data_7342 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; SOLUTION STRUCTURE OF THE ZN COMPLEX OF HIV-2 NCP(23-49) PEPTIDE, ENCOMPASSING PROTEIN CCHC-LINKER, DISTAL CCHC ZN-BINDING MOTIF AND C-TERMINAL TAIL ; _BMRB_accession_number 7342 _BMRB_flat_file_name bmr7342.str _Entry_type original _Submission_date 2006-12-01 _Accession_date 2006-12-05 _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 Amodeo P. . . 2 'Castiglione Morelli' M. A. . 3 Ostuni A. . . 4 Cristinziano P. . . 5 Bavoso A. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 168 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-05-26 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural Features of the C-Terminal Zinc Finger Domain of the HIV-2 Nc Protein (Residues 23-49).' _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 Amodeo P. . . 2 'Castiglione Morelli' M. A. . 3 Ostuni A. . . 4 Cristinziano P. . . 5 Bavoso A. . . stop_ _Journal_abbreviation . _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 NUCLEOCAPSID_PROTEIN _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'NUCLEOCAPSID PROTEIN' $NUCLEOCAPSID_PROTEIN 'ZINC ION' $ZN 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_NUCLEOCAPSID_PROTEIN _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common NUCLEOCAPSID_PROTEIN _Molecular_mass . _Mol_thiol_state 'all other bound' _Details ; FRAGMENT 23-49 OF NCP CORRESPONDS TO 405-431 OF THE WHOLE HIV-2 GAG PROTEIN CONTAINS ONE ZN ION IN A CCHC ZN-BINDING DOMAINS. ; ############################## # Polymer residue sequence # ############################## _Residue_count 27 _Mol_residue_sequence ; RAPRRQGCWKCGKTGHVMAK CPERQAG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 23 ARG 2 24 ALA 3 25 PRO 4 26 ARG 5 27 ARG 6 28 GLN 7 29 GLY 8 30 CYS 9 31 TRP 10 32 LYS 11 33 CYS 12 34 GLY 13 35 LYS 14 36 THR 15 37 GLY 16 38 HIS 17 39 VAL 18 40 MET 19 41 ALA 20 42 LYS 21 43 CYS 22 44 PRO 23 45 GLU 24 46 ARG 25 47 GLN 26 48 ALA 27 49 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-28 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 15196 Gag-Pol_polyprotein_(Pr160Gag-Pol) 100.00 27 100.00 100.00 8.62e-10 BMRB 15364 Gag_polyprotein_(Pr55Gag) 100.00 49 100.00 100.00 1.48e-09 BMRB 7384 Gag_polyprotein_(Pr55Gag) 100.00 49 100.00 100.00 1.48e-09 PDB 2E1X "Nmr Structure Of The Hiv-2 Nucleocapsid Protein" 100.00 27 100.00 100.00 8.62e-10 PDB 2EC7 "Solution Structure Of Human Immunodificiency Virus Type-2 Nucleocapsid Protein" 100.00 49 100.00 100.00 1.48e-09 PDB 2IWJ "Solution Structure Of The Zn Complex Of Hiv-2 Ncp(23-49) Peptide, Encompassing Protein Cchc-Linker, Distal Cchc Zn- Binding Mot" 100.00 27 100.00 100.00 8.62e-10 EMBL CAA32483 "unnamed protein product [Simian immunodeficiency virus]" 100.00 507 100.00 100.00 2.22e-09 GB AAA43932 "gag