data_11489
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
RNA aptamer against prion protein in complex with the partial binding peptide
;
_BMRB_accession_number 11489
_BMRB_flat_file_name bmr11489.str
_Entry_type original
_Submission_date 2012-03-08
_Accession_date 2012-03-11
_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 Mashima Tsukasa . .
2 Nishikawa Fumiko . .
3 Kamatari Yuji O .
4 Fujiwara Hiromichi . .
5 Nishikawa Satoshi . .
6 Kuwata Kazuo . .
7 Katahira Masato . .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 2
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 153
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2013-02-11 original author .
stop_
_Original_release_date 2013-02-11
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title 'Anti-prion activity of an RNA aptamer and its structural basis'
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID 23180780
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Mashima Tsukasa . .
2 Nishikawa Fumiko . .
3 Kamatari Yuji O .
4 Fujiwara Hiromichi . .
5 Saimura Masayuki . .
6 Nagata Takashi . .
7 Kodaki Tsutomu . .
8 Nishikawa Satoshi . .
9 Kuwata Kazuo . .
10 Katahira Masato . .
stop_
_Journal_abbreviation 'Nucleic Acids Res.'
_Journal_volume 41
_Journal_issue 2
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 1355
_Page_last 1362
_Year 2013
_Details .
save_
##################################
# Molecular system description #
##################################
save_assembly
_Saveframe_category molecular_system
_Mol_system_name 'RNA aptamer against prion protein'
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
'RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')_1' $RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')
'RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')_2' $RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')
entity_2_1 $P16
entity_2_2 $P16
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(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class RNA
_Name_common RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')
_Molecular_mass 4033.540
_Mol_thiol_state 'not present'
_Details .
##############################
# Polymer residue sequence #
##############################
_Residue_count 12
_Mol_residue_sequence GGAGGAGGAGGA
loop_
_Residue_seq_code
_Residue_label
1 G 2 G 3 A 4 G 5 G
6 A 7 G 8 G 9 A 10 G
11 G 12 A
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date .
save_
save_P16
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class protein
_Name_common P16
_Molecular_mass 1387.577
_Mol_thiol_state 'not present'
_Details .
_Residue_count 12
_Mol_residue_sequence GQWNKPSKPKTN
loop_
_Residue_seq_code
_Residue_author_seq_code
_Residue_label
1 25 GLY 2 26 GLN 3 27 TRP 4 28 ASN 5 29 LYS
6 30 PRO 7 31 SER 8 32 LYS 9 33 PRO 10 34 LYS
11 35 THR 12 36 ASN
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(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') . . . . . .
$P16 cow 9913 Eukaryota Metazoa . .
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(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') 'chemical synthesis' . . . . .
$P16 '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
$RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') 1 mM 'natural abundance'
$P16 1 mM 'natural abundance'
'potassium phosphate' 10 mM 'natural abundance'
'potassium chloride' 10 mM 'natural abundance'
DSS 0.01 mM 'natural abundance'
'sodium azide' 3 mM 'natural abundance'
H2O 95 % .
D2O 5 % .
stop_
save_
save_sample_2
_Saveframe_category sample
_Sample_type solution
_Details .
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
$RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') 1 mM 'natural abundance'
$P16 1 mM 'natural abundance'
'potassium phosphate' 10 mM 'natural abundance'
'potassium chloride' 10 mM 'natural abundance'
DSS 0.01 mM 'natural abundance'
'sodium azide' 3 mM 'natural abundance'
D2O 100 % .
stop_
save_
############################
# Computer software used #
############################
save_X-PLOR_NIH
_Saveframe_category software
_Name X-PLOR_NIH
_Version 2.26
loop_
_Vendor
_Address
_Electronic_address
'Schwieters, Kuszewski, Tjandra and Clore' . .
stop_
loop_
_Task
refinement
stop_
_Details .
save_
save_xwinnmr
_Saveframe_category software
_Name xwinnmr
_Version .
loop_
_Vendor
_Address
_Electronic_address
'Bruker Biospin' . .
stop_
loop_
_Task
collection
stop_
_Details .
