data_19583 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR assignment and structure of a peptide derived from the membrane proximal external region of HIV-1 gp41 in the presence of dodecylphosphocholine micelles ; _BMRB_accession_number 19583 _BMRB_flat_file_name bmr19583.str _Entry_type original _Submission_date 2013-10-24 _Accession_date 2013-10-24 _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 Serrano Soraya . . 2 Apellaniz Beatriz . . 3 Huarte Nerea . . 4 Nieva Jose L. . 5 Jimenez 'M. Angeles' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 203 "13C chemical shifts" 20 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-03-23 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 19582 'peptide derived from the membrane proximal external region of HIV-1 gp41 in the presence of hexafluoroisopropanol' stop_ _Original_release_date 2015-03-23 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and its Connection to the Inmmunogenic Membrane-proximal External Region' _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 Serrano Soraya . . 2 Apellaniz Beatriz . . 3 Huarte Nerea . . 4 Jimenez 'M. Angeles' . . 5 Nieva Jose L. . stop_ _Journal_abbreviation 'Not known' _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 'peptide derived from the membrane proximal external region of HIV-1 gp41' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label CpreTM $CpreTM stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_CpreTM _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common CpreTM _Molecular_mass 3489.345 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; KKKNWFDITNWLWYIKLFIM IVGGLVKK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 LYS 2 2 LYS 3 3 LYS 4 4 ASN 5 5 TRP 6 6 PHE 7 7 ASP 8 8 ILE 9 9 THR 10 10 ASN 11 11 TRP 12 12 LEU 13 13 TRP 14 14 TYR 15 15 ILE 16 16 LYS 17 17 LEU 18 18 PHE 19 19 ILE 20 20 MET 21 21 ILE 22 22 VAL 23 23 GLY 24 24 GLY 25 25 LEU 26 26 VAL 27 27 LYS 28 28 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-04-23 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 BMRB 19582 CpreTM 100.00 28 100.00 100.00 5.75e-09 PDB 2MG2 "Nmr Assignment And Structure Of A Peptide Derived From The Membrane Proximal External Region Of Hiv-1 Gp41 In The Presence Of H" 100.00 28 100.00 100.00 5.75e-09 PDB 2MG3 "Nmr Assignment And Structure Of A Peptide Derived From The Membrane Proximal External Region Of Hiv-1 Gp41 In The Presence Of D" 100.00 28 100.00 100.00 5.75e-09 GB AAC58893 "envelope glycoprotein [Human immunodeficiency virus 1]" 82.14 859 100.00 100.00 3.25e-06 GB AAD12142 "envelope glycoprotein [Simian-Human immunodeficiency virus]" 82.14 856 100.00 100.00 4.46e-06 GB AAS72624 "envelope glycoprotein, partial [Human immunodeficiency virus 1]" 50.00 130 100.00 100.00 2.89e+00 