protein [Human immunodeficiency virus 2]" 100.00 522 100.00 100.00 2.59e-09 GB AAB41427 "gag, partial [Simian immunodeficiency virus]" 100.00 149 100.00 100.00 8.13e-10 GB AAC68655 "Gag [Simian immunodeficiency virus]" 100.00 507 100.00 100.00 2.33e-09 GB AAL18230 "gag polyprotein [Simian immunodeficiency virus]" 51.85 389 100.00 100.00 3.76e+00 GB ADI24350 "gag protein [Simian immunodeficiency virus]" 100.00 507 100.00 100.00 2.40e-09 PRF 1509334A "gag gene" 100.00 507 100.00 100.00 2.22e-09 SP P12496 "RecName: Full=Gag polyprotein; AltName: Full=Pr55Gag; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: RecName: " 100.00 507 100.00 100.00 2.22e-09 SP P12502 "RecName: Full=Gag-Pol polyprotein; AltName: Full=Pr160Gag-Pol; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: " 100.00 1449 100.00 100.00 1.92e-09 SP P18041 "RecName: Full=Gag polyprotein; AltName: Full=Pr55Gag; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: RecName: " 100.00 522 100.00 100.00 2.59e-09 SP P18042 "RecName: Full=Gag-Pol polyprotein; AltName: Full=Pr160Gag-Pol; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: " 100.00 1464 100.00 100.00 1.73e-09 stop_ save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type non-polymer _Name_common "ZN (ZINC ION)" _BMRB_code . _PDB_code ZN _Molecular_mass 65.409 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Oct 7 14:15:35 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons ZN ZN ZN . 2 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single coordination 'NUCLEOCAPSID PROTEIN' 8 CYS SG 'ZINC ION' 1 ZN ZN single coordination 'NUCLEOCAPSID PROTEIN' 11 CYS SG 'ZINC ION' 1 ZN ZN single coordination 'NUCLEOCAPSID PROTEIN' 16 HIS NE2 'ZINC ION' 1 ZN ZN single coordination 'NUCLEOCAPSID PROTEIN' 21 CYS SG 'ZINC ION' 1 ZN ZN stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $NUCLEOCAPSID_PROTEIN HIV-2 11709 Viruses . Lentivirus HIV-2 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 $NUCLEOCAPSID_PROTEIN 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details '80% WATER/20% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $NUCLEOCAPSID_PROTEIN 2.6 mM 'natural abundance' H2O 80 % 'natural abundance' D2O 20 % 'natural abundance' TCEP.HCl 11.5 mM 'natural abundance' 'zinc chloride' 3.1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_MolMol _Saveframe_category software _Name MolMol _Version 2K.2 loop_ _Task 'data analysis' stop_ _Details Koradi save_ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1C loop_ _Task processing stop_ _Details Varian save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer VARIAN _Model UNITYINOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample save_ save_2D_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample 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' 130 . mM pH 7.0 . pH pressure 1.0 . atm temperature 298.0 . 