data_15937 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the equine infectious anemia virus p9 gag protein ; _BMRB_accession_number 15937 _BMRB_flat_file_name bmr15937.str _Entry_type new _Submission_date 2008-09-02 _Accession_date 2008-09-02 _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 Sharma Alok . . 2 Bruns Karsten . . 3 Roeder Rene . . 4 Henklein Peter . . 5 Votteler Joerg . . 6 Wray Victor . . 7 Sharma Ulrich . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 202 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-01-22 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of the equine infectious anemia virus p9 protein: a rationalization of its different ALIX binding requirements compared to the analogous HIV-p6 protein.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20015412 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sharma Alok . . 2 Bruns Karsten . . 3 Roeder Rene . . 4 Henklein Peter . . 5 Votteler Joerg . . 6 Wray Victor . . 7 Schubert Ulrich . . stop_ _Journal_abbreviation 'BMC Struct. Biol.' _Journal_name_full 'BMC structural biology' _Journal_volume 9 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 74 _Page_last 74 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'p9 (22-51)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'p9 (22-51)' $p9_(22-51) 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_p9_(22-51) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common p9_(22-51) _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; LYPDLSEIKKEYNVKEKDQV EDLNLDSLWE ; loop_ _Residue_seq_code _Residue_label 1 LEU 2 TYR 3 PRO 4 ASP 5 LEU 6 SER 7 GLU 8 ILE 9 LYS 10 LYS 11 GLU 12 TYR 13 ASN 14 VAL 15 LYS 16 GLU 17 LYS 18 ASP 19 GLN 20 VAL 21 GLU 22 ASP 23 LEU 24 ASN 25 LEU 26 ASP 27 SER 28 LEU 29 TRP 30 GLU 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 PDB 2K84 "Solution Structure Of The Equine Infectious Anemia Virus P9 Gag Protein" 100.00 30 100.00 100.00 2.06e-10 GB AAA43003 "gag protein [Equine infectious anemia virus]" 100.00 486 100.00 100.00 7.51e-10 GB AAA43011 "gag [Equine infectious anemia virus]" 100.00 512 100.00 100.00 8.84e-10 GB AAB59861 "gag protein [Equine infectious anemia virus]" 100.00 486 100.00 100.00 7.51e-10 GB AAC03760 "gag polyprotein [Equine infectious anemia virus]" 100.00 486 100.00 100.00 7.51e-10 GB AAC24014 "gag polyprotein [Equine infectious anemia virus]" 100.00 486 100.00 100.00 7.51e-10 REF NP_056901 "gag protein [Equine infectious anemia virus]" 100.00 486 100.00 100.00 7.51e-10 SP P69730 "RecName: Full=Gag polyprotein; Contains: RecName: Full=Matrix protein p15; Short=MA; Contains: RecName: Full=Capsid protein p26" 100.00 486 100.00 100.00 7.51e-10 SP P69731 "RecName: Full=Gag polyprotein; Contains: RecName: Full=Matrix protein p15; Short=MA; Contains: RecName: Full=Capsid protein p26" 100.00 486 100.00 100.00 7.51e-10 SP P69732 "RecName: Full=Gag polyprotein; Contains: RecName: Full=Matrix protein p15; Short=MA; Contains: RecName: Full=Capsid protein p26" 100.00 486 100.00 100.00 7.51e-10 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $p9_(22-51) HIV-1 11676 Viruses . Lentivirus 'Human immunodeficiency virus 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 $p9_(22-51) '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 $p9_(22-51) 2-3 