data_15389 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; solution structure of hiv-1 gp41 fusion domain bound to DPC micelle ; _BMRB_accession_number 15389 _BMRB_flat_file_name bmr15389.str _Entry_type original _Submission_date 2007-07-18 _Accession_date 2007-07-18 _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 Li Y . . 2 Tamm L. K. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 84 "15N chemical shifts" 21 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-18 original author . stop_ _Original_release_date 2008-06-18 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Combined NMR and EPR spectroscopy to determine structures of viral fusion domains in membranes' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17963720 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tamm Lukas K. . 2 Lai Alex L. . 3 Li Yinling . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_volume 1768 _Journal_issue 12 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3052 _Page_last 3060 _Year 2007 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'HIV fusion peptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'HIV fusion peptide' $Envelope_glycoprotein stop_ _System_molecular_weight 2902 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Envelope_glycoprotein _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Envelope_glycoprotein _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 31 _Mol_residue_sequence ; AVGIGALFLGFLGAAGSTVG AASGGGKKKKK ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 VAL 3 GLY 4 ILE 5 GLY 6 ALA 7 LEU 8 PHE 9 LEU 10 GLY 11 PHE 12 LEU 13 GLY 14 ALA 15 ALA 16 GLY 17 SER 18 THR 19 VAL 20 GLY 21 ALA 22 ALA 23 SER 24 GLY 25 GLY 26 GLY 27 LYS 28 LYS 29 LYS 30 LYS 31 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-31 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 PDB 2PJV "Solution Structure Of Hiv-1 Gp41 Fusion Domain Bound To Dpc Micelle" 100.00 31 100.00 100.00 2.94e-08 GB AAB68317 "envelope glycoprotein, partial [Human immunodeficiency virus 1]" 58.06 433 100.00 100.00 8.66e-02 GB AAB68318 "envelope glycoprotein, partial [Human immunodeficiency virus 1]" 58.06 434 100.00 100.00 8.67e-02 GB AAB68319 "envelope glycoprotein, partial [Human immunodeficiency virus 1]" 58.06 416 100.00 100.00 3.07e-01 GB AAB68320 "envelope glycoprotein, partial [Human immunodeficiency virus 1]" 58.06 416 100.00 100.00 2.06e-01 GB AAB68321 "envelope glycoprotein, partial [Human immunodeficiency virus 1]" 58.06 433 100.00 100.00 8.66e-02 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain _Gene_mnemonic $Envelope_glycoprotein HIV-1 11676 Viruses . Lentivirus HIV-1 LAVmal 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 $Envelope_glycoprotein 'recombinant technology' bacteria Escherichia coli BLR(DE3)pLysS PET31b(+) stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1 MM N15-PEPTIDE IN THE PRESENCE OF 200 MM D38-DPC IN 0.05% NAN3, 5 MM DTT, 20 MM D4-ACETIC ACID, 95% H2O/5% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Envelope_glycoprotein 1 mM [U-15N] D38-DPC 200 mM . NAN3 0.05 % . DTT 5 mM . 'D4-ACETIC ACID' 20 mM . H2O 95 % . D2O 5 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '2 MM PEPTIDE IN THE PRESENCE OF 400 MM D38-DPC IN 0.05% NAN3, 5 MM DTT, 20 MM D4-ACETIC ACID, 95% H2O/5% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Envelope_glycoprotein 2 mM . D38-DPC 400 mM . NAN3 0.05 % . DTT 5 mM . 'D4-ACETIC ACID' 20 mM . H2O 95 % . D2O 5 % . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 2.4 loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.110 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_OPAL _Saveframe_category software _Name OPAL _Version 2.6 loop_ _Vendor _Address _Electronic_address 'Luginbuhl, Guntert, Billeter and Wuthrich' . . 