702 26 LEU CA C 57.31 0.002 1 98 702 26 LEU N N 119.46 0.010 1 99 703 27 SER H H 8.14 0.002 1 100 703 27 SER C C 176.38 0.001 1 101 703 27 SER CA C 60.94 0.002 1 102 703 27 SER N N 114.50 0.010 1 103 704 28 LEU H H 7.72 0.002 1 104 704 28 LEU C C 178.05 0.001 1 105 704 28 LEU CA C 57.31 0.002 1 106 704 28 LEU N N 122.83 0.010 1 107 705 29 VAL H H 8.33 0.002 1 108 705 29 VAL C C 177.05 0.001 1 109 705 29 VAL CA C 65.70 0.002 1 110 705 29 VAL N N 118.40 0.010 1 111 706 30 ASN H H 8.18 0.002 1 112 706 30 ASN C C 176.62 0.001 1 113 706 30 ASN CA C 55.45 0.002 1 114 706 30 ASN N N 117.51 0.010 1 115 707 31 ARG H H 7.92 0.002 1 116 707 31 ARG C C 178.57 0.001 1 117 707 31 ARG CA C 58.14 0.002 1 118 707 31 ARG N N 119.29 0.010 1 119 708 32 VAL H H 8.14 0.002 1 120 708 32 VAL C C 178.01 0.001 1 121 708 32 VAL CA C 64.36 0.002 1 122 708 32 VAL N N 119.38 0.010 1 123 709 33 ARG H H 8.23 0.002 1 124 709 33 ARG C C 177.08 0.001 1 125 709 33 ARG CA C 57.72 0.002 1 126 709 33 ARG N N 120.17 0.010 1 127 710 34 GLN H H 7.80 0.002 1 128 710 34 GLN C C 176.34 0.001 1 129 710 34 GLN CA C 55.92 0.002 1 130 710 34 GLN N N 117.43 0.010 1 131 711 35 GLY H H 7.89 0.002 1 132 711 35 GLY C C 173.35 0.001 1 133 711 35 GLY CA C 44.51 0.002 1 134 711 35 GLY N N 107.77 0.010 1 135 712 36 TYR H H 7.89 0.002 1 136 712 36 TYR C C 174.74 0.001 1 137 712 36 TYR CA C 57.00 0.002 1 138 712 36 TYR N N 120.44 0.010 1 139 713 37 SER H H 8.06 0.002 1 140 713 37 SER C C 172.40 0.001 1 141 713 37 SER CA C 54.93 0.002 1 142 713 37 SER N N 118.58 0.010 1 143 714 38 PRO C C 176.01 0.001 1 144 715 39 LEU H H 8.12 0.002 1 145 715 39 LEU C C 175.94 0.001 1 146 715 39 LEU N N 120.44 0.010 1 147 716 40 SER H H 7.64 0.002 1 148 716 40 SER C C 177.94 0.001 1 149 716 40 SER N N 121.32 0.010 1 stop_ save_