data_34134 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR assignment and structure of a peptide derived from the fusion peptide of HIV-1 gp41 in the presence of dodecylphosphocholine micelles ; _BMRB_accession_number 34134 _BMRB_flat_file_name bmr34134.str _Entry_type original _Submission_date 2017-05-08 _Accession_date 2017-05-08 _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 Jimenez M. A. . 2 Serrano S. . . 3 Nieva J. L. . 4 Huarte N. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 211 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-11-28 original BMRB . stop_ _Original_release_date 2017-05-31 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure-Related Roles for the Conservation of the HIV-1 Fusion Peptide Sequence Revealed by Nuclear Magnetic Resonance ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28930470 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Serrano S. . . 2 Huarte N. . . 3 Rujas E. . . 4 Andreu D. . . 5 Nieva J. L. . 6 Jimenez M. A. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 56 _Journal_issue 41 _Journal_ISSN 1520-4995 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5503 _Page_last 5511 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name scrFP-tag,Gp41 _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 3822.411 _Mol_thiol_state 'not present' _Details ; Residues 1-4 and 12-15 are derived from gp41 fusion peptide and correspond to residues 514-517 and 525-528 of gp41. Residues 5-11 are residues 518-524 of gp41 in a scrambled order. Residues 19-35 are derived from gp41 MPER region and correspond to residues 655-671 of gp41. Residues 16-18 are the linker sequence. ; ############################## # Polymer residue sequence # ############################## _Residue_count 35 _Mol_residue_sequence ; GIGAFGLLGFLAAGSKKXKN EQELLELDKWASLWN ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 ILE 3 GLY 4 ALA 5 PHE 6 GLY 7 LEU 8 LEU 9 GLY 10 PHE 11 LEU 12 ALA 13 ALA 14 GLY 15 SER 16 LYS 17 LYS 18 ACA 19 LYS 20 ASN 21 GLU 22 GLN 23 GLU 24 LEU 25 LEU 26 GLU 27 LEU 28 ASP 29 LYS 30 TRP 31 ALA 32 SER 33 LEU 34 TRP 35 ASN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ACA _Saveframe_category polymer_residue _Mol_type 'PEPTIDE LINKING' _Name_common '6-AMINOHEXANOIC ACID' _BMRB_code ACA _PDB_code ACA _Standard_residue_derivative . _Molecular_mass 131.173 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? O1 O1 O . 0 . ? O2 O2 O . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? N6 N6 N . 0 . ? HO2 HO2 H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H31 H31 H . 0 . ? H32 H32 H . 0 . ? H41 H41 H . 0 . ? H42 H42 H . 0 . ? H51 H51 H . 0 . ? H52 H52 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? HN61 HN61 H . 