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AURELIA _Saveframe_category software _Name AURELIA _Version . loop_ _Vendor _Address _Electronic_address 'Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzer' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _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 temperature 300 . K pH 3 . pH pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'Internally referenced to the residual CH2-signal of trifluoroethanol (CF3CD2OH, TFE-d2) which was used as solvent in a 50% aqueous solution. The reference signal was set to 3.95 ppm.' 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 Trifluoroethanol H 1 'methylene protons' ppm 3.95 internal direct . . . 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 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 $chemical_shift_reference_1 _Mol_system_component_name 'p9 (22-51)' _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 LEU HA H 3.962 . 1 2 1 1 LEU HB2 H 1.714 . 1 3 1 1 LEU HB3 H 1.714 . 1 4 1 1 LEU HD1 H 0.968 . 1 5 1 1 LEU HD2 H 0.968 . 1 6 1 1 LEU HG H 1.646 . 1 7 2 2 TYR H H 8.225 . 1 8 2 2 TYR HA H 4.946 . 1 9 2 2 TYR HB2 H 3.161 . 2 10 2 2 TYR HB3 H 2.946 . 2 11 2 2 TYR HD1 H 7.22 . 1 12 2 2 TYR HD2 H 7.22 . 1 13 2 2 TYR HE1 H 6.898 . 1 14 2 2 TYR HE2 H 6.898 . 1 15 3 3 PRO HA H 4.448 . 1 16 3 3 PRO HB2 H 2.226 . 2 17 3 3 PRO HB3 H 1.938 . 2 18 3 3 PRO HD2 H 3.783 . 2 19 3 3 PRO HD3 H 3.561 . 2 20 3 3 PRO HG2 H 2.036 . 1 21 3 3 PRO HG3 H 2.036 . 1 22 4 4 ASP H H 8.005 . 1 23 4 4 ASP HA H 4.844 . 1 24 4 4 ASP HB2 H 3.036 . 2 25 4 4 ASP HB3 H 2.889 . 2 26 5 5 LEU H H 8.208 . 1 27 5 5 LEU HA H 4.222 . 1 28 5 5 LEU HB2 H 1.759 . 2 29 5 5 LEU HB3 H 1.759 . 2 30 5 5 LEU HD1 H 1.002 . 2 31 5 5 LEU HD2 H 0.924 . 2 32 5 5 LEU HG H 1.759 . 1 33 6 6 SER H H 8.31 . 1 34 6 6 SER HA H 4.166 . 1 35 6 6 SER HB2 H 4.019 . 1 36 6 6 SER HB3 H 4.019 . 1 37 7 7 GLU H H 7.756 . 1 38 7 7 GLU HA H 4.245 . 1 39 7 7 GLU HB2 H 2.214 . 1 40 7 7 GLU HB3 H 2.214 . 1 41 7 7 GLU HG2 H 2.552 . 1 42 7 7 GLU HG3 H 2.552 . 1 43 8 8 ILE H H 7.745 . 1 44 8 8 ILE HA H 3.838 . 1 45 8 8 ILE HB H 2.019 . 1 46 8 8 ILE HD1 H 0.89 . 1 47 8 8 ILE HG12 H 1.713 . 2 48 8 8 ILE HG13 H 1.25 . 2 49 8 8 ILE HG2 H 0.968 . 1 50 9 9 LYS H H 8.146 . 1 51 9 9 LYS HA H 4.086 . 1 52 9 9 LYS HB2 H 1.94 . 2 53 9 9 LYS HB3 H 1.724 . 2 54 9 9 LYS HD2 H 1.626 . 1 55 9 9 LYS HD3 H 1.626 . 1 56 9 9 LYS HE2 H 2.991 . 1 57 9 9 LYS HE3 H 2.991 . 1 58 9 9 LYS HG2 H 1.482 . 1 59 9 9 LYS HG3 H 1.482 . 1 60 9 9 LYS HZ H 7.613 . 1 61 10 10 LYS H H 7.847 . 1 62 10 10 LYS HA H 4.132 . 1 63 10 10 LYS HB2 H 2.028 . 2 64 10 10 LYS HB3 H 1.763 . 2 65 10 10 LYS HD2 H 1.67 . 1 66 10 10 LYS HD3 H 1.67 . 1 67 10 10 LYS HE2 H 3.002 . 1 68 10 10 LYS HE3 H 3.002 . 1 69 10 10 LYS HG2 H 1.467 . 1 70 10 10 LYS HG3 H 1.467 . 1 71 10 10 LYS HZ H 7.596 . 1 72 11 11 GLU H H 8.203 . 1 73 11 11 GLU HA H 4.121 . 1 74 11 11 GLU HB2 H 2.291 . 2 75 11 11 GLU HB3 H 2.201 . 2 76 11 11 GLU HG2 H 2.664 . 2 77 11 11 GLU HG3 H 2.472 . 2 78 12 12 TYR H H 8.592 . 1 79 12 12 TYR HA H 4.211 . 1 80 12 12 TYR HB2 H 3.172 . 1 81 12 12 TYR HB3 H 3.172 . 1 82 12 12 TYR HD1 H 7.151 . 1 83 12 12 TYR HD2 H 7.151 . 1 84 12 12 TYR HE1 H 6.818 . 1 85 12 12 TYR HE2 H 6.818 . 1 86 13 13 ASN H H 8.166 . 1 87 13 13 ASN HA H 4.516 . 1 88 13 13 ASN HB2 H 3.06 . 2 89 13 13 ASN HB3 H 2.864 . 