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 H 1 'methyl protons' ppm 0.00 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_chemical_shift_ch_A _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D DQF-COSY' '2D TOCSY' stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'NUCLEOCAPSID PROTEIN' _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 23 1 ARG HA H 4.03 0.02 1 2 23 1 ARG HB2 H 1.90 0.02 2 3 23 1 ARG HB3 H 1.82 0.02 2 4 23 1 ARG HD2 H 3.20 0.02 1 5 23 1 ARG HD3 H 3.20 0.02 1 6 23 1 ARG HG2 H 1.64 0.02 1 7 23 1 ARG HG3 H 1.64 0.02 1 8 23 1 ARG HH11 H 7.25 0.02 1 9 23 1 ARG HH12 H 7.25 0.02 1 10 24 2 ALA H H 8.79 0.02 1 11 24 2 ALA HA H 4.64 0.02 1 12 24 2 ALA HB H 1.38 0.02 1 13 25 3 PRO HA H 4.43 0.02 1 14 25 3 PRO HB2 H 2.09 0.02 2 15 25 3 PRO HB3 H 1.92 0.02 2 16 25 3 PRO HD2 H 3.80 0.02 2 17 25 3 PRO HD3 H 3.60 0.02 2 18 25 3 PRO HG2 H 2.30 0.02 1 19 25 3 PRO HG3 H 2.30 0.02 1 20 26 4 ARG H H 8.44 0.02 1 21 26 4 ARG HA H 4.53 0.02 1 22 26 4 ARG HB2 H 1.79 0.02 2 23 26 4 ARG HB3 H 1.63 0.02 2 24 26 4 ARG HD2 H 3.19 0.02 1 25 26 4 ARG HD3 H 3.19 0.02 1 26 26 4 ARG HG2 H 1.42 0.02 1 27 26 4 ARG HG3 H 1.42 0.02 1 28 26 4 ARG HH11 H 7.09 0.02 1 29 26 4 ARG HH12 H 7.09 0.02 1 30 27 5 ARG H H 8.40 0.02 1 31 27 5 ARG HA H 4.29 0.02 1 32 27 5 ARG HB2 H 1.78 0.02 2 33 27 5 ARG HB3 H 1.64 0.02 2 34 27 5 ARG HD2 H 3.15 0.02 1 35 27 5 ARG HD3 H 3.15 0.02 1 36 27 5 ARG HG2 H 1.42 0.02 1 37 27 5 ARG HG3 H 1.42 0.02 1 38 27 5 ARG HH11 H 7.16 0.02 1 39 27 5 ARG HH12 H 7.16 0.02 1 40 28 6 GLN H H 8.47 0.02 1 41 28 6 GLN HA H 4.36 0.02 1 42 28 6 GLN HB2 H 2.08 0.02 2 43 28 6 GLN HB3 H 1.96 0.02 2 44 28 6 GLN HG2 H 2.36 0.02 1 45 28 6 GLN HG3 H 2.36 0.02 1 46 29 7 GLY H H 8.26 0.02 1 47 29 7 GLY HA2 H 3.85 0.02 2 48 29 7 GLY HA3 H 3.55 0.02 2 49 30 8 CYS H H 8.25 0.02 1 50 30 8 CYS HA H 4.12 0.02 1 51 30 8 CYS HB2 H 2.95 0.02 2 52 30 8 CYS HB3 H 2.20 0.02 2 53 31 9 TRP H H 8.55 0.02 1 54 31 9 TRP HA H 4.52 0.02 1 55 31 9 TRP HB2 H 3.46 0.02 1 56 31 9 TRP HB3 H 3.46 0.02 1 57 31 9 TRP HD1 H 7.33 0.02 1 58 31 9 TRP HE1 H 10.00 0.02 1 59 31 9 TRP HE3 H 7.64 0.02 1 60 31 9 TRP HH2 H 7.27 0.02 1 61 31 9 TRP HZ2 H 7.55 0.02 1 62 31 9 TRP HZ3 H 7.18 0.02 1 63 32 10 LYS H H 9.30 0.02 1 64 32 10 LYS HA H 4.32 0.02 1 65 32 10 LYS HB2 H 2.26 0.02 1 66 32 10 LYS HB3 H 2.26 0.02 1 67 32 10 LYS HD2 H 1.30 0.02 1 68 32 10 LYS HD3 H 1.30 0.02 1 69 32 10 LYS HE2 H 2.96 0.02 1 70 32 10 LYS HE3 H 2.96 0.02 1 71 32 10 LYS HG2 H 1.70 0.02 1 72 32 10 LYS HG3 H 1.70 0.02 1 73 32 10 LYS HZ H 7.25 0.02 1 74 33 11 CYS H H 8.49 0.02 1 75 33 11 CYS HA H 4.98 0.02 1 76 33 11 CYS HB2 H 3.29 0.02 2 77 33 11 CYS HB3 H 2.55 0.02 2 78 34 12 GLY H H 8.20 0.02 1 79 34 12 GLY HA2 H 4.18 0.02 