0 . ? HN62 HN62 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 DOUB C1 O1 ? ? SING C1 O2 ? ? SING C1 C2 ? ? SING O2 HO2 ? ? SING C2 C3 ? ? SING C2 H21 ? ? SING C2 H22 ? ? SING C3 C4 ? ? SING C3 H31 ? ? SING C3 H32 ? ? SING C4 C5 ? ? SING C4 H41 ? ? SING C4 H42 ? ? SING C5 C6 ? ? SING C5 H51 ? ? SING C5 H52 ? ? SING C6 N6 ? ? SING C6 H61 ? ? SING C6 H62 ? ? SING N6 HN61 ? ? SING N6 HN62 ? ? stop_ 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 HIV-1 11676 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 micelle _Details '0.6 mM scrFP-tag, 20 mM [U-98% 2H] DPC, 2.0 mM HEPES, 90 % H2O, 10 % [U-99% 2H] D2O, 0.1 mM DSS, 90% H2O/10% D2O.' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling D2O 10 % '[U-99% 2H]' DPC 20 mM '[U-98% 2H]' DSS 0.1 mM 'natural abundance' H2O 90 % 'natural abundance' HEPES 2.0 mM 'natural abundance' $entity_1 0.6 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details 'Equipped with a cryoprobe' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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 'ionic strength' 2 . mM pH 6.8 . pH* pressure 1 . atm temperature 298 . 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 H 1 'methyl protons' ppm 0.000 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 1H-1H COSY' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 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 2 2 ILE HA H 4.170 0.003 1 2 2 2 ILE HB H 1.898 0.004 1 3 2 2 ILE HG12 H 1.257 0.003 2 4 2 2 ILE HG13 H 1.546 0.004 2 5 2 2 ILE HG2 H 0.941 0.001 1 6 2 2 ILE HD1 H 0.860 0.007 1 7 3 3 GLY H H 8.579 0.002 1 8 3 3 GLY HA2 H 3.990 0.000 2 9 3 3 GLY HA3 H 3.990 0.000 2 10 4 4 ALA H H 8.542 0.002 1 11 4 4 ALA HA H 4.080 0.001 1 12 4 4 ALA HB H 1.310 0.001 1 13 5 5 PHE H H 8.519 0.004 1 14 5 5 PHE HA H 4.367 0.005 1 15 5 5 PHE HB2 H 3.170 0.002 2 16 5 5 PHE HB3 H 3.170 0.002 2 17 5 5 PHE HD1 H 7.273 0.001 1 18 5 5 PHE HD2 H 7.273 0.001 1 19 6 6 GLY H H 8.272 0.002 1 20 6 6 GLY HA2 H 3.924 0.003 2 21 6 6 GLY HA3 H 3.924 0.003 2 22 7 7 LEU H H 8.179 0.003 1 23 7 7 LEU HA H 4.176 0.004 1 24 7 7 LEU HB2 H 1.688 0.001 2 25 7 7 LEU HB3 H 1.762 0.000 2 26 7 7 LEU HD1 H 0.885 0.000 2 27 7 7 LEU HD2 H 0.942 0.001 2 28 8 8 LEU H H 8.224 0.004 1 29 8 8 LEU HA H 4.059 0.003 1 30 8 8 LEU HB2 H 1.563 0.005 2 31 8 8 LEU HB3 H 1.781 0.002 2 32 8 8 LEU HG H 1.667 0.000 1 33 8 8 LEU HD1 H 0.861 0.003 2 34 8 8 LEU HD2 H 0.898 0.000 2 35 9 9 GLY H H 8.142 0.004 1 36 9 9 GLY HA2 H 3.755 0.003 2 37 9 9 GLY HA3 H 3.856 0.006 2 38 10 10 PHE H H 7.842 0.003 1 39 10 10 PHE HA H 4.411 0.002 1 40 10 10 PHE HB2 H 3.231 0.002 2 41 10 10 PHE HB3 H 3.231 0.002 2 42 10 10 PHE HD1 H 7.267 0.002 1 43 10 10 PHE HD2 H 7.267 0.002 1 44 10 10 PHE HE1 H 7.723 0.000 1 45 10 10 PHE HE2 H 7.723 0.000 1 46 11 