save_
save_TOPSPIN
_Saveframe_category software
_Name TOPSPIN
_Version .
loop_
_Vendor
_Address
_Electronic_address
'Bruker Biospin' . .
stop_
loop_
_Task
collection
stop_
_Details .
save_
save_SPARKY
_Saveframe_category software
_Name SPARKY
_Version .
loop_
_Vendor
_Address
_Electronic_address
Goddard . .
stop_
loop_
_Task
'chemical shift assignment'
'peak picking'
stop_
_Details .
save_
save_NMRPipe
_Saveframe_category software
_Name NMRPipe
_Version .
loop_
_Vendor
_Address
_Electronic_address
'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . .
stop_
loop_
_Task
processing
stop_
_Details .
save_
save_TALOS
_Saveframe_category software
_Name TALOS
_Version .
loop_
_Vendor
_Address
_Electronic_address
'Cornilescu, Delaglio and Bax' . .
stop_
loop_
_Task
'data analysis'
stop_
_Details .
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_spectrometer_1
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model DRX
_Field_strength 600
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_2D_1H-1H_NOESY_1
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H NOESY'
_Sample_label $sample_1
save_
save_2D_1H-1H_NOESY_2
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H NOESY'
_Sample_label $sample_1
save_
save_2D_1H-1H_NOESY_3
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H NOESY'
_Sample_label $sample_2
save_
save_2D_1H-1H_NOESY_4
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H NOESY'
_Sample_label $sample_2
save_
save_2D_1H-1H_TOCSY_5
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H TOCSY'
_Sample_label $sample_1
save_
save_2D_1H-1H_TOCSY_6
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H TOCSY'
_Sample_label $sample_2
save_
save_2D_DQF-COSY_7
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D DQF-COSY'
_Sample_label $sample_1
save_
save_2D_DQF-COSY_8
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D DQF-COSY'
_Sample_label $sample_2
save_
save_2D_1H-13C_HSQC_9
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-13C HSQC'
_Sample_label $sample_2
save_
save_JRHMBC_10
_Saveframe_category NMR_applied_experiment
_Experiment_name JRHMBC
_Sample_label $sample_1
save_
#######################
# Sample conditions #
#######################
save_sample_conditions_1
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
temperature 278 . K
pH 6.2 . pH
pressure 1 . atm
'ionic strength' 20 . mM
stop_
save_
save_sample_conditions_2
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
temperature 303 . K
pH 6.2 . pH
pressure 1 . atm
'ionic strength' 20 . mM
stop_
save_
####################
# NMR parameters #
####################
##############################
# Assigned chemical shifts #
##############################
################################
