data_5394 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Sculpting of the Eukaryotic Branch Site Recognition Motif by a Conserved Pseudouridine ; _BMRB_accession_number 5394 _BMRB_flat_file_name bmr5394.str _Entry_type original _Submission_date 2002-06-12 _Accession_date 2002-06-13 _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 Newby Meredith I. . 2 Greenbaum Nancy L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 95 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2005-11-14 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 5395 'unmodified U2 snRNA - Intron duplex' stop_ _Original_release_date 2002-06-13 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Sculpting of the Spliceosomal Branch Site Recognition Motif by a Conserved Pseudouridine ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22337323 _PubMed_ID 12426583 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Newby Meredith I. . 2 Greenbaum Nancy L. . stop_ _Journal_abbreviation 'Nat. Struct. Biol.' _Journal_volume 9 _Journal_issue 12 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 958 _Page_last 965 _Year 2002 _Details . loop_ _Keyword NMR 'U2 snRNA' 'branch site' pseudouridine stop_ save_ ################################## # Molecular system description # ################################## save_system_U2_snRNA_Intron_duplex _Saveframe_category molecular_system _Mol_system_name 'U2 snRNA - Intron duplex' _Abbreviation_common 'U2 snRNA - Intron duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'U2 snRNA strand' $U2_snRNA_Intron1 'Intron strand' $U2_snRNA_Intron2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_U2_snRNA_Intron1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'U2 snRNA - intron duplex' _Abbreviation_common 'U2 snRNA - Intron' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence ; GGUGXAGUA ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 U 4 G 5 PSU 6 A 7 G 8 U 9 A stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_U2_snRNA_Intron2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'U2 snRNA - intron duplex' _Abbreviation_common 'U2 snRNA - Intron' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 10 _Mol_residue_sequence ; UACUAACACC ; loop_ _Residue_seq_code _Residue_label 1 U 2 A 3 C 4 U 5 A 6 A 7 C 8 A 9 C 10 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_PSU _Saveframe_category polymer_residue _Mol_type 'RNA linking' _Name_common PSEUDOURIDINE-5'-MONOPHOSPHATE _BMRB_code . _PDB_code PSU _Standard_residue_derivative . _Molecular_mass 324.181 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jun 9 16:17:31 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O2 O2 O . 0 . ? O4 O4 O . 0 . ? C1' C1' C . 0 . ? C2' C2' C . 0 . ? O2' O2' O . 0 . ? C3' C3' C . 0 . ? C4' C4' C . 0 . ? O3' O3' O . 0 . ? O4' O4' O . 0 . ? C5' C5' C . 0 . ? O5' O5' O . 0 . ? P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? HN1 HN1 H . 0 . ? HN3 HN3 H . 0 . ? H6 H6 H . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? HO2' HO2' H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? HO3' HO3' H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N1 C2 ? ? SING N1 C6 ? ? SING N1 HN1 ? ? SING C2 N3 ? ? DOUB C2 O2 ? ? SING N3 C4 ? ? SING N3 HN3 ? ? SING C4 C5 ? ? DOUB C4 O4 ? ? DOUB C5 C6 ? ? SING C5 C1' ? ? SING C6 H6 ? ? SING C1' C2' ? ? SING C1' O4' ? ? SING C1' H1' ? ? SING C2' O2' ? ? SING C2' C3' ? ? SING C2' H2' ? ? SING O2' HO2' ? ? SING C3' C4' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING C4' O4' ? ? SING C4' C5' ? ? SING C4' H4' ? ? SING O3' HO3' ? ? SING C5' O5' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING O5' P ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? SING OP3 HOP3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $U2_snRNA_Intron1 "Baker's yeast" 4932 Eukaryota Fungi Saccharomyces cerevisiae 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 $U2_snRNA_Intron1 '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 $U2_snRNA_Intron1 1.0 mM . $U2_snRNA_Intron2 1.0 mM . 'sodium phosphate' 10 mM . D2O 10 % . H2O 90 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $U2_snRNA_Intron1 1.0 mM . $U2_snRNA_Intron2 1.0 mM . 