data_4298 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; A Synthetic Cyclic Peptide Corresponding to the Complete V3 Loop of the RF HIV-1 Strain in Water Solution ; _BMRB_accession_number 4298 _BMRB_flat_file_name bmr4298.str _Entry_type original _Submission_date 1999-01-21 _Accession_date 1999-01-25 _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 Vranken Wim F . 2 Budesinsky Milos . . 3 Martins Jose C . 4 Fant Franky . . 5 Boulez Kris . . 6 Gras-Masse Helene . . 7 Borremans Frans AM . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 213 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 1999-03-10 original author . stop_ _Original_release_date 1999-03-10 save_ ############################# # Citation for this entry # ############################# save_primary_citation _Saveframe_category entry_citation _Citation_full ; Vranken, W. F., Budesinsky, M., Martins, J. C., Fant, F., Boulez, K., Gras-Masse, H., and Borremans, F. A. M., "Conformational Features of a Synthetic Cyclic Peptide Corresponding to the Complete V3 Loop of the RF HIV-1 Strain in Water and Water/Trifluoroethanol Solutions," Eur. J. Biochem. 236, 100-108 (1996). ; _Citation_title ; Conformational Features of a Synthetic Cyclic Peptide Corresponding to the Complete V3 Loop of the RF HIV-1 Strain in Water and Water/Trifluoroethanol Solutions ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 96184885 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Vranken Wim F . 2 Budesinsky Milos . . 3 Martins Jose C . 4 Fant Franky . . 5 Boulez Kris . . 6 Gras-Masse Helene . . 7 Borremans Frans AM . stop_ _Journal_abbreviation 'Eur. J. Biochem.' _Journal_name_full 'European Journal of Biochemistry' _Journal_volume 236 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 100 _Page_last 108 _Year 1996 _Details . loop_ _Keyword 'amphipathic helix' CD 'human immunodeficiency virus type 1' NMR 'RF V3 loop' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_citation_one _Saveframe_category citation _Citation_full ; Wishart, D. S., Bigam, C. G., Yao, J., Abildgaard, F., Dyson, H. J., Oldfield, E., Markley, J. L., and Sykes, B. D. J. Biomol. NMR 6, 135-140 (1995). ; _Citation_title '1H, 13C and 15N chemical shift referencing in biomolecular NMR.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8589602 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wishart 'D S' S. . 2 Bigam 'C G' G. . 3 Yao J . . 4 Abildgaard F . . 5 Dyson 'H J' J. . 6 Oldfield E . . 7 Markley 'J L' L. . 8 Sykes 'B D' D. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 6 _Journal_issue 2 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 135 _Page_last 140 _Year 1995 _Details ; A considerable degree of variability exists in the way that 1H, 13C and 15N chemical shifts are reported and referenced for biomolecules. In this article we explore some of the reasons for this situation and propose guidelines for future chemical shift referencing and for conversion from many common 1H, 13C and 15N chemical shift standards, now used in biomolecular NMR, to those proposed here. ; save_ ################################## # Molecular system description # ################################## save_RF_HIV-1_gp120_envelope_protein _Saveframe_category molecular_system _Mol_system_name 'V3 loop peptide of RF HIV-1 gp120 envelope protein' _Abbreviation_common 'V3 loop' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label V3_loop $V3_loop stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state . loop_ _Biological_function 'crucial in viral infection process of HIV-1' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_V3_loop _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'V3 loop' _Name_variant RF _Abbreviation_common 'V3 loop' _Molecular_mass 3880.4 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 35 _Mol_residue_sequence ; CTRPNNNTRKSITKGPGRVI YATGQIIGDIRKAHC ; loop_ _Residue_seq_code _Residue_label 1 CYS 2 THR 3 ARG 4 PRO 5 ASN 6 ASN 7 ASN 8 THR 9 ARG 10 LYS 11 SER 12 ILE 13 THR 14 LYS 15 GLY 16 PRO 17 GLY 18 ARG 19 VAL 20 ILE 21 TYR 22 ALA 23 THR 24 GLY 25 GLN 26 ILE 27 ILE 28 GLY 29 ASP 30 ILE 31 ARG 32 LYS 33 ALA 34 HIS 35 CYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-03-16 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 GB AAA45057 "envelope polyprotein [Human immunodeficiency virus 1]" 100.00 865 100.00 100.00 1.80e-15 GB AAA45315 "envelope protein, partial [Human immunodeficiency virus 1]" 100.00 35 97.14 97.14 7.82e-15 GB AAC21522 "envelope glycoprotein [Human immunodeficiency virus 1]" 100.00 202 97.14 97.14 1.16e-14 GB AAQ82893 "envelope glycoprotein, partial [Human immunodeficiency virus 1]" 100.00 76 100.00 100.00 1.81e-16 GB AGI37066 "envelope glycoprotein, partial [Human immunodeficiency virus 1]" 100.00 395 100.00 100.00 1.41e-14 SP P04579 "RecName: Full=Envelope glycoprotein gp160; AltName: Full=Env polyprotein; Contains: RecName: Full=Surface protein gp120; Short=" 100.00 865 100.00 100.00 1.80e-15 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Variant _Gene_mnemonic $V3_loop 'Human Immunodefiency Virus' 12721 . . Lentivirus 'Human immunodeficiency virus' 'RF HIV-1' 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 $V3_loop 'chemically synthesized' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $V3_loop 4.0 mM . stop_ save_ ############################ # Computer software used # ############################ save_UXNMR _Saveframe_category software _Name UXNMR _Version . loop_ _Task 'Spectrum processing' stop_ _Details . save_ save_PRONTO _Saveframe_category software _Name PRONTO _Version . loop_ _Task 'Analysis of spectra' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AM-500 _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_magnitude_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'magnitude COSY' _Sample_label $sample_one save_ save_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_one save_ save_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_one save_ save_CT-NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name CT-NOESY _Sample_label $sample_one save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 2.5 0.1 n/a temperature 275 0.2 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _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 _Indirect_shift_ratio_citation_label DSS H 1 'methyl protons' ppm 0.00 . direct . . . 