GB AAV28703 "env [Simian-Human immunodeficiency virus]" 82.14 856 100.00 100.00 4.59e-06 GB AAV39368 "envelope glycoprotein [Human immunodeficiency virus 1]" 71.43 143 100.00 100.00 1.77e-04 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $CpreTM HIV 12721 Viruses . Lentivirus 'Human immunodeficiency virus' 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 $CpreTM 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $CpreTM 0.5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % '[U-100% 2H]' DPC 20 mM '[U-99% 2H]' HEPES 2 mM 'natural abundance' DSS 0.1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . 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_ ############################# # 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_ save_2D_1H-13C_HSQC_aliphatic_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . 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 7.0 . pH pressure 1 . atm temperature 298 . 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 C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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 1H-1H COSY' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-13C HSQC aliphatic' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name CpreTM _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 1 1 LYS HA H 3.75 0.010 1 2 1 1 LYS HB2 H 1.76 0.010 2 3 1 1 LYS HB3 H 1.76 0.010 2 4 1 1 LYS HG2 H 1.41 0.010 2 5 1 1 LYS HG3 H 1.41 0.010 2 6 1 1 LYS HD2 H 1.68 0.010 2 7 1 1 LYS HD3 H 1.68 0.010 2 8 2 2 LYS HA H 4.30 0.010 1 9 2 2 LYS HB2 H 1.75 0.010 2 10 2 2 LYS HB3 H 1.79 0.010 2 11 2 2 LYS HG2 H 1.42 0.010 2 12 2 2 LYS HG3 H 1.42 0.010 2 13 2 2 LYS HD2 H 1.67 0.010 2 14 2 2 LYS HD3 H 1.67 0.010 2 15 2 2 LYS HE2 H 2.98 0.010 2 16 2 2 LYS HE3 H 2.98 0.010 2 17 3 3 LYS H H 8.19 0.010 1 18 3 3 LYS HA H 4.27 0.010 1 19 3 3 LYS HB2 H 1.67 0.010 2 20 3 3 LYS HB3 H 1.67 0.010 2 21 3 3 LYS HG2 H 1.33 0.010 2 22 3 3 LYS HG3 H 1.38 0.010 2 23 3 3 LYS HD2 H 1.61 0.010 2 24 3 3 LYS HD3 H 1.61 0.010 2 25 3 3 LYS HE2 H 2.91 0.010 2 26 3 3 LYS HE3 H 2.91 0.010 2 27 4 4 ASN H H 8.56 0.010 1 28 4 4 ASN HA H 4.74 0.010 1 29 4 4 ASN HB2 H 2.62 0.010 2 30 4 4 ASN HB3 H 2.62 0.010 2 31 4 4 ASN HD21 H 7.72 0.010 2 32 4 4 ASN HD22 H 6.96 0.010 2 33 5 5 TRP H H 8.54 0.010 1 34 5 5 TRP HA H 4.40 0.010 1 35 5 5 TRP HB2 H 3.19 0.010 2 36 5 5 TRP HB3 H 3.25 0.010 2 37 5 5 TRP HD1 H 7.38 0.010 1 38 5 5 TRP HE1 H 10.74 0.010 1 39 5 5 TRP HE3 H 7.50 0.010 1 40 5 5 TRP HZ2 H 7.50 0.010 1 41 5 5 TRP HZ3 H 6.99 0.010 1 42 5 5 TRP HH2 H 7.09 0.010 1 43 6 6 PHE H H 7.48 0.010 1 44 6 6 PHE HA H 4.41 0.010 1 45 6 6 PHE HB2 H 2.69 0.010 2 46 6 6 PHE HB3 H 2.74 0.010 2 47 6 6 PHE HD1 H 6.91 0.010 3 48 6 6 PHE HD2 H 6.91 0.010 3 49 6 6 PHE HE1 H 7.14 0.010 3 50 6 6 PHE HE2 H 7.14 