data_15799 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; HIV-1 Gag p6 C-terminal ; _BMRB_accession_number 15799 _BMRB_flat_file_name bmr15799.str _Entry_type new _Submission_date 2008-06-09 _Accession_date 2008-06-09 _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 Salgado Gilmar F.J. . 2 Bouaziz Serge . . 3 Marquante Rodrigue . . 4 Vogel Alexander . . 5 Alves Isabel . . 6 Morellet Nelly . . 7 Feller Scott . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 126 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-02 update BMRB 'edit assembly name' 2009-04-02 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural Studies of HIV-1 Gag p6ct and Its Interaction with Vpr Determined by Solution Nuclear Magnetic Resonance' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19254034 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Salgado Gilmar F. . 2 Marquante Rodrigue . . 3 Vogel Alexander . . 4 Alves Isabel D. . 5 Feller Scott E. . 6 Morellet Nelly . . 7 Bouaziz Serge . . stop_ _Journal_abbreviation Biochemistry _Journal_volume 48 _Journal_issue 11 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2355 _Page_last 2367 _Year 2009 _Details . loop_ _Keyword 'HIV-1 Gag p6' Vpr 'protein-protein interaction' DPC 'Molecular Dynamics' NMR stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name HIV-1_Gag_p6ct _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label HIV-1_Gag_p6ct $HIV-1_Gag_p6ct 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_HIV-1_Gag_p6ct _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common HIV-1_Gag_p6ct _Molecular_mass 2312.555 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; DKELYPLASLRSLFGSDPSS Q ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 32 ASP 2 33 LYS 3 34 GLU 4 35 LEU 5 36 TYR 6 37 PRO 7 38 LEU 8 39 ALA 9 40 SER 10 41 LEU 11 42 ARG 12 43 SER 13 44 LEU 14 45 PHE 15 46 GLY 16 47 SER 17 48 ASP 18 49 PRO 19 50 SER 20 51 SER 21 52 GLN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 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 15957 HIV-1_p6_C-terminal 100.00 21 100.00 100.00 2.25e-04 PDB 2C55 "Solution Structure Of The Human Immunodeficiency Virus Type 1 P6 Protein" 100.00 52 100.00 100.00 1.67e-04 DBJ BAF34641 "gag polyprotein [HIV-1 vector pNL-DT5R]" 100.00 498 100.00 100.00 7.27e-04 DBJ BAO09775 "gag protein [Human immunodeficiency virus 1]" 100.00 500 100.00 100.00 6.68e-04 DBJ BAO09817 "gag protein [Human immunodeficiency virus 1]" 100.00 500 100.00 100.00 6.36e-04 DBJ BAO09912 "gag protein [Human immunodeficiency virus 1]" 100.00 500 100.00 100.00 9.00e-04 DBJ BAO09940 "gag protein [Human immunodeficiency virus 1]" 100.00 500 100.00 100.00 6.87e-04 EMBL CBI61180 "gag polyprotein [HIV-1 M:B 2003_KC005]" 85.71 497 100.00 100.00 3.28e-02 EMBL CBI61181 "gag polyprotein [HIV-1 M:B 2003_KC005]" 85.71 497 100.00 100.00 3.10e-02 EMBL CBI61182 "gag polyprotein [HIV-1 M:B 2003_KC005]" 85.71 497 100.00 100.00 3.07e-02 EMBL CBI61183 "gag polyprotein [HIV-1 M:B 2003_KC005]" 85.71 497 100.00 100.00 3.16e-02 EMBL CBI61184 "gag polyprotein [HIV-1 M:B 2003_KC005]" 85.71 497 100.00 100.00 3.19e-02 GB AAA44987 "gag polyprotein [Human immunodeficiency virus 1]" 100.00 500 100.00 100.00 5.78e-04 GB AAB04036 "gag [Human immunodeficiency virus 1]" 100.00 500 100.00 100.00 6.68e-04 GB AAB60571 "Gag polyprotein precursor [Human immunodeficiency virus 1]" 100.00 500 100.00 100.00 5.72e-04 GB AAC28445 "gag protein [Human immunodeficiency virus 1]" 100.00 500 100.00 100.00 5.89e-04 GB AAG28735 "gag protein [synthetic construct]" 100.00 500 100.00 100.00 6.74e-04 SP P12493 "RecName: Full=Gag polyprotein; AltName: Full=Pr55Gag; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: RecName: " 100.00 500 100.00 100.00 5.78e-04 SP P35962 "RecName: Full=Gag polyprotein; AltName: Full=Pr55Gag; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: RecName: " 100.00 500 100.00 100.00 6.74e-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 $HIV-1_Gag_p6ct . . . . . . 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 $HIV-1_Gag_p6ct 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelle _Details ; 1 mM polypeptide 100 mM dodecylphosphocoline (DPC-d38) 30 mM NaCl pH 3.4 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HIV-1_Gag_p6ct 1 mM 'natural abundance' dodecylphosphocoline 100 mM . NaCl 30 mM . H2O 95 % 'natural abundance' D2O 5 % . stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.114 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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 temperature 296 1 K pH 3.4 0.1 pH pressure 1 . atm 'ionic strength' 0.03 2 M 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 0.00 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 NOESY' 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 HIV-1_Gag_p6ct _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 32 1 ASP HA H 4.345 . 1 2 32 1 ASP HB2 H 2.940 . 2 3 32 1 ASP HB3 H 2.890 . 2 4 33 2 LYS H H 8.943 . 1 5 33 2 LYS HA H 4.329 . 1 6 33 2 LYS HB2 H 1.852 . . 7 33 2 LYS HB3 H 1.852 . . 8 33 2 LYS HD2 H 1.741 . . 9 33 2 LYS HD3 H 1.741 . . 10 33 2 LYS HE2 H 3.037 . . 11 33 2 LYS HE3 H 3.037 . . 12 33 2 LYS HG2 H 1.494 . . 13 33 2 LYS HG3 H 1.494 . . 14 33 2 LYS HZ H 7.724 . . 15 34 3 GLU H H 8.549 . 1 16 34 3 GLU HA H 4.352 . 1 17 34 3 GLU HB2 H 2.043 . . 18 34 3 GLU HB3 H 2.043 . . 19 34 3 GLU HG2 H 2.438 . . 20 34 3 GLU HG3 H 2.438 . . 21 35 4 LEU H H 8.406 . 1 22 35 4 LEU HA H 4.188 . 1 23 35 4 LEU HB2 H 1.643 . . 24 35 4 LEU HB3 H 1.643 . . 25 35 4 LEU HD1 H 0.985 . . 26 35 4 LEU HD2 H 0.912 . . 27 35 4 LEU HG H 1.493 . 1 28 36 5 TYR H H 8.151 . 