data_1656 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; C-Terminal Retroviral-Type Zinc Finger Domain from the HIV-1 Nucleocapsid Protein Is Structurally Similar to the N-Terminal Zinc Finger Domain ; _BMRB_accession_number 1656 _BMRB_flat_file_name bmr1656.str _Entry_type update _Submission_date 1995-07-31 _Accession_date 1996-04-13 _Entry_origination BMRB _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 South Terri L. . 2 Blake Paul R. . 3 Hare Dennis R. . 4 Summers Michael F. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 109 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-15 revision BMRB 'Complete natural source information' 1999-06-14 revision BMRB 'Converted to BMRB NMR-STAR V 2.1 format' 1996-04-13 revision BMRB 'Link to the Protein Data Bank added' 1996-03-25 reformat BMRB 'Converted to the BMRB 1996-03-01 STAR flat-file format' 1995-07-31 original BMRB 'Last release in original BMRB flat-file format' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; South, Terri L., Blake, Paul R., Hare, Dennis R., Summers, Michael F., "C-Terminal Retroviral-Type Zinc Finger Domain from the HIV-1 Nucleocapsid Protein Is Structurally Similar to the N-Terminal Zinc Finger Domain," Biochemistry 30, 6342-6349 (1991). ; _Citation_title ; C-Terminal Retroviral-Type Zinc Finger Domain from the HIV-1 Nucleocapsid Protein Is Structurally Similar to the N-Terminal Zinc Finger Domain ; _Citation_status published _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 South Terri L. . 2 Blake Paul R. . 3 Hare Dennis R. . 4 Summers Michael F. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 30 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6342 _Page_last 6349 _Year 1991 _Details . save_ ################################## # Molecular system description # ################################## save_system_nucleocapsid_protein _Saveframe_category molecular_system _Mol_system_name 'nucleocapsid protein' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'nucleocapsid protein' $nucleocapsid_protein stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic ? _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' _Name_variant 'zinc finger Zn-HIV1-F2' _Molecular_mass . _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence KGCWKCGKEGHQMKDCTE loop_ _Residue_seq_code _Residue_label 1 LYS 2 GLY 3 CYS 4 TRP 5 LYS 6 CYS 7 GLY 8 LYS 9 GLU 10 GLY 11 HIS 12 GLN 13 MET 14 LYS 15 ASP 16 CYS 17 THR 18 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-04-17 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 17216 NCp7(12-55) 100.00 44 100.00 100.00 2.53e-03 BMRB 17228 C-terminal_zinc_knuckle_of_the_HIVNCp7 100.00 19 100.00 100.00 4.39e-03 BMRB 17229 C-terminal_zinc_knuckle_of_the_HIVNCp7 100.00 19 100.00 100.00 4.39e-03 BMRB 18980 entity_1 100.00 55 100.00 100.00 1.99e-03 BMRB 2217 "nucleocapsid protein" 100.00 39 100.00 100.00 3.72e-03 BMRB 25532 Gag 100.00 432 100.00 100.00 1.79e-03 PDB 1A1T "Structure Of The Hiv-1 Nucleocapsid Protein Bound To The Sl3 Psi-Rna Recognition Element, Nmr, 25 Structures" 100.00 55 100.00 100.00 2.16e-03 PDB 1BJ6 "1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES" 100.00 42 100.00 100.00 3.36e-03 PDB 1ESK "Solution Structure Of Ncp7 From Hiv-1" 100.00 42 100.00 100.00 3.36e-03 PDB 1F6U "Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bound To Stem-Loop Sl2 Of The Psi-Rna Packaging Signal. Implications For Genome" 100.00 56 100.00 100.00 2.13e-03 PDB 1MFS "Dynamical Behavior Of The Hiv-1 Nucleocapsid Protein; Nmr, 30 Structures" 100.00 55 100.00 100.00 2.16e-03 PDB 1NCP "Structural Characterization Of A 39 Residue Synthetic Peptide Containing The Two Zinc Binding Domains From The Hiv-1 P7 Nucleoc" 100.00 18 100.00 100.00 5.04e-03 PDB 1Q3Y "Nmr Structure Of The Cys28his Mutant (D Form) Of The Nucleocapsid Protein Ncp7 Of Hiv-1." 100.00 42 100.00 100.00 2.70e-03 PDB 1Q3Z "Nmr Structure Of The Cys28his Mutant (e Form) Of The Nucleocapsid Protein Ncp7 Of Hiv-1" 100.00 42 100.00 100.00 2.70e-03 PDB 2EXF "Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7(12-55)) Complexed With The Dna (-) Primer Binding Site" 100.00 44 100.00 100.00 2.53e-03 PDB 2JZW "How The Hiv-1 Nucleocapsid Protein Binds And Destabilises The (-)primer Binding Site During Reverse Transcription" 100.00 44 100.00 100.00 2.53e-03 PDB 2L44 "C-Terminal Zinc Knuckle Of The Hivncp7" 100.00 19 100.00 100.00 4.39e-03 PDB 2L45 "C-Terminal Zinc Knuckle Of The Hivncp7 With Dna" 100.00 19 100.00 100.00 4.39e-03 PDB 2L46 "C-Terminal Zinc Finger Of The Hivncp7 With Platinated Dna" 100.00 19 100.00 100.00 4.39e-03 PDB 2L4L "Structural Insights Into The Ctar Dna Recognition By The Hiv-1 Nucleocapsid Protein: Role Of Sugar Deoxyriboses In The Binding " 100.00 45 100.00 100.00 2.55e-03 PDB 2M3Z "Nmr Solution Structure Of Hiv-1 Nucleocapsid Protein In Complex With An Inhibitor Displaying A 2 Inhibitors:1 Nc Stoichiometry" 100.00 55 100.00 100.00 1.99e-03 DBJ BAA12988 "Gag [Human immunodeficiency virus 1]" 100.00 512 100.00 100.00 1.67e-04 DBJ BAA12996 "Gag [Human immunodeficiency virus 1]" 100.00 512 100.00 100.00 1.82e-04 DBJ BAA84661 "gag-pol fusion polyprotein [Human immunodeficiency virus 1]" 100.00 1433 100.00 100.00 2.85e-03 DBJ BAA84662 "gag polyprotein precursor [Human immunodeficiency virus 1]" 100.00 498 100.00 100.00 2.28e-03 DBJ BAA84669 "gag-pol fusion polyprotein [Human immunodeficiency virus 1]" 100.00 1433 100.00 100.00 2.74e-03 EMBL CAA28011 "gag polyprotein [Human immunodeficiency virus 1]" 100.00 505 100.00 100.00 1.72e-03 EMBL CAA42971 "p24/p25/p7 [Human immunodeficiency virus 1]" 100.00 75 100.00 100.00 8.68e-04 EMBL CAA42973 "p24/p25/p7 [Human immunodeficiency virus 1]" 83.33 66 100.00 100.00 1.58e-01 EMBL CAA73647 "gag protein [Human immunodeficiency virus 1]" 100.00 467 100.00 100.00 1.73e-03 EMBL CAA77483 "p24/p25/p7, partial [Human immunodeficiency virus 1]" 100.00 76 100.00 100.00 