data_30472 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Oligomeric Structure of the HIV gp41 MPER-TMD in Phospholipid Bilayers ; _BMRB_accession_number 30472 _BMRB_flat_file_name bmr30472.str _Entry_type original _Submission_date 2018-06-01 _Accession_date 2018-06-01 _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 Kwon B. . . 2 Lee M. . . 3 Waring A. J. . 4 Hong M. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 23 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-08-03 original BMRB . stop_ _Original_release_date 2018-06-26 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Oligomeric Structure of the HIV gp41 MPER-TMD in Phospholipid Bilayers ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kwon B. . . 2 Lee M. . . 3 Hong M. . . 4 Waring A. J. . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _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 'Transmembrane protein gp41' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, 1' $entity_1 'entity_1, 2' $entity_1 'entity_1, 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 entity_1 _Molecular_mass 4672.646 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 39 _Mol_residue_sequence ; KWASLWNWFNITNWLWYIKL FIMIVGGLVGLRIVFAVLS ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 TRP 3 ALA 4 SER 5 LEU 6 TRP 7 ASN 8 TRP 9 PHE 10 ASN 11 ILE 12 THR 13 ASN 14 TRP 15 LEU 16 TRP 17 TYR 18 ILE 19 LYS 20 LEU 21 PHE 22 ILE 23 MET 24 ILE 25 VAL 26 GLY 27 GLY 28 LEU 29 VAL 30 GLY 31 LEU 32 ARG 33 ILE 34 VAL 35 PHE 36 ALA 37 VAL 38 LEU 39 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 $entity_1 'isolate HXB2' 11706 Viruses . Lentivirus HIV-1 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 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type membrane _Details ; 33 % w/w 4-19F-F699 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 33 '% w/w' 4-19F-F699 'HEPES buffer' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type membrane _Details ; 33 % w/w [U-13C; U-15N]-L684,I686, G694, 19F-5F-W678, 19F-4F-F699 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 33 '% w/w' '[U-13C; U-15N]-L684,I686, G694, 19F-5F-W678, 19F-4F-F699' 'HEPES buffer' 10 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type membrane _Details ; 33 % w/w [U-13C; U-15N]-L669,I686, A700, 13C'-G694, 19F-5F-W680 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 33 '% w/w' "[U-13C; U-15N]-L669,I686, A700, 13C'-G694, 19F-5F-W680" 'HEPES buffer' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name Matlab _Version . loop_ _Vendor _Address _Electronic_address Mathwork . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name GROMACS _Version . loop_ _Vendor _Address _Electronic_address 'University of GroningenRoyal Institute of TechnologyUppsala University' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name CHARMM-GUI _Version . loop_ _Vendor _Address _Electronic_address 'Lehigh University / Department of Biological Sciences / Department of Bioengineering/ Im Lab' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Bruker _Field_strength 400 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Bruker _Field_strength 600 _Details . save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Bruker _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_13C-13C_DARR_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR' _Sample_label $sample_3 save_ save_2D_water_Edited_DARR_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D water Edited DARR' _Sample_label $sample_3 save_ save_13C-19F_REDOR_3 _Saveframe_category NMR_applied_experiment _Experiment_name '13C-19F REDOR' _Sample_label $sample_2 save_ save_2D_water_Edited_DARR_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D water Edited DARR' _Sample_label $sample_2 save_ save_19F_CODEX_5 _Saveframe_category NMR_applied_experiment _Experiment_name '19F CODEX' _Sample_label $sample_1 save_ save_19F_CODEX_6 _Saveframe_category NMR_applied_experiment _Experiment_name '19F CODEX' _Sample_label $sample_3 save_ save_19F_CODEX_7 _Saveframe_category NMR_applied_experiment _Experiment_name '19F CODEX' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.5 . pH pressure 1 . atm temperature 263 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.5 . pH pressure 1 . atm temperature 233 . 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 'N-formyl-Met-Leu-Phe-OH (f-MLF)' C 13 'methyl carbons' ppm 14 internal indirect . . . 1.0 Teflon F 19 fluorine ppm -122 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 13C-13C DARR' '2D water Edited DARR' '13C-19F REDOR' '19F CODEX' stop_ loop_ _Sample_label $sample_3 $sample_2 $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 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 5 5 LEU C C 175.8 0.5 1 2 5 5 LEU CA C 55.1 0.5 1 3 5 5 LEU CB C 40.2 0.5 1 4 5 5 LEU CG C 24.6 0.5 1 5 5 5 LEU CD1 C 23.1 0.8 2 6 5 5 LEU CD2 C 22.1 0.8 2 7 20 20 LEU C C 175.8 0.5 1 8 20 20 LEU CA C 55.9 0.5 1 9 20 20 LEU CB C 38.8 0.5 1 10 20 20 LEU CG C 24.8 0.5 1 11 20 20 LEU CD1 C 21.6 0.8 2 12 20 20 LEU CD2 C 21.6 0.8 2 13 22 22 ILE C C 175.7 0.5 1 14 22 22 ILE CA C 63.6 0.5 1 15 22 22 ILE CB C 35.5 0.5 1 16 22 22 ILE CG1 C 27.8 0.5 1 17 22 22 ILE CG2 C 15.8 0.5 1 18 22 22 ILE CD1 C 12.1 0.5 1 19 30 30 GLY C C 173.0 0.5 1 20 30 30 GLY CA C 45.8 0.5 1 21 36 36 ALA C C 178.5 0.5 1 22 36 36 ALA CA C 53.0 0.5 1 23 36 36 ALA CB C 16.4 0.5 1 stop_ save_