1.0 $citation_one 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_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name V3_loop _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 CYS H H 8.70 0.01 1 2 . 1 CYS HA H 4.76 0.01 1 3 . 1 CYS HB2 H 3.22 0.01 2 4 . 1 CYS HB3 H 2.92 0.01 2 5 . 2 THR H H 8.64 0.01 1 6 . 2 THR HA H 4.38 0.01 1 7 . 2 THR HB H 4.19 0.01 1 8 . 2 THR HG2 H 1.20 0.01 1 9 . 3 ARG H H 8.64 0.01 1 10 . 3 ARG HA H 4.64 0.01 1 11 . 3 ARG HB2 H 1.85 0.01 2 12 . 3 ARG HB3 H 1.75 0.01 2 13 . 3 ARG HG2 H 1.69 0.01 1 14 . 3 ARG HG3 H 1.69 0.01 1 15 . 3 ARG HD2 H 3.22 0.01 1 16 . 3 ARG HD3 H 3.22 0.01 1 17 . 3 ARG HE H 7.30 0.01 1 18 . 4 PRO HA H 4.41 0.01 1 19 . 4 PRO HB2 H 2.29 0.01 2 20 . 4 PRO HB3 H 2.02 0.01 2 21 . 4 PRO HG2 H 1.90 0.01 1 22 . 4 PRO HG3 H 1.90 0.01 1 23 . 4 PRO HD2 H 3.84 0.01 2 24 . 4 PRO HD3 H 3.65 0.01 2 25 . 5 ASN H H 8.76 0.01 1 26 . 5 ASN HA H 4.68 0.01 1 27 . 5 ASN HB2 H 2.85 0.01 2 28 . 5 ASN HB3 H 2.81 0.01 2 29 . 5 ASN HD21 H 7.80 0.01 2 30 . 5 ASN HD22 H 7.07 0.02 2 31 . 6 ASN H H 8.65 0.01 1 32 . 6 ASN HA H 4.72 0.01 1 33 . 6 ASN HB2 H 2.87 0.02 2 34 . 6 ASN HB3 H 2.80 0.02 2 35 . 6 ASN HD21 H 7.79 0.01 2 36 . 6 ASN HD22 H 7.07 0.02 2 37 . 7 ASN H H 8.65 0.01 1 38 . 7 ASN HA H 4.77 0.01 1 39 . 7 ASN HB2 H 2.88 0.02 2 40 . 7 ASN HB3 H 2.81 0.02 2 41 . 7 ASN HD21 H 7.75 0.01 2 42 . 7 ASN HD22 H 7.07 0.01 2 43 . 8 THR H H 8.26 0.01 1 44 . 8 THR HA H 4.29 0.01 1 45 . 8 THR HB H 4.27 0.01 1 46 . 8 THR HG2 H 1.22 0.01 1 47 . 9 ARG H H 8.47 0.01 1 48 . 9 ARG HA H 4.33 0.01 1 49 . 9 ARG HB2 H 1.85 0.01 2 50 . 9 ARG HB3 H 1.78 0.01 2 51 . 9 ARG HG2 H 1.66 0.01 2 52 . 9 ARG HG3 H 1.63 0.01 2 53 . 9 ARG HD2 H 3.19 0.01 1 54 . 9 ARG HD3 H 3.19 0.01 1 55 . 9 ARG HE H 7.26 0.01 1 56 . 10 LYS H H 8.52 0.01 1 57 . 10 LYS HA H 4.33 0.01 1 58 . 10 LYS HB2 H 1.84 0.01 2 59 . 10 LYS HB3 H 1.77 0.01 2 60 . 10 LYS HG2 H 1.47 0.02 1 61 . 10 LYS HG3 H 1.47 0.02 1 62 . 10 LYS HD2 H 1.68 0.01 1 63 . 10 LYS HD3 H 1.68 0.01 1 64 . 10 LYS HE2 H 3.00 0.01 1 65 . 10 LYS HE3 H 3.00 0.01 1 66 . 10 LYS HZ H 7.65 0.01 1 67 . 11 SER H H 8.52 0.01 1 68 . 11 SER HA H 4.47 0.01 1 69 . 11 SER HB2 H 3.85 0.01 1 70 . 11 SER HB3 H 3.85 0.01 1 71 . 12 ILE H H 8.50 0.01 1 72 . 12 ILE HA H 4.30 0.01 1 73 . 12 ILE HB H 1.92 0.01 1 74 . 12 ILE HG12 H 1.48 0.01 2 75 . 12 ILE HG13 H 1.19 0.01 2 76 . 12 ILE HG2 H 0.92 0.01 1 77 . 12 ILE HD1 H 0.87 0.02 1 78 . 13 THR H H 8.42 0.01 1 79 . 13 THR HA H 4.35 0.01 1 80 . 13 THR HB H 4.17 0.01 1 81 . 13 THR HG2 H 1.20 0.01 1 82 . 14 LYS H H 8.58 0.01 1 83 . 14 LYS HA H 4.40 0.01 1 84 . 14 LYS HB2 H 1.86 0.01 2 85 . 14 LYS HB3 H 1.77 0.01 2 86 . 14 LYS HG2 H 1.46 0.01 1 87 . 14 LYS HG3 H 1.46 0.01 1 88 . 14 LYS HD2 H 1.68 0.01 1 89 . 14 LYS HD3 H 1.68 0.01 1 90 . 14 LYS HE2 H 2.99 0.01 1 91 . 14 LYS HE3 H 2.99 0.01 1 92 . 14 LYS HZ H 7.62 0.01 1 93 . 15 GLY H H 8.50 0.01 1 94 . 15 GLY HA2 H 4.12 0.01 1 95 . 15 GLY HA3 H 4.12 0.01 1 96 . 16 PRO HA H 4.46 0.01 1 97 . 16 PRO HB2 H 2.29 0.01 2 98 . 16 PRO HB3 H 2.01 0.02 2 99 . 16 PRO HG2 H 2.04 0.02 1 100 . 16 PRO HG3 H 2.04 0.02 1 101 . 16 PRO HD2 H 3.66 0.01 2 102 . 16 PRO HD3 H 3.63 0.01 2 103 . 17 GLY H H 8.69 0.01 1 104 . 17 GLY HA2 H 3.93 0.02 1 105 . 17 GLY HA3 H 3.93 0.02 1 106 . 18 ARG H H 8.31 0.01 1 107 . 18 ARG HA H 4.33 0.01 1 108 . 