data_17401 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1 ; _BMRB_accession_number 17401 _BMRB_flat_file_name bmr17401.str _Entry_type original _Submission_date 2011-01-07 _Accession_date 2011-01-07 _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 Parkesh Raman . . 2 Fountain Matthew A. . 3 Disney Matthew D. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 48 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-02-04 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)(2) Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21204525 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Parkesh Raman . . 2 Fountain Matthew . . 3 Disney Matthew D. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 50 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 599 _Page_last 601 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_1' $RNA_(5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_ 'RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_2' $RNA_(5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_ 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_RNA_(5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_ _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_ _Molecular_mass 2862.776 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence CCGCUGCGG loop_ _Residue_seq_code _Residue_label 1 C 2 C 3 G 4 C 5 U 6 G 7 C 8 G 9 G 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 $RNA_(5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_ Human 9606 Eukaryota 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 $RNA_(5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_ 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_rCCGCUGCGG _Saveframe_category sample _Sample_type solution _Details 'pH 7.2, 0.1 M NaCl, and 0.05 mM EDTA' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_ 1.5 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.111 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 11 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $rCCGCUGCGG save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $rCCGCUGCGG save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $rCCGCUGCGG save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'pH 7.2, 0.1 M NaCl, and 0.05 mM EDTA' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 7.2 . pH pressure 1 . atm 'ionic strength' 0.1 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 water H 1 protons ppm 4.65 internal direct . . . 1 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_r(CCGCUGCGG) _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D DQF-COSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $rCCGCUGCGG stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_1' _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 1 C H1' H 5.438 . 1 2 1 1 C H2' H 4.461 . 1 3 1 1 C H3' H 4.493 . 1 4 1 1 C H4' H 4.338 . 1 5 1 1 C H5 H 6.009 . 1 6 1 1 C H5' H 4.055 . 2 7 1 1 C H5'' H 3.929 . 2 8 1 1 C H6 H 8.048 . 1 9 2 2 C H1' H 5.642 . 1 10 2 2 C H2' H 4.597 . 1 11 2 2 C H3' H 4.694 . 1 12 2 2 C H5 H 5.636 . 1 13 2 2 C H6 H 7.983 . 1 14 3 3 G H1' H 5.774 . 1 15 3 3 G H2' H 4.557 . 1 16 3 3 G H3' H 4.690 . 1 17 3 3 G H5'' H 4.185 . 2 18 3 3 G H8 H 7.656 . 1 19 4 4 C H1' H 5.568 . 1 20 4 4 C H2' H 4.385 . 1 21 4 4 C H3' H 4.455 . 1 22 4 4 C H5 H 5.290 . 1 23 4 4 C H6 H 7.622 . 1 24 5 5 U H1' H 5.531 . 1 25 5 5 U H2' H 4.324 . 1 26 5 5 U H3' H 4.465 . 1 27 5 5 U H5 H 5.542 . 1 28 5 5 U H5'' H 4.134 . 2 29 5 5 U H6 H 7.651 . 1 30 6 6 G H1' H 5.808 . 1 31 6 6 G H2' H 4.556 . 1 32 6 6 G H3' H 4.678 . 1 33 6 6 G H5' H 4.165 . 2 34 6 6 G H8 H 7.838 . 1 35 7 7 C H1' H 5.586 . 1 36 7 7 C H2' H 4.618 . 1 37 7 7 C H3' H 4.521 . 1 38 7 7 C H5 H 5.270 . 1 39 7 7 C H6 H 7.677 . 1 40 8 8 G H1' H 5.763 . 1 41 8 8 G H2' H 4.588 . 1 42 8 8 G H3' H 4.530 . 1 43 8 8 G H5'' H 4.141 . 2 44 8 8 G H8 H 7.499 . 1 45 9 9 G H1' H 5.862 . 1 46 9 9 G H2' H 4.086 . 1 47 9 9 G H3' H 4.255 . 1 48 9 9 G H8 H 7.364 . 1 stop_ save_