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 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_2 save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_2 save_ save_3D_15N-separated_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name 3D_15N-separated_NOESY _Sample_label $sample_1 save_ save_HNHA_4 _Saveframe_category NMR_applied_experiment _Experiment_name HNHA _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 pH 7.4 . pH pressure 1 1 atm temperature 303 . 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 DSS H 1 'methyl protons' ppm 0 external direct . . . 1 DSS N 15 'methyl protons' ppm 0 external indirect . . . 0.1 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 NOESY' stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'HIV fusion peptide' _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 VAL HA H 4.253 0.042 . 2 2 2 VAL HB H 2.168 0.009 . 3 2 2 VAL HG1 H 1.028 0.009 . 4 2 2 VAL HG2 H 1.028 0.009 . 5 3 3 GLY H H 8.521 0.010 . 6 3 3 GLY HA2 H 4.207 0.003 . 7 3 3 GLY HA3 H 4.102 0.002 . 8 3 3 GLY N N 111.710 0.036 . 9 4 4 ILE H H 8.772 0.007 . 10 4 4 ILE HA H 3.934 0.009 . 11 4 4 ILE HB H 1.965 0.009 . 12 4 4 ILE HD1 H 0.958 0.005 . 13 4 4 ILE HG12 H 1.641 0.005 . 14 4 4 ILE HG13 H 1.352 0.005 . 15 4 4 ILE HG2 H 0.990 0.005 . 16 4 4 ILE N N 121.300 0.068 . 17 5 5 GLY H H 9.112 0.005 . 18 5 5 GLY HA2 H 3.940 0.003 . 19 5 5 GLY HA3 H 3.773 0.009 . 20 5 5 GLY N N 109.870 0.033 . 21 6 6 ALA H H 8.132 0.007 . 22 6 6 ALA HA H 4.144 0.008 . 23 6 6 ALA HB H 1.502 0.006 . 24 6 6 ALA N N 122.981 0.056 . 25 7 7 LEU H H 8.031 0.005 . 26 7 7 LEU HA H 4.136 0.007 . 27 7 7 LEU HB2 H 1.908 0.009 . 28 7 7 LEU HB3 H 1.706 0.022 . 29 7 7 LEU HD1 H 0.951 0.005 . 30 7 7 LEU HD2 H 0.914 0.005 . 31 7 7 LEU HG H 1.655 0.052 . 32 7 7 LEU N N 120.130 0.055 . 33 8 8 PHE H H 8.392 0.008 . 34 8 8 PHE HA H 4.377 0.010 . 35 8 8 PHE N N 118.680 0.069 . 36 9 9 LEU H H 8.510 0.007 . 37 9 9 LEU HA H 4.208 0.006 . 38 9 9 LEU HB2 H 1.949 0.005 . 39 9 9 LEU HB3 H 1.918 0.005 . 40 9 9 LEU HD1 H 0.988 0.006 . 41 9 9 LEU HD2 H 0.964 0.008 . 42 9 9 LEU HG H 1.600 0.006 . 43 9 9 LEU N N 118.147 0.165 . 44 10 10 GLY H H 8.239 0.008 . 45 10 10 GLY HA2 H 3.947 0.002 . 46 10 10 GLY HA3 H 3.947 0.002 . 47 10 10 GLY N N 107.291 0.049 . 48 11 11 PHE H H 8.065 0.005 . 49 11 11 PHE HA H 4.493 0.023 . 50 11 11 PHE HB2 H 3.271 0.016 . 51 11 11 PHE HB3 H 3.271 0.016 . 52 11 11 PHE N N 122.459 0.127 . 53 12 12 LEU H H 8.027 0.006 . 54 12 12 LEU HA H 3.958 0.009 . 55 12 12 LEU HB2 H 1.762 0.007 . 56 12 12 LEU HB3 H 1.724 0.006 . 57 12 12 LEU HD1 H 0.851 0.007 . 58 12 12 LEU HD2 H 0.834 0.016 . 59 12 12 LEU HG H 1.553 0.013 . 60 12 12 LEU N N 117.843 0.195 . 61 13 13 GLY H H 8.080 0.016 . 62 13 13 GLY HA2 H 3.954 0.006 . 63 13 13 GLY HA3 H 3.913 0.006 . 64 13 13 GLY N N 105.014 0.140 . 65 14 14 ALA H H 7.965 0.052 . 66 14 14 ALA HA H 4.369 0.009 . 67 14 14 ALA HB H 1.472 0.002 . 68 14 14 ALA N N 123.634 0.140 . 69 15 15 ALA H H 8.254 0.005 . 70 15 15 ALA HA H 4.203 0.010 . 71 15 15 ALA HB H 1.358 0.002 . 72 15 15 ALA N N 121.566 0.032 . 73 16 16 GLY H H 8.359 0.005 . 74 16 16 GLY HA2 H 3.939 0.004 . 75 16 16 GLY HA3 H 3.939 0.004 . 76 16 16 GLY N N 105.920 0.037 . 77 17 17 SER H H 8.024 0.023 . 78 17 17 SER HA H 4.253 0.005 . 79 17 17 SER N N 115.091 0.016 . 80 18 18 THR H H 8.164 0.006 . 81 18 18 THR HA H 4.344 0.017 . 82 18 18 THR HB H 4.312 0.009 . 83 18 18 THR HG2 H 1.265 0.009 . 84 18 18 THR N N 116.174 0.088 . 85 19 19 VAL H H 8.031 0.003 . 86 19 19 VAL HA H 4.106 0.008 . 87 19 19 VAL HB H 2.185 0.008 . 88 19 19 VAL HG1 H 1.022 0.007 . 89 19 19 VAL HG2 H 0.992 0.005 . 90 19 19 VAL N N 120.323 0.018 . 91 20 20 GLY H H 8.412 0.005 . 92 20 20 GLY HA2 H 3.975 0.006 . 93 20 20 GLY HA3 H 3.975 0.006 . 94 20 20 GLY N N 110.759 0.091 . 95 21 21 ALA H H 8.084 0.004 . 96 21 21 ALA HA H 4.344 0.016 . 97 21 21 ALA HB H 1.488 0.008 . 98 21 21 ALA N N 123.556 0.011 . 99 22 22 ALA H H 8.303 0.004 . 100 22 22 ALA HA H 4.392 0.008 . 101 22 22 ALA HB H 1.460 0.003 . 102 22 22 ALA N N 122.426 0.129 . 103 23 23 SER H H 8.210 0.003 . 104 23 23 SER HA H 4.475 0.003 . 105 23 23 SER N N 114.254 0.087 . stop_ save_