0.010 3 51 6 6 PHE HZ H 7.08 0.010 1 52 7 7 ASP H H 7.82 0.010 1 53 7 7 ASP HA H 4.64 0.010 1 54 7 7 ASP HB2 H 2.54 0.010 2 55 7 7 ASP HB3 H 2.82 0.010 2 56 8 8 ILE H H 8.19 0.010 1 57 8 8 ILE HA H 3.94 0.010 1 58 8 8 ILE HB H 1.93 0.010 1 59 8 8 ILE HG12 H 1.26 0.010 2 60 8 8 ILE HG13 H 1.46 0.010 2 61 8 8 ILE HG2 H 0.86 0.010 1 62 8 8 ILE HD1 H 0.88 0.010 1 63 8 8 ILE CG2 C 17.9 0.100 1 64 8 8 ILE CD1 C 14.2 0.100 1 65 9 9 THR H H 8.21 0.010 1 66 9 9 THR HA H 3.94 0.010 1 67 9 9 THR HB H 4.16 0.010 1 68 9 9 THR HG2 H 1.23 0.010 1 69 9 9 THR CG2 C 22.0 0.100 1 70 10 10 ASN H H 8.28 0.010 1 71 10 10 ASN HA H 4.66 0.010 1 72 10 10 ASN HB2 H 2.71 0.010 2 73 10 10 ASN HB3 H 2.77 0.010 2 74 10 10 ASN HD21 H 7.76 0.010 2 75 10 10 ASN HD22 H 6.91 0.010 2 76 11 11 TRP H H 8.04 0.010 1 77 11 11 TRP HA H 4.74 0.010 1 78 11 11 TRP HB2 H 3.33 0.010 2 79 11 11 TRP HB3 H 3.46 0.010 2 80 11 11 TRP HD1 H 7.33 0.010 1 81 11 11 TRP HE1 H 10.62 0.010 1 82 11 11 TRP HE3 H 7.43 0.010 1 83 11 11 TRP HZ2 H 7.46 0.010 1 84 11 11 TRP HZ3 H 6.85 0.010 1 85 11 11 TRP HH2 H 7.04 0.010 1 86 12 12 LEU H H 8.13 0.010 1 87 12 12 LEU HA H 4.07 0.010 1 88 12 12 LEU HB2 H 1.67 0.010 2 89 12 12 LEU HB3 H 1.90 0.010 2 90 12 12 LEU HG H 1.84 0.010 1 91 12 12 LEU HD1 H 0.93 0.010 2 92 12 12 LEU HD2 H 1.00 0.010 2 93 12 12 LEU CD1 C 24.2 0.100 1 94 12 12 LEU CD2 C 25.0 0.100 1 95 13 13 TRP H H 8.27 0.010 1 96 13 13 TRP HA H 4.06 0.010 1 97 13 13 TRP HB2 H 3.14 0.010 2 98 13 13 TRP HB3 H 3.31 0.010 2 99 13 13 TRP HD1 H 7.25 0.010 1 100 13 13 TRP HE1 H 10.55 0.010 1 101 13 13 TRP HE3 H 6.46 0.010 1 102 13 13 TRP HZ2 H 7.43 0.010 1 103 13 13 TRP HZ3 H 6.74 0.010 1 104 13 13 TRP HH2 H 7.00 0.010 1 105 14 14 TYR H H 7.62 0.010 1 106 14 14 TYR HA H 4.05 0.010 1 107 14 14 TYR HB2 H 3.08 0.010 2 108 14 14 TYR HB3 H 3.25 0.010 2 109 14 14 TYR HD1 H 7.24 0.010 3 110 14 14 TYR HD2 H 7.24 0.010 3 111 14 14 TYR HE1 H 6.88 0.010 3 112 14 14 TYR HE2 H 6.88 0.010 3 113 15 15 ILE H H 8.22 0.010 1 114 15 15 ILE HA H 3.77 0.010 1 115 15 15 ILE HB H 2.13 0.010 1 116 15 15 ILE HG12 H 1.19 0.010 2 117 15 15 ILE HG13 H 2.02 0.010 2 118 15 15 ILE HG2 H 1.01 0.010 1 119 15 15 ILE HD1 H 0.98 0.010 1 120 15 15 ILE CG2 C 17.8 0.100 1 121 15 15 ILE CD1 C 13.5 0.100 1 122 16 16 LYS H H 8.43 0.010 1 123 16 16 LYS HA H 3.83 0.010 1 124 16 16 LYS HB2 H 1.82 0.010 2 125 16 16 LYS HB3 H 1.82 0.010 2 126 16 16 LYS HG2 H 1.31 0.010 2 127 16 16 LYS HG3 H 1.57 0.010 2 128 16 16 LYS HD2 H 1.68 0.010 2 129 16 16 LYS HD3 H 1.68 0.010 2 130 16 16 LYS HE2 H 2.83 0.010 2 131 16 16 LYS HE3 H 2.89 0.010 2 132 17 17 LEU H H 7.73 0.010 1 133 17 17 LEU HA H 3.87 0.010 1 134 17 17 LEU HB2 H 1.08 0.010 2 135 17 17 LEU HB3 H 1.59 0.010 2 136 17 17 LEU HG H 1.37 0.010 1 137 17 17 LEU HD1 H 0.59 0.010 2 138 17 17 LEU HD2 H 0.73 