1 29 36 5 TYR HA H 4.828 . 1 30 36 5 TYR HB2 H 3.099 . 2 31 36 5 TYR HB3 H 3.010 . 2 32 36 5 TYR HD1 H 7.171 . . 33 36 5 TYR HD2 H 7.171 . . 34 36 5 TYR HE1 H 6.856 . . 35 36 5 TYR HE2 H 6.856 . . 36 37 6 PRO HA H 4.579 . 1 37 37 6 PRO HB2 H 2.295 . . 38 37 6 PRO HB3 H 2.295 . . 39 37 6 PRO HD2 H 3.834 . 2 40 37 6 PRO HD3 H 3.686 . 2 41 37 6 PRO HG2 H 2.067 . . 42 37 6 PRO HG3 H 2.067 . . 43 38 7 LEU H H 8.456 . 1 44 38 7 LEU HA H 4.185 . 1 45 38 7 LEU HB2 H 1.885 . . 46 38 7 LEU HB3 H 1.835 . 2 47 38 7 LEU HD1 H 1.067 . . 48 38 7 LEU HD2 H 0.991 . . 49 38 7 LEU HG H 1.740 . 1 50 39 8 ALA H H 8.489 . 1 51 39 8 ALA HA H 4.160 . 1 52 39 8 ALA HB H 1.548 . 1 53 40 9 SER H H 8.247 . 1 54 40 9 SER HA H 4.372 . 1 55 40 9 SER HB2 H 4.024 . 2 56 40 9 SER HB3 H 3.961 . 2 57 41 10 LEU H H 8.065 . 1 58 41 10 LEU HA H 4.204 . 1 59 41 10 LEU HB2 H 1.995 . 2 60 41 10 LEU HB3 H 1.918 . 2 61 41 10 LEU HD1 H 1.060 . . 62 41 10 LEU HD2 H 0.989 . . 63 41 10 LEU HG H 1.749 . 1 64 42 11 ARG H H 8.262 . 1 65 42 11 ARG HA H 4.046 . 1 66 42 11 ARG HB2 H 2.060 . 2 67 42 11 ARG HB3 H 1.970 . 2 68 42 11 ARG HD2 H 3.272 . . 69 42 11 ARG HD3 H 3.272 . . 70 42 11 ARG HE H 7.721 . 1 71 42 11 ARG HG2 H 1.747 . 2 72 42 11 ARG HG3 H 1.876 . 2 73 43 12 SER H H 7.948 . 1 74 43 12 SER HA H 4.388 . 1 75 43 12 SER HB2 H 4.051 . . 76 43 12 SER HB3 H 4.051 . . 77 44 13 LEU H H 7.713 . 1 78 44 13 LEU HA H 4.107 . 1 79 44 13 LEU HB2 H 1.689 . . 80 44 13 LEU HB3 H 1.689 . . 81 44 13 LEU HD1 H 0.921 . . 82 44 13 LEU HD2 H 0.827 . . 83 44 13 LEU HG H 1.292 . 1 84 45 14 PHE H H 7.731 . 1 85 45 14 PHE HA H 4.651 . 1 86 45 14 PHE HB2 H 3.415 . 2 87 45 14 PHE HB3 H 2.982 . 2 88 45 14 PHE HD1 H 7.422 . . 89 45 14 PHE HD2 H 7.422 . . 90 45 14 PHE HE1 H 7.259 . . 91 45 14 PHE HE2 H 7.259 . . 92 45 14 PHE HZ H 7.150 . 1 93 46 15 GLY H H 8.067 . 1 94 46 15 GLY HA2 H 4.119 . . 95 46 15 GLY HA3 H 4.119 . . 96 47 16 SER H H 8.334 . 1 97 47 16 SER HA H 4.541 . 1 98 47 16 SER HB2 H 3.895 . . 99 47 16 SER HB3 H 3.895 . . 100 48 17 ASP H H 8.741 . 1 101 48 17 ASP HA H 5.002 . 1 102 48 17 ASP HB2 H 2.967 . 2 103 48 17 ASP HB3 H 2.736 . 2 104 49 18 PRO HA H 4.512 . 1 105 49 18 PRO HB2 H 2.365 . . 106 49 18 PRO HB3 H 2.365 . . 107 49 18 PRO HD2 H 3.893 . 2 108 49 18 PRO HD3 H 3.837 . 2 109 49 18 PRO HG2 H 2.061 . . 110 49 18 PRO HG3 H 2.061 . . 111 50 19 SER H H 8.483 . 1 112 50 19 SER HA H 4.499 . 1 113 50 19 SER HB2 H 3.961 . . 114 50 19 SER HB3 H 3.961 . . 115 51 20 SER H H 8.306 . 1 116 51 20 SER HA H 4.526 . 1 117 51 20 SER HB2 H 3.955 . . 118 51 20 SER HB3 H 3.955 . . 119 52 21 GLN H H 8.143 . 1 120 52 21 GLN HA H 4.298 . 1 121 52 21 GLN HB2 H 2.212 . 2 122 52 21 GLN HB3 H 2.005 . 2 123 52 21 GLN HE21 H 7.479 . 2 124 52 21 GLN HE22 H 6.920 . 2 125 52 21 GLN HG2 H 2.375 . . 126 52 21 GLN HG3 H 2.375 . . stop_ save_