2 80 34 12 GLY HA3 H 3.95 0.02 2 81 35 13 LYS H H 8.25 0.02 1 82 35 13 LYS HA H 4.25 0.02 1 83 35 13 LYS HB2 H 2.05 0.02 2 84 35 13 LYS HB3 H 1.85 0.02 2 85 35 13 LYS HD2 H 1.68 0.02 1 86 35 13 LYS HD3 H 1.68 0.02 1 87 35 13 LYS HE2 H 3.25 0.02 1 88 35 13 LYS HE3 H 3.25 0.02 1 89 35 13 LYS HG2 H 1.40 0.02 1 90 35 13 LYS HG3 H 1.40 0.02 1 91 36 14 THR H H 8.20 0.02 1 92 36 14 THR HA H 4.36 0.02 1 93 36 14 THR HB H 4.25 0.02 1 94 36 14 THR HG2 H 1.19 0.02 1 95 37 15 GLY H H 8.56 0.02 1 96 37 15 GLY HA2 H 4.33 0.02 2 97 37 15 GLY HA3 H 3.76 0.02 2 98 38 16 HIS H H 7.18 0.02 1 99 38 16 HIS HA H 4.95 0.02 1 100 38 16 HIS HB2 H 3.25 0.02 2 101 38 16 HIS HB3 H 3.18 0.02 2 102 38 16 HIS HD2 H 6.91 0.02 1 103 38 16 HIS HE1 H 7.54 0.02 1 104 39 17 VAL H H 7.95 0.02 1 105 39 17 VAL HA H 4.64 0.02 1 106 39 17 VAL HB H 2.42 0.02 1 107 39 17 VAL HG1 H 0.93 0.02 1 108 39 17 VAL HG2 H 0.93 0.02 1 109 40 18 MET H H 8.85 0.02 1 110 40 18 MET HA H 4.45 0.02 1 111 40 18 MET HB2 H 2.22 0.02 1 112 40 18 MET HB3 H 2.22 0.02 1 113 40 18 MET HG2 H 2.62 0.02 1 114 40 18 MET HG3 H 2.62 0.02 1 115 41 19 ALA H H 8.54 0.02 1 116 41 19 ALA HA H 4.16 0.02 1 117 41 19 ALA HB H 1.43 0.02 1 118 42 20 LYS H H 7.91 0.02 1 119 42 20 LYS HA H 4.52 0.02 1 120 42 20 LYS HB2 H 2.14 0.02 1 121 42 20 LYS HB3 H 2.14 0.02 1 122 42 20 LYS HD2 H 1.66 0.02 1 123 42 20 LYS HD3 H 1.66 0.02 1 124 42 20 LYS HE2 H 2.97 0.02 1 125 42 20 LYS HE3 H 2.97 0.02 1 126 42 20 LYS HG2 H 1.44 0.02 2 127 42 20 LYS HG3 H 1.27 0.02 2 128 42 20 LYS HZ H 7.56 0.02 1 129 43 21 CYS H H 7.58 0.02 1 130 43 21 CYS HA H 4.06 0.02 1 131 43 21 CYS HB2 H 2.85 0.02 2 132 43 21 CYS HB3 H 3.25 0.02 2 133 44 22 PRO HA H 4.43 0.02 1 134 44 22 PRO HB2 H 2.09 0.02 2 135 44 22 PRO HB3 H 1.97 0.02 2 136 44 22 PRO HD2 H 3.58 0.02 2 137 44 22 PRO HD3 H 3.72 0.02 2 138 44 22 PRO HG2 H 2.30 0.02 1 139 44 22 PRO HG3 H 2.30 0.02 1 140 45 23 GLU H H 8.69 0.02 1 141 45 23 GLU HA H 4.31 0.02 1 142 45 23 GLU HB2 H 2.15 0.02 2 143 45 23 GLU HB3 H 2.02 0.02 2 144 45 23 GLU HG2 H 2.36 0.02 2 145 45 23 GLU HG3 H 2.26 0.02 2 146 46 24 ARG H H 8.01 0.02 1 147 46 24 ARG HA H 4.28 0.02 1 148 46 24 ARG HB2 H 1.90 0.02 2 149 46 24 ARG HB3 H 1.82 0.02 2 150 46 24 ARG HD2 H 3.20 0.02 1 151 46 24 ARG HD3 H 3.20 0.02 1 152 46 24 ARG HE H 7.23 0.02 1 153 46 24 ARG HG2 H 1.64 0.02 1 154 46 24 ARG HG3 H 1.64 0.02 1 155 47 25 GLN H H 8.35 0.02 1 156 47 25 GLN HA H 4.33 0.02 1 157 47 25 GLN HB2 H 2.15 0.02 2 158 47 25 GLN HB3 H 2.01 0.02 2 159 47 25 GLN HE21 H 6.87 0.02 2 160 47 25 GLN HE22 H 7.56 0.02 2 161 47 25 GLN HG2 H 2.37 0.02 1 162 47 25 GLN HG3 H 2.37 0.02 1 163 48 26 ALA H H 8.65 0.02 1 164 48 26 ALA HA H 4.29 0.02 1 165 48 26 ALA HB H 1.36 0.02 1 166 49 27 GLY H H 7.98 0.02 1 167 49 27 GLY HA2 H 3.77 0.02 1 168 49 27 GLY HA3 H 3.77 0.02 1 stop_ save_