# Chemical shift referencing #
################################
save_chemical_shift_reference_1
_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
DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000
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_assigned_chem_shift_list_1_1
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Experiment_label
'2D 1H-1H NOESY'
stop_
loop_
_Sample_label
$sample_2
stop_
_Sample_conditions_label $sample_conditions_2
_Chem_shift_reference_set_label $chemical_shift_reference_1
_Mol_system_component_name 'RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-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 G H1' H 5.556 0.03 1
2 1 1 G H2' H 4.944 0.03 1
3 1 1 G H3' H 4.96 0.03 1
4 1 1 G H4' H 4.727 0.03 1
5 1 1 G H5' H 4.211 0.03 2
6 1 1 G H5'' H 4.273 0.03 2
7 1 1 G H8 H 7.418 0.03 1
8 2 2 G H1' H 5.447 0.03 1
9 2 2 G H2' H 4.292 0.03 1
10 2 2 G H3' H 4.559 0.03 1
11 2 2 G H4' H 3.137 0.03 1
12 2 2 G H5' H 3.097 0.03 2
13 2 2 G H5'' H 3.752 0.03 2
14 2 2 G H8 H 7.848 0.03 1
15 3 3 A H1' H 5.707 0.03 1
16 3 3 A H2 H 8.509 0.03 1
17 3 3 A H2' H 4.435 0.03 1
18 3 3 A H3' H 5.111 0.03 1
19 3 3 A H4' H 4.493 0.03 1
20 3 3 A H5' H 3.878 0.03 2
21 3 3 A H5'' H 4.287 0.03 2
22 3 3 A H8 H 7.78 0.03 1
23 4 4 G H1' H 5.78 0.03 1
24 4 4 G H2' H 5.534 0.03 1
25 4 4 G H4' H 4.787 0.03 1
26 4 4 G H5' H 4.568 0.03 2
27 4 4 G H5'' H 4.61 0.03 2
28 4 4 G H8 H 7.721 0.03 1
29 5 5 G H1' H 6.276 0.03 1
30 5 5 G H2' H 4.966 0.03 1
31 5 5 G H3' H 4.825 0.03 1
32 5 5 G H4' H 4.825 0.03 1
33 5 5 G H5' H 4.227 0.03 2
34 5 5 G H5'' H 4.647 0.03 2
35 5 5 G H8 H 8.083 0.03 1
36 6 6 A H1' H 6.334 0.03 1
37 6 6 A H2 H 9.041 0.03 1
38 6 6 A H2' H 5.895 0.03 1
39 6 6 A H3' H 5.302 0.03 1
40 6 6 A H4' H 4.855 0.03 1
41 6 6 A H5' H 4.685 0.03 1
42 6 6 A H5'' H 4.685 0.03 1
43 6 6 A H8 H 8.384 0.03 1
44 7 7 G H1' H 5.609 0.03 1
45 7 7 G H2' H 5.168 0.03 1
46 7 7 G H3' H 5.081 0.03 1
47 7 7 G H4' H 5.012 0.03 1
48 7 7 G H5' H 4.349 0.03 2
49 7 7 G H5'' H 4.513 0.03 2
50 7 7 G H8 H 8.17 0.03 1
51 8 8 G H1' H 5.41 0.03 1
52 8 8 G H2' H 4.305 0.03 1
53 8 8 G H3' H 4.499 0.03 1
54 8 8 G H4' H 3.108 0.03 1
55 8 8 G H5' H 2.888 0.03 2
56 8 8 G H5'' H 3.716 0.03 2
57 8 8 G H8 H 7.902 0.03 1
58 9 9 A H1' H 5.714 0.03 1
59 9 9 A H2 H 8.492 0.03 1
60 9 9 A H2' H 4.342 0.03 1
61 9 9 A H3' H 5.228 0.03 1
62 9 9 A H4' H 4.46 0.03 1
63 9 9 A H5' H 3.77 0.03 2
64 9 9 A H5'' H 4.293 0.03 2
65 9 9 A H8 H 7.875 0.03 1
66 10 10 G H1' H 5.864 0.03 1
67 10 10 G H2' H 4.612 0.03 1
68 10 10 G H3' H 4.654 0.03 1
69 10 10 G H4' H 4.739 0.03 1
70 10 10 G H8 H 7.792 0.03 1
71 11 11 G H1' H 5.423 0.03 1
72 11 11 G H2' H 4.556 0.03 1
73 11 11 G H3' H 4.905 0.03 1
74 11 11 G H4' H 4.825 0.03 1
75 11 11 G H5' H 4.316 0.03 2
76 11 11 G H5'' H 4.705 0.03 2