0.010 2 139 17 17 LEU CD1 C 23.9 0.100 1 140 17 17 LEU CD2 C 25.4 0.100 1 141 18 18 PHE H H 8.37 0.010 1 142 18 18 PHE HA H 4.06 0.010 1 143 18 18 PHE HB2 H 3.20 0.010 2 144 18 18 PHE HB3 H 3.41 0.010 2 145 18 18 PHE HD1 H 7.06 0.010 3 146 18 18 PHE HD2 H 7.06 0.010 3 147 18 18 PHE HE1 H 7.03 0.010 3 148 18 18 PHE HE2 H 7.03 0.010 3 149 18 18 PHE HZ H 6.96 0.010 1 150 19 19 ILE H H 8.48 0.010 1 151 19 19 ILE HA H 3.45 0.010 1 152 19 19 ILE HB H 2.02 0.010 1 153 19 19 ILE HG12 H 1.19 0.010 2 154 19 19 ILE HG13 H 2.00 0.010 2 155 19 19 ILE HG2 H 0.91 0.010 1 156 19 19 ILE HD1 H 0.88 0.010 1 157 19 19 ILE CG2 C 17.6 0.100 1 158 19 19 ILE CD1 C 14.0 0.100 1 159 20 20 MET H H 8.14 0.010 1 160 20 20 MET HA H 4.06 0.010 1 161 20 20 MET HB2 H 2.14 0.010 2 162 20 20 MET HB3 H 2.27 0.010 2 163 20 20 MET HG2 H 2.46 0.010 2 164 20 20 MET HG3 H 2.73 0.010 2 165 20 20 MET HE H 2.03 0.010 1 166 20 20 MET CE C 17.0 0.100 1 167 21 21 ILE H H 8.34 0.010 1 168 21 21 ILE HA H 3.67 0.010 1 169 21 21 ILE HB H 1.88 0.010 1 170 21 21 ILE HG12 H 1.03 0.010 2 171 21 21 ILE HG2 H 0.80 0.010 1 172 21 21 ILE HD1 H 0.81 0.010 1 173 21 21 ILE CG2 C 17.0 0.100 1 174 21 21 ILE CD1 C 13.7 0.100 1 175 22 22 VAL H H 8.40 0.010 1 176 22 22 VAL HA H 3.40 0.010 1 177 22 22 VAL HB H 1.77 0.010 1 178 22 22 VAL HG1 H 0.48 0.010 2 179 22 22 VAL HG2 H 0.72 0.010 2 180 22 22 VAL CG1 C 22.9 0.100 1 181 22 22 VAL CG2 C 22.1 0.100 1 182 23 23 GLY H H 8.57 0.010 1 183 23 23 GLY HA2 H 3.63 0.010 2 184 23 23 GLY HA3 H 3.88 0.010 2 185 24 24 GLY H H 7.86 0.010 1 186 24 24 GLY HA2 H 3.71 0.010 2 187 24 24 GLY HA3 H 3.89 . 2 188 25 25 LEU H H 8.00 0.010 1 189 25 25 LEU HA H 4.11 0.010 1 190 25 25 LEU HB2 H 1.43 0.010 2 191 25 25 LEU HB3 H 1.98 0.010 2 192 25 25 LEU HG H 1.90 0.010 1 193 25 25 LEU HD1 H 0.83 0.010 2 194 25 25 LEU HD2 H 0.83 0.010 2 195 25 25 LEU CD1 C 23.5 0.100 1 196 25 25 LEU CD2 C 26.0 0.100 1 197 26 26 VAL H H 8.19 0.010 1 198 26 26 VAL HA H 3.72 0.010 1 199 26 26 VAL HB H 2.19 0.010 1 200 26 26 VAL HG1 H 0.93 0.010 2 201 26 26 VAL HG2 H 1.01 0.010 2 202 26 26 VAL CG1 C 21.8 0.100 1 203 26 26 VAL CG2 C 22.7 0.100 1 204 27 27 LYS H H 7.73 0.010 1 205 27 27 LYS HA H 4.08 0.010 1 206 27 27 LYS HB2 H 1.91 0.010 2 207 27 27 LYS HB3 H 1.91 0.010 2 208 27 27 LYS HG2 H 1.49 0.010 2 209 27 27 LYS HG3 H 1.58 0.010 2 210 27 27 LYS HD2 H 1.68 0.010 2 211 27 27 LYS HD3 H 1.68 0.010 2 212 27 27 LYS HE2 H 2.94 0.010 2 213 27 27 LYS HE3 H 2.94 0.010 2 214 28 28 LYS H H 7.71 0.010 1 215 28 28 LYS HA H 4.15 0.010 1 216 28 28 LYS HB2 H 1.91 0.010 2 217 28 28 LYS HB3 H 1.91 0.010 2 218 28 28 LYS HG2 H 1.53 0.010 2 219 28 28 LYS HG3 H 1.53 0.010 2 220 28 28 LYS HD2 H 1.69 0.010 2 221 28 28 LYS HD3 H 1.69 0.010 2 222 28 28 LYS HE2 H 2.94 0.010 2 223 28 28 LYS HE3 H 2.94 0.010 2 stop_ save_