18 ARG HB2 H 1.79 0.01 2 109 . 18 ARG HB3 H 1.74 0.01 2 110 . 18 ARG HG2 H 1.59 0.01 2 111 . 18 ARG HG3 H 1.56 0.01 2 112 . 18 ARG HD2 H 3.17 0.01 1 113 . 18 ARG HD3 H 3.17 0.01 1 114 . 18 ARG HE H 7.26 0.01 1 115 . 19 VAL H H 8.38 0.01 1 116 . 19 VAL HA H 4.00 0.01 1 117 . 19 VAL HB H 1.93 0.01 1 118 . 19 VAL HG1 H 0.90 0.01 2 119 . 19 VAL HG2 H 0.76 0.01 2 120 . 20 ILE H H 8.48 0.01 1 121 . 20 ILE HA H 4.34 0.01 1 122 . 20 ILE HB H 1.52 0.02 2 123 . 20 ILE HG12 H 1.54 0.02 2 124 . 20 ILE HG13 H 1.42 0.01 2 125 . 20 ILE HG2 H 0.90 0.01 1 126 . 20 ILE HD1 H 0.81 0.01 1 127 . 21 TYR H H 8.36 0.01 1 128 . 21 TYR HA H 4.59 0.01 1 129 . 21 TYR HB2 H 3.05 0.01 2 130 . 21 TYR HB3 H 2.89 0.01 2 131 . 21 TYR HD1 H 7.10 0.01 1 132 . 21 TYR HD2 H 7.10 0.01 1 133 . 21 TYR HE1 H 6.79 0.01 1 134 . 21 TYR HE2 H 6.79 0.01 1 135 . 22 ALA H H 8.50 0.01 1 136 . 22 ALA HA H 4.39 0.01 1 137 . 22 ALA HB H 1.39 0.01 1 138 . 23 THR H H 8.34 0.01 1 139 . 23 THR HA H 4.30 0.01 1 140 . 23 THR HB H 4.26 0.01 1 141 . 23 THR HG2 H 1.25 0.01 1 142 . 24 GLY H H 8.64 0.01 1 143 . 24 GLY HA2 H 4.02 0.01 2 144 . 24 GLY HA3 H 3.93 0.01 2 145 . 25 GLN H H 8.32 0.01 1 146 . 25 GLN HA H 4.31 0.01 1 147 . 25 GLN HB2 H 2.06 0.01 2 148 . 25 GLN HB3 H 1.98 0.01 2 149 . 25 GLN HG2 H 2.31 0.01 1 150 . 25 GLN HG3 H 2.31 0.01 1 151 . 25 GLN HE21 H 7.71 0.01 2 152 . 25 GLN HE22 H 7.02 0.01 2 153 . 26 ILE H H 8.50 0.01 1 154 . 26 ILE HA H 4.15 0.01 1 155 . 26 ILE HB H 1.85 0.02 1 156 . 26 ILE HG12 H 1.49 0.02 2 157 . 26 ILE HG13 H 1.17 0.02 2 158 . 26 ILE HG2 H 0.86 0.01 1 159 . 26 ILE HD1 H 0.85 0.02 1 160 . 27 ILE H H 8.53 0.01 1 161 . 27 ILE HA H 4.10 0.01 1 162 . 27 ILE HB H 1.84 0.02 1 163 . 27 ILE HG12 H 1.49 0.02 2 164 . 27 ILE HG13 H 1.18 0.02 2 165 . 27 ILE HG2 H 0.91 0.01 1 166 . 27 ILE HD1 H 0.85 0.02 1 167 . 28 GLY H H 8.66 0.01 1 168 . 28 GLY HA2 H 3.94 0.02 1 169 . 28 GLY HA3 H 3.94 0.02 1 170 . 29 ASP H H 8.42 0.01 1 171 . 29 ASP HA H 4.71 0.01 1 172 . 29 ASP HB2 H 2.90 0.01 2 173 . 29 ASP HB3 H 2.80 0.01 2 174 . 30 ILE H H 8.32 0.01 1 175 . 30 ILE HA H 4.14 0.01 1 176 . 30 ILE HB H 1.91 0.01 1 177 . 30 ILE HG12 H 1.48 0.01 2 178 . 30 ILE HG13 H 1.20 0.01 2 179 . 30 ILE HG2 H 0.91 0.01 1 180 . 30 ILE HD1 H 0.86 0.01 1 181 . 31 ARG H H 8.55 0.01 1 182 . 31 ARG HA H 4.33 0.01 1 183 . 31 ARG HB2 H 1.84 0.01 2 184 . 31 ARG HB3 H 1.77 0.01 2 185 . 31 ARG HG2 H 1.66 0.01 2 186 . 31 ARG HG3 H 1.62 0.01 2 187 . 31 ARG HD2 H 3.20 0.01 1 188 . 31 ARG HD3 H 3.20 0.01 1 189 . 31 ARG HE H 7.32 0.01 1 190 . 32 LYS H H 8.43 0.01 1 191 . 32 LYS HA H 4.28 0.02 1 192 . 32 LYS HB2 H 1.84 0.01 2 193 . 32 LYS HB3 H 1.74 0.01 2 194 . 32 LYS HG2 H 1.46 0.01 1 195 . 32 LYS HG3 H 1.46 0.01 1 196 . 32 LYS HD2 H 1.69 0.01 1 197 . 32 LYS HD3 H 1.69 0.01 1 198 . 32 LYS HE2 H 3.00 0.01 1 199 . 32 LYS HE3 H 3.00 0.01 1 200 . 32 LYS HZ H 7.65 0.01 1 201 . 33 ALA H H 8.48 0.01 1 202 . 33 ALA HA H 4.26 0.01 1 203 . 33 ALA HB H 1.36 0.01 1 204 . 34 HIS H H 8.58 0.01 1 205 . 34 HIS HA H 4.71 0.01 1 206 . 34 HIS HB2 H 3.27 0.01 1 207 . 34 HIS HB3 H 3.27 0.01 1 208 . 34 HIS HD2 H 7.34 0.01 1 209 . 34 HIS HE1 H 8.36 0.01 1 210 . 35 CYS H H 8.62 0.01 1 211 . 35 CYS HA H 4.59 0.01 1 212 . 35 CYS HB2 H 3.32 0.01 2 213 . 35 CYS HB3 H 3.00 0.01 2 stop_ save_