77 11 11 G H8 H 7.992 0.03 1
78 12 12 A H1' H 5.958 0.03 1
79 12 12 A H2 H 7.831 0.03 1
80 12 12 A H2' H 4.436 0.03 1
81 12 12 A H3' H 4.403 0.03 1
82 12 12 A H4' H 4.409 0.03 1
83 12 12 A H5' H 4.279 0.03 2
84 12 12 A H5'' H 4.411 0.03 2
85 12 12 A H8 H 8.114 0.03 1
stop_
save_
save_assigned_chem_shift_list_1_3
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Experiment_label
'2D 1H-1H NOESY'
stop_
loop_
_Sample_label
$sample_2
stop_
_Sample_conditions_label $sample_conditions_2
_Chem_shift_reference_set_label $chemical_shift_reference_1
_Mol_system_component_name entity_2_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 25 1 GLY HA2 H 3.673 0.03 2
2 25 1 GLY HA3 H 3.621 0.03 2
3 26 2 GLN HA H 3.919 0.03 1
4 26 2 GLN HB2 H 1.627 0.03 1
5 26 2 GLN HB3 H 1.627 0.03 1
6 26 2 GLN HG2 H 1.905 0.03 1
7 26 2 GLN HG3 H 1.905 0.03 1
8 27 3 TRP HA H 4.129 0.03 1
9 27 3 TRP HB2 H 2.793 0.03 2
10 27 3 TRP HB3 H 2.652 0.03 2
11 27 3 TRP HD1 H 6.519 0.03 1
12 27 3 TRP HE3 H 6.978 0.03 1
13 27 3 TRP HZ2 H 6.848 0.03 1
14 27 3 TRP HZ3 H 6.459 0.03 1
15 27 3 TRP HH2 H 6.581 0.03 1
16 28 4 ASN HA H 4.151 0.03 1
17 28 4 ASN HB2 H 2.209 0.03 2
18 28 4 ASN HB3 H 2.164 0.03 2
19 29 5 LYS HA H 3.934 0.03 1
20 29 5 LYS HB2 H 1.428 0.03 2
21 29 5 LYS HB3 H 1.294 0.03 2
22 29 5 LYS HG2 H 1.066 0.03 1
23 29 5 LYS HG3 H 1.066 0.03 1
24 29 5 LYS HD2 H 1.405 0.03 1
25 29 5 LYS HD3 H 1.405 0.03 1
26 29 5 LYS HE2 H 2.752 0.03 1
27 29 5 LYS HE3 H 2.752 0.03 1
28 30 6 PRO HA H 4.197 0.03 1
29 30 6 PRO HB2 H 2.072 0.03 2
30 30 6 PRO HB3 H 1.704 0.03 2
31 30 6 PRO HG2 H 1.713 0.03 1
32 30 6 PRO HG3 H 1.713 0.03 1
33 30 6 PRO HD2 H 3.424 0.03 2
34 30 6 PRO HD3 H 3.264 0.03 2
35 31 7 SER HA H 4.302 0.03 1
36 31 7 SER HB2 H 3.729 0.03 1
37 31 7 SER HB3 H 3.729 0.03 1
38 32 8 LYS HA H 4.555 0.03 1
39 32 8 LYS HB2 H 1.762 0.03 2
40 32 8 LYS HB3 H 1.661 0.03 2
41 32 8 LYS HG2 H 1.399 0.03 1
42 32 8 LYS HG3 H 1.399 0.03 1
43 32 8 LYS HD2 H 1.65 0.03 1
44 32 8 LYS HD3 H 1.65 0.03 1
45 32 8 LYS HE2 H 2.954 0.03 1
46 32 8 LYS HE3 H 2.954 0.03 1
47 33 9 PRO HA H 4.36 0.03 1
48 33 9 PRO HB2 H 2.253 0.03 2
49 33 9 PRO HB3 H 1.849 0.03 2
50 33 9 PRO HG2 H 1.984 0.03 2
51 33 9 PRO HG3 H 1.948 0.03 2
52 33 9 PRO HD2 H 3.762 0.03 2
53 33 9 PRO HD3 H 3.575 0.03 2
54 34 10 LYS HA H 4.361 0.03 1
55 34 10 LYS HB2 H 1.86 0.03 2
56 34 10 LYS HB3 H 1.759 0.03 2
57 34 10 LYS HG2 H 1.48 0.03 2
58 34 10 LYS HG3 H 1.432 0.03 2
59 34 10 LYS HD2 H 1.673 0.03 1
60 34 10 LYS HD3 H 1.673 0.03 1
61 34 10 LYS HE2 H 2.996 0.03 1
62 34 10 LYS HE3 H 2.996 0.03 1
63 35 11 THR HA H 4.354 0.03 1
64 35 11 THR HB H 4.255 0.03 1
65 35 11 THR HG2 H 1.169 0.03 1
66 36 12 ASN HA H 4.47 0.03 1
67 36 12 ASN HB2 H 2.757 0.03 2
68 36 12 ASN HB3 H 2.686 0.03 2
stop_
save_