2 90 13 13 ASN HD21 H 7.474 . 2 91 13 13 ASN HD22 H 6.801 . 2 92 14 14 VAL H H 8.118 . 1 93 14 14 VAL HA H 3.748 . 1 94 14 14 VAL HB H 2.245 . 1 95 14 14 VAL HG1 H 1.126 . 2 96 14 14 VAL HG2 H 1.014 . 2 97 15 15 LYS H H 8.146 . 1 98 15 15 LYS HA H 4.086 . 1 99 15 15 LYS HB2 H 1.941 . 2 100 15 15 LYS HB3 H 1.709 . 2 101 15 15 LYS HD2 H 1.613 . 1 102 15 15 LYS HD3 H 1.613 . 1 103 15 15 LYS HE2 H 3.01 . 1 104 15 15 LYS HE3 H 3.01 . 1 105 15 15 LYS HG2 H 1.478 . 1 106 15 15 LYS HG3 H 1.478 . 1 107 15 15 LYS HZ H 7.595 . 1 108 16 16 GLU H H 8.265 . 1 109 16 16 GLU HA H 4.119 . 1 110 16 16 GLU HB2 H 2.082 . 1 111 16 16 GLU HB3 H 2.082 . 1 112 16 16 GLU HG2 H 2.405 . 2 113 16 16 GLU HG3 H 2.33 . 2 114 17 17 LYS H H 7.982 . 1 115 17 17 LYS HA H 4.076 . 1 116 17 17 LYS HB2 H 1.985 . 2 117 17 17 LYS HB3 H 1.736 . 2 118 17 17 LYS HD2 H 1.59 . 1 119 17 17 LYS HD3 H 1.59 . 1 120 17 17 LYS HE2 H 3.037 . 1 121 17 17 LYS HE3 H 3.037 . 1 122 17 17 LYS HG2 H 1.515 . 1 123 17 17 LYS HG3 H 1.515 . 1 124 17 17 LYS HZ H 7.575 . 1 125 18 18 ASP H H 8.361 . 1 126 18 18 ASP HA H 4.551 . 1 127 18 18 ASP HB2 H 3.047 . 2 128 18 18 ASP HB3 H 2.945 . 2 129 19 19 GLN H H 8.073 . 1 130 19 19 GLN HA H 4.234 . 1 131 19 19 GLN HB2 H 2.246 . 1 132 19 19 GLN HB3 H 2.246 . 1 133 19 19 GLN HE21 H 7.129 . 2 134 19 19 GLN HE22 H 6.672 . 2 135 19 19 GLN HG2 H 2.506 . 2 136 19 19 GLN HG3 H 2.427 . 2 137 20 20 VAL H H 8.05 . 1 138 20 20 VAL HA H 3.872 . 1 139 20 20 VAL HB H 2.239 . 1 140 20 20 VAL HG1 H 1.093 . 2 141 20 20 VAL HG2 H 1.002 . 2 142 21 21 GLU H H 8.265 . 1 143 21 21 GLU HA H 4.211 . 1 144 21 21 GLU HB2 H 2.213 . 1 145 21 21 GLU HB3 H 2.213 . 1 146 21 21 GLU HG2 H 2.63 . 2 147 21 21 GLU HG3 H 2.518 . 2 148 22 22 ASP H H 8.214 . 1 149 22 22 ASP HA H 4.618 . 1 150 22 22 ASP HB2 H 3.038 . 2 151 22 22 ASP HB3 H 2.972 . 2 152 23 23 LEU H H 8.011 . 1 153 23 23 LEU HA H 4.268 . 1 154 23 23 LEU HB2 H 1.862 . 2 155 23 23 LEU HB3 H 1.798 . 2 156 23 23 LEU HD1 H 0.946 . 1 157 23 23 LEU HD2 H 0.946 . 1 158 23 23 LEU HG H 1.658 . 1 159 24 24 ASN H H 8.146 . 1 160 24 24 ASN HA H 4.63 . 1 161 24 24 ASN HB2 H 2.878 . 1 162 24 24 ASN HB3 H 2.878 . 1 163 24 24 ASN HD21 H 7.417 . 2 164 24 24 ASN HD22 H 6.621 . 2 165 25 25 LEU H H 8.163 . 1 166 25 25 LEU HA H 4.2 . 1 167 25 25 LEU HB2 H 1.782 . 1 168 25 25 LEU HB3 H 1.782 . 1 169 25 25 LEU HD1 H 0.978 . 2 170 25 25 LEU HD2 H 0.89 . 2 171 25 25 LEU HG H 1.601 . 1 172 26 26 ASP H H 8.27 . 1 173 26 26 ASP HA H 4.527 . 1 174 26 26 ASP HB2 H 2.978 . 2 175 26 26 ASP HB3 H 2.926 . 2 176 27 27 SER H H 7.954 . 1 177 27 27 SER HA H 4.324 . 1 178 27 27 SER HB2 H 3.985 . 2 179 27 27 SER HB3 H 3.934 . 2 180 28 28 LEU H H 7.745 . 1 181 28 28 LEU HA H 4.222 . 1 182 28 28 LEU HB2 H 1.672 . 1 183 28 28 LEU HB3 H 1.672 . 1 184 28 28 LEU HD1 H 0.915 . 2 185 28 28 LEU HD2 H 0.835 . 2 186 28 28 LEU HG H 1.48 . 1 187 29 29 TRP H H 7.694 . 1 188 29 29 TRP HA H 4.697 . 1 189 29 29 TRP HB2 H 3.364 . 1 190 29 29 TRP HB3 H 3.364 . 1 191 29 29 TRP HD1 H 7.265 . 1 192 29 29 TRP HE1 H 9.683 . 1 193 29 29 TRP HE3 H 7.732 . 1 194 29 29 TRP HH2 H 7.152 . 1 195 29 29 TRP HZ2 H 7.457 . 1 196 29 29 TRP HZ3 H 7.219 . 1 197 30 30 GLU H H 7.768 . 1 198 30 30 GLU HA H 4.245 . 1 199 30 30 GLU HB2 H 2.114 . 2 200 30 30 GLU HB3 H 1.942 . 2 201 30 30 GLU HG2 H 2.303 . 1 202 30 30 GLU HG3 H 2.303 . 1 stop_ save_