data_17216 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; How the HIV-1 Nucleocapsid Protein Binds and Destabilises the (-)Primer Binding Site During Reverse Transcription ; _BMRB_accession_number 17216 _BMRB_flat_file_name bmr17216.str _Entry_type new _Submission_date 2010-09-29 _Accession_date 2010-09-29 _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 Bourbigot Sarah . . 2 Ramalanjaona Nick . . 3 Boudier Christian . . 4 Salgado Gilmar F.J. . 5 Roques Bernard P. . 6 Mely Yves . . 7 Bouaziz Serge . . 8 Morellet Nelly . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count kinetic_rates 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-11-10 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'How the HIV-1 Nucleocapsid Protein Binds and Destabilises the (-)Primer Binding Site During Reverse Transcription' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18773912 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bourbigot Sarah . . 2 Ramalanjaona Nick . . 3 Boudier Christian . . 4 Salgado Gilmar F.J. . 5 Roques Bernard P. . 6 Mely Yves . . 7 Bouaziz Serge . . 8 Morellet Nelly . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of Molecular Biology' _Journal_volume 383 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1112 _Page_last 1128 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'PPBS/NCp7(12-55) exchange' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label PPBS $PPBS NCp7(12-55) $NCp7(12-55) 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_PPBS _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common PPBS _Molecular_mass . _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GCCCTGTTGGGC loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DC 4 DC 5 DT 6 DG 7 DT 8 DT 9 DG 10 DG 11 DG 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_NCp7(12-55) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common NCp7(12-55) _Molecular_mass . _Mol_thiol_state 'not reported' _Details . _Residue_count 44 _Mol_residue_sequence ; NVKCFNCGKEGHTARNCRAP RKKGCWKCGKEGHQMKDCTE RQAN ; loop_ _Residue_seq_code _Residue_label 1 ASN 2 VAL 3 LYS 4 CYS 5 PHE 6 ASN 7 CYS 8 GLY 9 LYS 10 GLU 11 GLY 12 HIS 13 THR 14 ALA 15 ARG 16 ASN 17 CYS 18 ARG 19 ALA 20 PRO 21 ARG 22 LYS 23 LYS 24 GLY 25 CYS 26 TRP 27 LYS 28 CYS 29 GLY 30 LYS 31 GLU 32 GLY 33 HIS 34 GLN 35 MET 36 LYS 37 ASP 38 CYS 39 THR 40 GLU 41 ARG 42 GLN 43 ALA 44 ASN 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 2217 "nucleocapsid protein" 88.64 39 100.00 100.00 1.09e-18 BMRB 25532 Gag 97.73 432 100.00 100.00 4.78e-22 PDB 1BJ6 "1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES" 93.18 42 100.00 100.00 3.64e-20 PDB 1ESK "Solution Structure Of Ncp7 From Hiv-1" 93.18 42 100.00 100.00 3.64e-20 PDB 1Q3Y "Nmr Structure Of The Cys28his Mutant (D Form) Of The Nucleocapsid Protein Ncp7 Of Hiv-1." 95.45 42 97.62 97.62 1.34e-19 PDB 1Q3Z "Nmr Structure Of The Cys28his Mutant (e Form) Of The Nucleocapsid Protein Ncp7 Of Hiv-1" 95.45 42 97.62 97.62 1.34e-19 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 2.36e-22 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 2.36e-22 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 2.28e-22 DBJ BAA12988 "Gag [Human immunodeficiency virus 1]" 97.73 512 97.67 97.67 3.14e-21 DBJ BAA12996 "Gag [Human immunodeficiency virus 1]" 97.73 512 100.00 100.00 7.15e-22 DBJ BAB85751 "Gag-pol fusion polyprotein [Human immunodeficiency virus 1]" 97.73 1434 97.67 97.67 2.28e-23 DBJ BAB85752 "Gag protein [Human immunodeficiency virus 1]" 97.73 