data_4247 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H Chemical Shift Assignments of the 8mer Chimeric Hybrid Duplex r(GCAGUGGC).r(RCCA)d(CTGC) ; _BMRB_accession_number 4247 _BMRB_flat_file_name bmr4247.str _Entry_type update _Submission_date 1998-10-15 _Accession_date 1998-10-15 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; The data reported here represent the 1H chemical shifts of a 8mer chimeric hybrid RNA/RNA-DNA duplex comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Szyperski Thomas . . 2 Goette Matthias . . 3 Billeter Martin . . 4 Perola Emanuele . . 5 Celai Luciano . . 6 Heumann Hermann . . 7 Wuthrich Kurt . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 3 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 145 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update author 'update DNA residue label to two-letter code' 2000-03-03 update author 'The chemical shift tables have been extensively revised' 2000-03-03 update BMRB 'Format updated to NMR-STAR version 2.1.1' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Szyperski, T., Goette, M., Billeter, M., Perola, E., Celai, L., Heumann, H., and Wuthrich, K., "NMR Structure of the Chimeric Hybrid Duplex r(gcaguggc). r(gcca)d(CTGC) Comprising the tRNA-DNA Junction Formed During Initiation of HIV-1 Reverse Trancription." J. Biomol. NMR, 13(4), 343-355 (1999). ; _Citation_title ; NMR Structure of the Chimeric Hybrid Duplex r(gcaguggc). r(gcca)d(CTGC) Comprising the tRNA-DNA Junction Formed During Initiation of HIV-1 Reverse Trancription ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 99281462 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Szyperski Thomas . . 2 Goette Matthias . . 3 Billeter Martin . . 4 Perola Emanuele . . 5 Celai Luciano . . 6 Heumann Hermann . . 7 Wuthrich Kurt . . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of Biomolecular NMR' _Journal_volume 13 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 343 _Page_last 355 _Year 1999 _Details . loop_ _Keyword AIDS 'chimeric hybrid duplex' 'NMR spectroscopy' 'NMR structure' 'Nucleic acids' 'reverse transcription' 'sequential resonance assignment' stop_ save_ ################################## # Molecular system description # ################################## save_system_CHD _Saveframe_category molecular_system _Mol_system_name '8mer chimeric hybrid RNA/RNA-DNA duplex with tRNA-DNA junction' _Abbreviation_common CHD _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label CHDA $CHDA 'CHDB RNA' $CHDB_RNA 'CHDB DNA' $CHDB_DNA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function ; The chimeric hybrid duplex is formed during the initiation of HIV-1 reverse transcription, i.e. (-)DNA synthesis. ; stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_CHDA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common CHD_strand_A _Name_variant CHDA _Abbreviation_common CHDA _Molecular_mass . _Mol_thiol_state . _Details 'plus strand, 8mer' ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence GCAGUGGC loop_ _Residue_seq_code _Residue_label 1 G 2 C 3 A 4 G 5 U 6 G 7 G 8 