8.06e-04 GB AAA43911 "core protein, partial [Human immunodeficiency virus 1]" 100.00 492 100.00 100.00 1.73e-03 GB AAA44201 "gag polyprotein precursor [Human immunodeficiency virus 1]" 100.00 512 100.00 100.00 1.70e-04 GB AAA44313 "gag protein, partial [Human immunodeficiency virus 1]" 100.00 492 100.00 100.00 3.46e-04 GB AAA44314 "gag protein, partial [Human immunodeficiency virus 1]" 100.00 484 100.00 100.00 1.92e-03 GB AAA44317 "gag protein, partial [Human immunodeficiency virus 1]" 100.00 486 100.00 100.00 1.91e-03 PIR FOVWLV "gag polyprotein - human immunodeficiency virus type 1 (isolate LAV-1a)" 100.00 500 100.00 100.00 2.33e-04 PRF 1102247B "protein gag" 100.00 512 100.00 100.00 1.70e-04 PRF 1103299C "gag gene" 100.00 478 100.00 100.00 2.04e-03 REF NP_057849 "Gag-Pol [Human immunodeficiency virus 1]" 100.00 1435 100.00 100.00 2.85e-03 REF NP_057850 "Pr55(Gag) [Human immunodeficiency virus 1]" 100.00 500 100.00 100.00 2.33e-04 REF NP_579881 "nucleocapsid [Human immunodeficiency virus 1]" 100.00 55 100.00 100.00 1.89e-03 SP O89939 "RecName: Full=Gag polyprotein; AltName: Full=Pr55Gag; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: RecName: " 100.00 495 100.00 100.00 1.85e-03 SP O89940 "RecName: Full=Gag-Pol polyprotein; AltName: Full=Pr160Gag-Pol; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: " 100.00 1433 100.00 100.00 2.57e-03 SP P03347 "RecName: Full=Gag polyprotein; AltName: Full=Pr55Gag; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: RecName: " 100.00 512 100.00 100.00 1.70e-04 SP P03348 "RecName: Full=Gag polyprotein; AltName: Full=Pr55Gag; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: RecName: " 100.00 512 100.00 100.00 1.67e-04 SP P03366 "RecName: Full=Gag-Pol polyprotein; AltName: Full=Pr160Gag-Pol; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: " 100.00 1447 100.00 100.00 2.69e-03 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain $nucleocapsid_protein HIV 12721 Virus . HIV . generic 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 'not available' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_list _Saveframe_category NMR_spectrometer _Manufacturer unknown _Model unknown _Field_strength 0 _Details 'spectrometer information not available' save_ ############################# # NMR applied experiments # ############################# save__1 _Saveframe_category NMR_applied_experiment _Sample_label $sample_one save_ ####################### # Sample conditions # ####################### save_sample_condition_set_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . na temperature 271 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_par_set_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_citation_label _Correction_value_citation_label H2O/HDO H . . ppm 5.03 . . . . . $entry_citation $entry_citation 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_assignment_data_set_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_condition_set_one _Chem_shift_reference_set_label $chem_shift_reference_par_set_one _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 . 