11 LEU H H 7.959 0.003 1 47 11 11 LEU HA H 3.990 0.003 1 48 11 11 LEU HB2 H 1.844 0.003 2 49 11 11 LEU HB3 H 1.844 0.003 2 50 11 11 LEU HG H 1.485 0.004 1 51 11 11 LEU HD1 H 0.865 0.003 2 52 11 11 LEU HD2 H 0.865 0.003 2 53 12 12 ALA H H 8.082 0.004 1 54 12 12 ALA HA H 4.128 0.003 1 55 12 12 ALA HB H 1.423 0.002 1 56 13 13 ALA H H 7.810 0.004 1 57 13 13 ALA HA H 4.206 0.002 1 58 13 13 ALA HB H 1.439 0.003 1 59 14 14 GLY H H 8.262 0.004 1 60 14 14 GLY HA2 H 3.765 0.005 2 61 14 14 GLY HA3 H 3.865 0.002 2 62 15 15 SER H H 8.065 0.003 1 63 15 15 SER HA H 4.283 0.004 1 64 15 15 SER HB2 H 3.853 0.003 2 65 15 15 SER HB3 H 3.896 0.002 2 66 16 16 LYS H H 8.073 0.004 1 67 16 16 LYS HA H 4.264 0.003 1 68 16 16 LYS HB2 H 1.792 0.005 2 69 16 16 LYS HB3 H 1.882 0.000 2 70 16 16 LYS HG2 H 1.480 0.000 2 71 16 16 LYS HG3 H 1.480 0.000 2 72 16 16 LYS HD2 H 1.674 0.000 2 73 16 16 LYS HD3 H 1.674 0.000 2 74 17 17 LYS H H 8.014 0.004 1 75 17 17 LYS HA H 4.200 0.003 1 76 17 17 LYS HB2 H 1.740 0.004 2 77 17 17 LYS HB3 H 1.794 0.008 2 78 17 17 LYS HG2 H 1.427 0.007 2 79 17 17 LYS HG3 H 1.427 0.007 2 80 17 17 LYS HD2 H 1.672 0.002 2 81 17 17 LYS HD3 H 1.672 0.002 2 82 17 17 LYS HE2 H 2.950 0.000 2 83 17 17 LYS HE3 H 2.950 0.000 2 84 18 18 ACA H21 H 2.258 0.003 2 85 18 18 ACA H22 H 2.313 0.003 2 86 18 18 ACA H31 H 1.577 0.004 2 87 18 18 ACA H32 H 1.577 0.004 2 88 18 18 ACA H41 H 1.276 0.004 2 89 18 18 ACA H42 H 1.276 0.004 2 90 18 18 ACA H51 H 1.480 0.003 2 91 18 18 ACA H52 H 1.480 0.003 2 92 18 18 ACA H61 H 3.089 0.004 2 93 18 18 ACA H62 H 3.208 0.004 2 94 18 18 ACA HN61 H 7.794 0.002 1 95 19 19 LYS H H 8.389 0.003 1 96 19 19 LYS HA H 4.237 0.001 1 97 19 19 LYS HB2 H 1.733 0.002 2 98 19 19 LYS HB3 H 1.776 0.005 2 99 19 19 LYS HG2 H 1.415 0.004 2 100 19 19 LYS HG3 H 1.415 0.004 2 101 19 19 LYS HD2 H 1.667 0.001 2 102 19 19 LYS HD3 H 1.667 0.001 2 103 19 19 LYS HE2 H 2.957 0.004 2 104 19 19 LYS HE3 H 2.957 0.004 2 105 20 20 ASN H H 8.324 0.001 1 106 20 20 ASN HA H 4.678 0.003 1 107 20 20 ASN HB2 H 2.888 0.003 2 108 20 20 ASN HB3 H 2.888 0.003 2 109 20 20 ASN HD21 H 6.921 0.001 2 110 20 20 ASN HD22 H 7.631 0.001 2 111 21 21 GLU H H 8.691 0.002 1 112 21 21 GLU HA H 4.131 0.002 1 113 21 21 GLU HB2 H 1.992 0.003 2 114 21 21 GLU HB3 H 2.071 0.006 2 115 21 21 GLU HG2 H 2.262 0.004 2 116 21 21 GLU HG3 H 2.262 0.004 2 117 22 22 GLN H H 8.280 0.003 1 118 22 22 GLN HA H 4.170 0.004 1 119 22 22 GLN HB2 H 2.092 0.003 2 120 22 22 GLN HB3 H 2.092 0.003 2 121 22 22 GLN HG2 H 2.375 0.001 2 122 22 22 GLN HG3 H 2.375 0.001 2 123 22 22 GLN HE21 H 6.851 0.000 2 124 22 22 GLN HE22 H 7.634 0.001 2 125 23 23 GLU H H 8.319 0.002 1 126 23 23 GLU HA H 4.188 0.003 1 127 23 23 GLU HB2 H 1.972 0.004 2 128 23 23 GLU HB3 H 2.058 0.004 2 129 23 23 GLU HG2 H 2.253 0.005 2 