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_CHDB_RNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common CHD_strand_B_RNA _Abbreviation_common CHDB_RNA _Molecular_mass . _Mol_thiol_state . _Details ; First 4 (RNA) residues of RNA/DNA hybrid 8mer minus strand Complete strand: r(GCCA)d(CTGC) ; _Residue_count 4 _Mol_residue_sequence GCCA loop_ _Residue_seq_code _Residue_label 1 G 2 C 3 C 4 A stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_CHDB_DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common CHD_strand_B_DNA _Abbreviation_common CHDB_DNA _Molecular_mass . _Mol_thiol_state . _Details ; Last 4 (DNA) residues of RNA/DNA hybrid 8mer minus strand Complete strand: r(GCCA)d(CTGC) ; _Residue_count 4 _Mol_residue_sequence CTGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 5 DC 2 6 DT 3 7 DG 4 8 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $CHDA human 9606 Eucaryota Metazoa Homo sapiens 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 $CHDA 'Chemical synthesis' . . . . . $CHDB_RNA 'Chemical synthesis' . . . . . $CHDB_DNA 'Chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $system_CHD 1.5 mM . KPO4 20 mM . NaCL 100 mM . D2O 10 % . H2O 90 % . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 500 _Details . save_ save_NMR_spectrometer_two _Saveframe_category NMR_spectrometer _Manufacturer BRUKER _Model AMX _Field_strength 600 _Details . save_ save_NMR_spectrometer_three _Saveframe_category NMR_spectrometer _Manufacturer VARIAN _Model UNITY_PLUS _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save__1 _Saveframe_category NMR_applied_experiment _Sample_label $sample_one save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 . pH temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . $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_one _Saveframe_category assigned_chemical_shifts _Details ; RNA-DNA chimeric hybrid duplex, sequence number (5') 1-8 (3'): RNA plus strand r(GCAGUGGC) ; loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name CHDA _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 G H5' H 3.84 . 2 2 . 1 G H5'' H 3.94 . 2 3 . 1 G H4' H 4.23 . 1 4 . 1 G H3' H 4.47 . 1 5 . 1 G H2' H 4.69 . 1 6 . 1 G H1' H 5.59 . 1 7 . 1 G H8 H 7.91 . 1 8 . 2 C H5' H 4.14 . 2 9 . 2 C H5'' H 4.51 . 2 10 . 2 C H4' H 4.45 . 1 11 . 2 C H3' H 4.57 . 1 12 . 2 C H2' H 4.63 . 1 13 . 2 C H1' H 5.52 . 1 14 . 2 C H41 H 8.43 . 2 15 . 2 C H42 H 6.70 . 2 16 . 2 C H5 H 5.25 . 1 17 . 2 C H6 H 7.78 . 1 18 . 3 A H5' H 4.17 . 2 19 . 3 A H5'' H 4.56 . 2 20 . 3 A H4' H 4.51 . 1 21 . 3 A H3' H 4.69 . 1 22 . 3 A H2' H 4.79 . 1 23 . 3 A H1' H 5.96 . 1 24 . 3 A H2 H 7.25 . 1 25 . 3 A H8 H 8.02 . 1 26 . 4 G H5' H 4.05 . 2 27 . 4 G H5'' H 4.42 . 2 28 . 4 G H4' H 4.47 . 1 29 . 4 G H3' H 4.33 . 1 30 . 4 G H2' H 4.32 . 1 31 . 4 G H1' H 5.47 . 1 32 . 4 G H1 H 13.27 . 1 33 . 4 G H8 H 7.12 . 1 34 . 5 U H5' H 4.07 . 2 35 . 5 U H5'' H 4.55 . 2 36 . 5 U H4' H 4.42 . 1 37 . 5 U H3' H 4.56 . 1 38 . 5 U H2' H 4.59 . 1 39 . 5 U H1' H 5.55 . 1 40 . 5 U H3 H 13.63 . 1 41 . 5 U H5 H 5.00 . 1 42 . 5 U H6 H 7.70 . 1 43 . 6 G H5' H 4.14 . 2 44 . 6 G H5'' H 4.48 . 2 45 . 6 G H4' H 4.51 . 1 46 . 