1 LYS HA H 3.93 . 1 2 . 1 LYS HB2 H 1.84 . 1 3 . 1 LYS HB3 H 1.84 . 1 4 . 1 LYS HG2 H 1.42 . 1 5 . 1 LYS HG3 H 1.42 . 1 6 . 1 LYS HD2 H 1.64 . 1 7 . 1 LYS HD3 H 1.64 . 1 8 . 1 LYS HE2 H 2.89 . 1 9 . 1 LYS HE3 H 2.89 . 1 10 . 2 GLY H H 8.74 . 1 11 . 2 GLY HA2 H 3.37 . 2 12 . 2 GLY HA3 H 3.74 . 2 13 . 3 CYS H H 8.19 . 1 14 . 3 CYS HA H 3.96 . 1 15 . 3 CYS HB2 H 2 . 2 16 . 3 CYS HB3 H 2.84 . 2 17 . 4 TRP H H 8.79 . 1 18 . 4 TRP HA H 4.36 . 1 19 . 4 TRP HB2 H 3.35 . 2 20 . 4 TRP HB3 H 3.46 . 2 21 . 4 TRP HD1 H 7.31 . 1 22 . 4 TRP HE1 H 10.16 . 1 23 . 4 TRP HE3 H 7.57 . 1 24 . 4 TRP HZ2 H 7.46 . 1 25 . 4 TRP HZ3 H 7.1 . 1 26 . 4 TRP HH2 H 7.19 . 1 27 . 5 LYS H H 9.39 . 1 28 . 5 LYS HA H 4.16 . 1 29 . 5 LYS HB2 H 2.26 . 1 30 . 5 LYS HB3 H 2.26 . 1 31 . 5 LYS HG2 H 1.64 . 1 32 . 5 LYS HG3 H 1.64 . 1 33 . 5 LYS HD2 H 1.25 . 1 34 . 5 LYS HD3 H 1.25 . 1 35 . 5 LYS HE2 H 2.88 . 1 36 . 5 LYS HE3 H 2.88 . 1 37 . 6 CYS H H 8.5 . 1 38 . 6 CYS HA H 4.89 . 1 39 . 6 CYS HB2 H 2.49 . 2 40 . 6 CYS HB3 H 3.17 . 2 41 . 7 GLY H H 8.16 . 1 42 . 7 GLY HA2 H 3.8 . 2 43 . 7 GLY HA3 H 4.07 . 2 44 . 8 LYS H H 8.46 . 1 45 . 8 LYS HA H 4.34 . 1 46 . 8 LYS HB2 H 1.85 . 1 47 . 8 LYS HB3 H 1.85 . 1 48 . 8 LYS HG2 H 1.39 . 1 49 . 8 LYS HG3 H 1.39 . 1 50 . 8 LYS HD2 H 1.56 . 1 51 . 8 LYS HD3 H 1.56 . 1 52 . 8 LYS HE2 H 2.94 . 1 53 . 8 LYS HE3 H 2.94 . 1 54 . 9 GLU H H 8.58 . 1 55 . 9 GLU HA H 4.16 . 1 56 . 9 GLU HB2 H 1.79 . 2 57 . 9 GLU HB3 H 1.98 . 2 58 . 9 GLU HG2 H 2.14 . 2 59 . 9 GLU HG3 H 2.26 . 2 60 . 10 GLY H H 8.75 . 1 61 . 10 GLY HA2 H 4.36 . 2 62 . 10 GLY HA3 H 3.66 . 2 63 . 11 HIS H H 7.16 . 1 64 . 11 HIS HA H 4.78 . 1 65 . 11 HIS HB2 H 3.16 . 1 66 . 11 HIS HB3 H 3.16 . 1 67 . 11 HIS HD2 H 6.8 . 1 68 . 11 HIS HE1 H 7.44 . 1 69 . 12 GLN H H 9.03 . 1 70 . 12 GLN HA H 4.63 . 1 71 . 12 GLN HB2 H 1.89 . 2 72 . 12 GLN HB3 H 2.03 . 2 73 . 12 GLN HG2 H 2.03 . 1 74 . 12 GLN HG3 H 2.03 . 1 75 . 13 MET H H 9.03 . 1 76 . 13 MET HA H 4.76 . 1 77 . 13 MET HB2 H 2.16 . 1 78 . 13 MET HB3 H 2.16 . 1 79 . 13 MET HG2 H 2.49 . 1 80 . 13 MET HG3 H 2.49 . 1 81 . 13 MET HE H 2.1 . 1 82 . 14 LYS H H 8.77 . 1 83 . 14 LYS HA H 4.12 . 1 84 . 14 LYS HB2 H 1.71 . 1 85 . 14 LYS HB3 H 1.71 . 1 86 . 14 LYS HG2 H 1.85 . 1 87 . 14 LYS HG3 H 1.85 . 1 88 . 14 LYS HD2 H 1.21 . 1 89 . 14 LYS HD3 H 1.21 . 1 90 . 14 LYS HE2 H 2.87 . 1 91 . 14 LYS HE3 H 2.87 . 1 92 . 15 ASP H H 7.96 . 1 93 . 15 ASP HA H 4.88 . 1 94 . 15 ASP HB2 H 2.51 . 2 95 . 15 ASP HB3 H 2.94 . 2 96 . 16 CYS H H 7.75 . 1 97 . 16 CYS HA H 3.65 . 1 98 . 16 CYS HB2 H 2.85 . 2 99 . 16 CYS HB3 H 3.28 . 2 100 . 17 THR H H 8.44 . 1 101 . 17 THR HA H 4.43 . 1 102 . 17 THR HB H 4.43 . 1 103 . 17 THR HG2 H 1.06 . 1 104 . 18 GLU H H 8.67 . 1 105 . 18 GLU HA H 4.04 . 1 106 . 18 GLU HB2 H 1.82 . 1 107 . 18 GLU HB3 H 1.82 . 1 108 . 18 GLU HG2 H 2.34 . 2 109 . 18 GLU HG3 H 2.16 . 2 stop_ save_