130 23 23 GLU HG3 H 2.370 0.003 2 131 24 24 LEU H H 8.103 0.002 1 132 24 24 LEU HA H 4.206 0.007 1 133 24 24 LEU HB2 H 1.585 0.001 2 134 24 24 LEU HB3 H 1.773 0.001 2 135 24 24 LEU HG H 1.692 0.000 1 136 24 24 LEU HD1 H 0.865 0.005 2 137 24 24 LEU HD2 H 0.907 0.000 2 138 25 25 LEU H H 7.926 0.002 1 139 25 25 LEU HA H 4.347 0.001 1 140 25 25 LEU HB2 H 1.590 0.002 2 141 25 25 LEU HB3 H 1.749 0.006 2 142 25 25 LEU HG H 1.684 0.005 1 143 25 25 LEU HD1 H 0.852 0.001 2 144 25 25 LEU HD2 H 0.886 0.001 2 145 26 26 GLU H H 8.035 0.002 1 146 26 26 GLU HA H 4.321 0.003 1 147 26 26 GLU HB2 H 2.035 0.006 2 148 26 26 GLU HB3 H 2.098 0.004 2 149 26 26 GLU HG2 H 2.251 0.001 2 150 26 26 GLU HG3 H 2.331 0.001 2 151 27 27 LEU H H 8.235 0.003 1 152 27 27 LEU HA H 4.094 0.003 1 153 27 27 LEU HB2 H 1.648 0.006 2 154 27 27 LEU HB3 H 1.772 0.004 2 155 27 27 LEU HG H 1.758 0.003 1 156 27 27 LEU HD1 H 0.840 0.005 2 157 27 27 LEU HD2 H 0.921 0.004 2 158 28 28 ASP H H 8.513 0.002 1 159 28 28 ASP HA H 4.383 0.004 1 160 28 28 ASP HB2 H 2.690 0.003 2 161 28 28 ASP HB3 H 2.690 0.003 2 162 29 29 LYS H H 7.816 0.002 1 163 29 29 LYS HA H 4.085 0.003 1 164 29 29 LYS HB2 H 1.675 0.002 2 165 29 29 LYS HB3 H 1.793 0.005 2 166 29 29 LYS HG2 H 1.150 0.005 2 167 29 29 LYS HG3 H 1.300 0.003 2 168 29 29 LYS HD2 H 1.537 0.003 2 169 29 29 LYS HD3 H 1.537 0.003 2 170 29 29 LYS HE2 H 2.773 0.003 2 171 29 29 LYS HE3 H 2.807 0.005 2 172 30 30 TRP H H 7.789 0.004 1 173 30 30 TRP HA H 4.470 0.003 1 174 30 30 TRP HB2 H 3.228 0.005 2 175 30 30 TRP HB3 H 3.414 0.004 2 176 30 30 TRP HD1 H 7.319 0.001 1 177 30 30 TRP HE1 H 10.640 0.000 1 178 30 30 TRP HE3 H 7.514 0.003 1 179 30 30 TRP HZ2 H 7.443 0.003 1 180 30 30 TRP HZ3 H 6.941 0.001 1 181 30 30 TRP HH2 H 7.069 0.001 1 182 31 31 ALA H H 8.221 0.001 1 183 31 31 ALA HA H 3.866 0.002 1 184 31 31 ALA HB H 1.461 0.004 1 185 32 32 SER H H 7.941 0.002 1 186 32 32 SER HA H 4.262 0.002 1 187 32 32 SER HB2 H 3.952 0.003 2 188 32 32 SER HB3 H 3.952 0.003 2 189 33 33 LEU H H 7.735 0.002 1 190 33 33 LEU HA H 4.145 0.003 1 191 33 33 LEU HB2 H 1.788 0.003 2 192 33 33 LEU HB3 H 1.894 0.001 2 193 33 33 LEU HG H 1.554 0.002 1 194 33 33 LEU HD1 H 0.884 0.006 2 195 33 33 LEU HD2 H 0.939 0.003 2 196 34 34 TRP H H 7.723 0.002 1 197 34 34 TRP HA H 4.533 0.001 1 198 34 34 TRP HB2 H 3.228 0.002 2 199 34 34 TRP HB3 H 3.319 0.001 2 200 34 34 TRP HD1 H 7.178 0.001 1 201 34 34 TRP HE1 H 10.391 0.001 1 202 34 34 TRP HE3 H 7.500 0.004 1 203 34 34 TRP HZ2 H 7.445 0.002 1 204 34 34 TRP HZ3 H 6.980 0.002 1 205 34 34 TRP HH2 H 7.069 0.001 1 206 35 35 ASN H H 7.985 0.002 1 207 35 35 ASN HA H 4.535 0.003 1 208 35 35 ASN HB2 H 2.715 0.002 2 209 35 35 ASN HB3 H 2.784 0.001 2 210 35 35 ASN HD21 H 6.975 0.001 2 211 35 35 ASN HD22 H 7.551 0.002 2 stop_ save_