6 G H3' H 4.59 . 1 47 . 6 G H2' H 4.61 . 1 48 . 6 G H1' H 5.81 . 1 49 . 6 G H1 H 12.12 . 1 50 . 6 G H8 H 7.66 . 1 51 . 7 G H5' H 4.06 . 2 52 . 7 G H5'' H 4.48 . 2 53 . 7 G H4' H 4.47 . 1 54 . 7 G H3' H 4.40 . 1 55 . 7 G H2' H 4.41 . 1 56 . 7 G H1' H 5.68 . 1 57 . 7 G H1 H 13.34 . 1 58 . 7 G H8 H 7.27 . 1 59 . 8 C H5' H 4.22 . 2 60 . 8 C H4' H 4.16 . 1 61 . 8 C H3' H 4.06 . 1 62 . 8 C H2' H 3.99 . 1 63 . 8 C H1' H 5.66 . 1 64 . 8 C H41 H 8.26 . 2 65 . 8 C H42 H 6.87 . 2 66 . 8 C H5 H 5.21 . 1 67 . 8 C H6 H 7.44 . 1 stop_ save_ save_chemical_shift_assignment_two _Saveframe_category assigned_chemical_shifts _Details ; RNA portion of minus strand of RNA-DNA chimeric hybrid duplex, sequence number (5') 1-4 (3'): Complete strand: r(GCCA)d(CTGC) ; loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name 'CHDB RNA' _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 G H5' H 3.83 . 2 2 . 1 G H5'' H 3.94 . 2 3 . 1 G H4' H 4.23 . 1 4 . 1 G H3' H 4.47 . 1 5 . 1 G H2' H 4.65 . 1 6 . 1 G H1' H 5.60 . 1 7 . 1 G H8 H 7.91 . 1 8 . 2 C H5' H 4.12 . 2 9 . 2 C H5'' H 4.58 . 2 10 . 2 C H4' H 4.46 . 1 11 . 2 C H3' H 4.54 . 1 12 . 2 C H2' H 4.46 . 1 13 . 2 C H1' H 5.62 . 1 14 . 2 C H41 H 8.69 . 2 15 . 2 C H42 H 6.76 . 2 16 . 2 C H5 H 5.22 . 1 17 . 2 C H6 H 7.89 . 1 18 . 3 C H5' H 4.49 . 2 19 . 3 C H5'' H 4.59 . 2 20 . 3 C H4' H 4.44 . 1 21 . 3 C H3' H 4.59 . 1 22 . 3 C H2' H 4.50 . 1 23 . 3 C H1' H 5.48 . 1 24 . 3 C H41 H 8.41 . 2 25 . 3 C H42 H 6.87 . 2 26 . 3 C H5 H 5.57 . 1 27 . 3 C H6 H 7.79 . 1 28 . 4 A H5' H 4.03 . 2 29 . 4 A H5'' H 4.14 . 2 30 . 4 A H4' H 4.48 . 1 31 . 4 A H3' H 4.68 . 1 32 . 4 A H2' H 4.60 . 1 33 . 4 A H1' H 5.94 . 1 34 . 4 A H2 H 7.38 . 1 35 . 4 A H8 H 8.08 . 1 stop_ save_ save_chemical_shift_assignment_three _Saveframe_category assigned_chemical_shifts _Details ; DNA portion of RNA-DNA chimeric hybrid duplex minus strand, author sequence number (5') 5-8 (3') Complete strand: r(GCCA)d(CTGC) ; loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name 'CHDB DNA' _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 DC H5' H 4.05 . 2 2 . 1 DC H5'' H 4.39 . 2 3 . 1 DC H4' H 4.18 . 1 4 . 1 DC H3' H 4.44 . 1 5 . 1 DC H2' H 2.26 . 2 6 . 1 DC H2'' H 2.52 . 2 7 . 1 DC H1' H 5.60 . 1 8 . 1 DC H41 H 8.27 . 2 9 . 1 DC H42 H 6.95 . 2 10 . 1 DC H5 H 5.26 . 1 11 . 1 DC H6 H 7.31 . 1 12 . 2 DT H5' H 4.11 . 2 13 . 2 DT H5'' H 4.14 . 2 14 . 2 DT H4' H 4.25 . 1 15 . 2 DT H3' H 4.87 . 1 16 . 2 DT H2' H 2.43 . 1 17 . 2 DT H2'' H 2.66 . 1 18 . 2 DT H1' H 6.05 . 1 19 . 2 DT H3 H 13.47 . 1 20 . 2 DT H6 H 7.69 . 1 21 . 2 DT H71 H 1.44 . 3 22 . 2 DT H72 H 1.44 . 3 23 . 2 DT H73 H 1.44 . 3 24 . 3 DG H5' H 4.16 . 2 25 . 3 DG H5'' H 4.20 . 2 26 . 3 DG H4' H 4.38 . 1 27 . 3 DG H3' H 4.90 . 1 28 . 3 DG H2' H 2.51 . 1 29 . 3 DG H2'' H 2.69 . 1 30 . 3 DG H1' H 6.03 . 1 31 . 3 DG H1 H 12.24 . 1 32 . 3 DG H8 H 7.74 . 1 33 . 4 DC H5' H 4.10 . 2 34 . 4 DC H5'' H 4.26 . 2 35 . 4 DC H4' H 4.08 . 1 36 . 4 DC H3' H 4.47 . 1 37 . 4 DC H2' H 2.09 . 2 38 . 4 DC H2'' H 2.24 . 2 39 . 4 DC H1' H 6.16 . 1 40 . 4 DC H41 H 8.21 . 2 41 . 4 DC H42 H 6.59 . 2 42 . 4 DC H5 H 5.15 . 1 43 . 4 DC H6 H 7.36 . 1 stop_ save_