499 97.67 97.67 3.63e-21 DBJ BAC02530 "gag-pol polyprotein [Human immunodeficiency virus 1]" 97.73 872 97.67 97.67 2.90e-23 EMBL CAB58976 "GAG protein [Human immunodeficiency virus 1]" 97.73 491 97.67 97.67 2.97e-21 EMBL CAB58988 "GAG protein [Human immunodeficiency virus 1]" 97.73 494 97.67 97.67 3.17e-21 EMBL CAB98186 "GAG protein [Human immunodeficiency virus 1]" 100.00 502 97.73 100.00 1.62e-22 EMBL CAP69989 "gag polyprotein [Human immunodeficiency virus 1]" 97.73 491 97.67 97.67 3.64e-21 EMBL CAP69993 "gag polyprotein [Human immunodeficiency virus 1]" 97.73 500 97.67 97.67 4.71e-21 GB AAA44201 "gag polyprotein precursor [Human immunodeficiency virus 1]" 97.73 512 100.00 100.00 7.15e-22 GB AAA45076 "gag protein, partial [Human immunodeficiency virus 1]" 97.73 495 97.67 97.67 3.32e-21 GB AAA76686 "gag [Human immunodeficiency virus 1]" 97.73 500 97.67 97.67 3.51e-21 GB AAB05598 "gag polyprotein [Human immunodeficiency virus 1]" 97.73 498 97.67 97.67 3.13e-21 GB AAB21888 "nucleocapsid protein, NCp7, NC71 [human immunodeficiency virus type 1, HIV-1, Peptide Recombinant, 71 aa]" 97.73 71 100.00 100.00 9.68e-22 PIR FOVWLV "gag polyprotein - human immunodeficiency virus type 1 (isolate LAV-1a)" 97.73 500 97.67 97.67 3.02e-21 PRF 1102247B "protein gag" 97.73 512 100.00 100.00 7.15e-22 PRF 1103299C "gag gene" 97.73 478 100.00 100.00 9.42e-22 REF NP_057849 "Gag-Pol [Human immunodeficiency virus 1]" 97.73 1435 100.00 100.00 4.24e-24 REF NP_057850 "Pr55(Gag) [Human immunodeficiency virus 1]" 97.73 500 100.00 100.00 7.17e-22 REF NP_579881 "nucleocapsid [Human immunodeficiency virus 1]" 97.73 55 100.00 100.00 8.61e-22 SP P03347 "RecName: Full=Gag polyprotein; AltName: Full=Pr55Gag; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: RecName: " 97.73 512 100.00 100.00 7.15e-22 SP P03348 "RecName: Full=Gag polyprotein; AltName: Full=Pr55Gag; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: RecName: " 97.73 512 97.67 97.67 3.14e-21 SP P03366 "RecName: Full=Gag-Pol polyprotein; AltName: Full=Pr160Gag-Pol; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: " 97.73 1447 100.00 100.00 4.47e-24 SP P03367 "RecName: Full=Gag-Pol polyprotein; AltName: Full=Pr160Gag-Pol; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: " 97.73 1447 97.67 97.67 1.89e-23 SP P04585 "RecName: Full=Gag-Pol polyprotein; AltName: Full=Pr160Gag-Pol; Contains: RecName: Full=Matrix protein p17; Short=MA; Contains: " 97.73 1435 100.00 100.00 4.24e-24 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _ICTVdb_decimal_code _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $PPBS 'Human immunodeficiency virus 1' 00.061.1.06.009.05.001. 11676 . . Lentivirus . 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 $PPBS 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'pH was adjusted with NaOH or DCl' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $PPBS 1 mM 'natural abundance' $NCp7(12-55) 1 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'pH was adjusted with NaOH or DCl' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $PPBS 1 mM 'natural abundance' $NCp7(12-55) 1 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_Felix _Saveframe_category software _Name Felix _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_EXSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D EXSY' _Sample_label $sample_1 save_ save_2D_EXSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D EXSY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 293 . K pH 6.5 . pH pressure ambient . atm stop_ save_