'sodium phosphate' 10 mM . D2O 100 % . stop_ save_ ############################ # Computer software used # ############################ save_VNMR1 _Saveframe_category software _Name VNMR _Version 5.3 loop_ _Task collection stop_ _Details 'Varian, Inc.' save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.69 loop_ _Task 'data analysis' stop_ _Details 'T.D. Goddard and D.G. Kneller' save_ save_X_PLOR _Saveframe_category software _Name X-PLOR _Version 3.851 loop_ _Task refinement 'structure Solution' stop_ _Details Brunger save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UNITYplus _Field_strength 720 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 50 . mM pH 6.4 0.1 pH pressure 1 . atm temperature 278 0.5 K stop_ save_ save_sample_cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 50 . mM pH 6.4 0.1 pH pressure 1 . atm temperature 293 0.5 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details ; The water proton resonance was referenced to 5.08 ppm at 5 degrees (exchangeable protons) and 4.8 ppm for 20 degrees (non-exchangeable protons). ; 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 0.0 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_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D TOCSY' DQF-COSY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'U2 snRNA strand' _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 H8 H 8.08 0.01 1 2 . 1 G H1' H 5.8 0.01 1 3 . 1 G H2' H 4.64 0.01 1 4 . 2 G H1 H 13.4 0.01 1 5 . 2 G H8 H 7.47 0.01 1 6 . 2 G H1' H 5.88 0.01 1 7 . 2 G H2' H 4.46 0.01 1 8 . 2 G H3' H 4.52 0.01 1 9 . 3 U H3 H 13.85 0.01 1 10 . 3 U H6 H 7.73 0.01 1 11 . 3 U H5 H 5.1 0.01 1 12 . 3 U H1' H 5.54 0.01 1 13 . 3 U H2' H 4.44 0.01 1 14 . 3 U H3' H 4.52 0.01 1 15 . 4 G H1 H 13.58 0.01 1 16 . 4 G H8 H 7.72 0.01 1 17 . 4 G H1' H 5.8 0.01 1 18 . 4 G H2' H 4.65 0.01 1 19 . 4 G H3' H 4.45 0.01 1 20 . 5 PSU HN3 H 10.55 0.01 1 21 . 5 PSU H6 H 7.05 0.01 1 22 . 5 PSU H1' H 4.42 0.01 1 23 . 5 PSU H2' H 4.43 0.01 1 24 . 5 PSU H3' H 4.6 0.01 1 25 . 6 A H8 H 8.04 0.01 1 26 . 6 A H2 H 6.84 0.01 1 27 . 6 A H1' H 5.77 0.01 1 28 . 6 A H2' H 4.57 0.01 1 29 . 6 A H3' H 4.68 0.01 1 30 . 7 G H1 H 12.65 0.01 1 31 . 7 G H8 H 7.23 0.01 1 32 . 7 G H1' H 5.38 0.01 1 33 . 7 G H2' H 4.25 0.01 1 34 . 7 G H3' H 4.35 0.01 1 35 . 8 U H6 H 7.6 0.01 1 36 . 8 U H5 H 5.05 0.01 1 37 . 8 U H1' H 5.45 0.01 1 38 . 8 U H2' H 4.22 0.01 1 39 . 8 U H3' H 4.46 0.01 1 40 . 9 A H8 H 8.11 0.01 1 41 . 9 A H2 H 7.41 0.01 1 42 . 9 A H1' H 6.03 0.01 1 43 . 9 A H2' H 4.12 0.01 1 44 . 9 A H3' H 4.26 0.01 1 stop_ save_ save_chemical_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D TOCSY' DQF-COSY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'Intron strand' _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 U H6 H 8.09 0.01 1 2 . 1 U H5 H 5.82 0.01 1 3 . 1 U H1' H 5.58 0.01 1 4 . 1 U H2' H 4.57 0.01 1 5 . 1 U H3' H 4.31 0.01 1 6 . 2 A H8 H 8.39 0.01 1 7 . 2 A H2 H 7.43 0.01 1 8 . 2 A H1' H 6.02 0.01 1 9 . 2 A H2' H 4.64 0.01 1 10 . 2 A H3' H 4.54 0.01 1 11 . 3 C H6 H 7.59 0.01 1 12 . 3 C H5 H 5.27 0.01 1 13 . 3 C H1' H 5.38 0.01 1 14 . 3 C H2' H 4.16 0.01 1 15 . 3 C H3' H 4.37 0.01 1 16 . 4 U H3 H 13.11 0.01 1 17 . 4 U H6 H 7.78 0.01 1 18 . 4 U H5 H 5.37 0.01 1 19 . 4 U H1' H 5.69 0.01 1 20 . 4 U H2' H 4.27 0.01 1 21 . 4 U H3' H 4.60 0.01 1 22 . 5 A H8 H 8.26 0.01 1 23 . 5 A H2 H 7.64 0.01 1 24 . 5 A H1' H 6.04 0.01 1 25 . 5 A H2' H 4.56 0.01 1 26 . 5 A H3' H 4.36 0.01 1 27 . 6 A H8 H 8.23 0.01 1 28 . 6 A H2 H 7.85 0.01 1 29 . 6 A H1' H 5.91 0.01 1 30 . 6 A H2' H 4.62 0.01 1 31 . 6 A H3' H 4.37 0.01 1 32 . 7 C H6 H 7.55 0.01 1 33 . 7 C H5 H 5.09 0.01 1 34 . 7 C H1' H 5.4 0.01 1 35 . 7 C H2' H 4.36 0.01 1 36 . 7 C H3' H 4.43 0.01 1 37 . 8 A H8 H 8.1 0.01 1 38 . 8 A H2 H 7.48 0.01 1 39 . 8 A H1' H 5.92 0.01 1 40 . 8 A H2' H 4.53 0.01 1 41 . 8 A H3' H 4.33 0.01 1 42 . 9 C H6 H 7.55 0.01 1 43 . 9 C H5 H 5.16 0.01 1 44 . 9 C H1' H 5.4 0.01 1 45 . 9 C H2' H 4.11 0.01 1 46 . 9 C H3' H 4.34 0.01 1 47 . 10 C H6 H 7.64 0.01 1 48 . 10 C H5 H 5.41 0.01 1 49 . 10 C H1' H 5.66 0.01 1 50 . 10 C H2' H 3.98 0.01 1 51 . 10 C H3' H 4.12 0.01 1 stop_ save_