data_15500
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
Solution Structure of the EDA-ID-related C417F mutant of human NEMO zinc finger
;
_BMRB_accession_number 15500
_BMRB_flat_file_name bmr15500.str
_Entry_type new
_Submission_date 2007-09-28
_Accession_date 2007-09-28
_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 Cordier Florence . .
2 Vinolo Emilie . .
3 Veron Michel . .
4 Delepierre Muriel . .
5 Agou Fabrice . .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 1
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 159
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2008-07-03 update BMRB 'complete entry citation'
2008-03-13 original author 'original release'
stop_
loop_
_Related_BMRB_accession_number
_Relationship
15499 'wild type zinc fingers of the NEMO protein'
stop_
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title 'Solution Structure of NEMO Zinc Finger and Impact of an Anhidrotic Ectodermal Dysplasia with Immunodeficiency-related Point Mutation'
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID 18313693
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Cordier Florence . .
2 Vinolo Emilie . .
3 Veron Michel . .
4 Delepierre Muriel . .
5 Agou Fabrice . .
stop_
_Journal_abbreviation 'J. Mol. Biol.'
_Journal_volume 377
_Journal_issue 5
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 1419
_Page_last 1432
_Year 2008
_Details .
loop_
_Keyword
NF-kappaB
NEMO
'zinc finger'
EDA-ID
NMR
stop_
save_
##################################
# Molecular system description #
##################################
save_assembly
_Saveframe_category molecular_system
_Mol_system_name ZF-C417F:ZN
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
'ZINC ION' $ZN
'NEMO ZF-C417F' $NEMO_ZF-C417F
stop_
_System_molecular_weight .
_System_physical_state native
_System_oligomer_state ?
_System_paramagnetic no
_System_thiol_state .
_Database_query_date .
_Details 'zinc-bound form of NEMO ZF-C417F'
save_
########################
# Monomeric polymers #
########################
save_NEMO_ZF-C417F
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class protein
_Name_common NEMO_ZF-C417F
_Molecular_mass .
_Mol_thiol_state 'free and other bound'
loop_
_Biological_function
'NEMO is a regulatory protein of the NF-kappaB signaling pathway'
stop_
_Details 'The C417F point mutation was identified in patients with anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID)'
##############################
# Polymer residue sequence #
##############################
_Residue_count 28
_Mol_residue_sequence
;
SSDFCCPKCQYQAPDMDTLQ
IHVMEFIE
;
loop_
_Residue_seq_code
_Residue_label
1 SER 2 SER 3 ASP 4 PHE 5 CYS
6 CYS 7 PRO 8 LYS 9 CYS 10 GLN
11 TYR 12 GLN 13 ALA 14 PRO 15 ASP
16 MET 17 ASP 18 THR 19 LEU 20 GLN
21 ILE 22 HIS 23 VAL 24 MET 25 GLU
26 PHE 27 ILE 28 GLU
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date .
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
UNP Q9Y6K9 NEMO_HUMAN . . . . .
stop_
save_
#############
# Ligands #
#############
save_ZN
_Saveframe_category ligand
_Mol_type non-polymer
_Name_common "ZN (ZINC ION)"
_BMRB_code .
_PDB_code ZN
_Molecular_mass 65.409
_Mol_charge 2
_Mol_paramagnetic .
_Mol_aromatic no
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Aug 21 03:50:37 2007
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
ZN ZN ZN N 2 . ?
stop_
_Mol_thiol_state .
_Sequence_homology_query_date .
save_
########################################
# Molecular bond linkage definitions #
########################################
save_crosslink_bonds
_Saveframe_category crosslink_bonds
loop_
_Bond_order
_Bond_type
_Atom_one_mol_system_component_name
_Atom_one_residue_seq_code
_Atom_one_residue_label
_Atom_one_atom_name
_Atom_two_mol_system_component_name
_Atom_two_residue_seq_code
_Atom_two_residue_label
_Atom_two_atom_name
single coordination 'NEMO ZF-C417F' 6 CYS SG 'ZINC ION' . . ZN
single coordination 'NEMO ZF-C417F' 9 CYS SG 'ZINC ION' . . ZN
single coordination 'NEMO ZF-C417F' 22 HIS NE2 'ZINC ION' . . ZN
stop_
loop_
_Deleted_atom_mol_system_component_name
_Deleted_atom_residue_seq_code
_Deleted_atom_residue_label
_Deleted_atom_name
'ZINC ION' 6 CYS HG
'ZINC ION' 9 CYS HG
'ZINC ION' 22 HIS HE2
stop_
save_
####################
# Natural source #
####################
save_natural_source
_Saveframe_category natural_source
loop_
_Mol_label
_Organism_name_common
_NCBI_taxonomy_ID
_Superkingdom
_Kingdom
_Genus
_Species
$NEMO_ZF-C417F 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
_Details
$NEMO_ZF-C417F 'chemical synthesis' . . . . . 'synthetic peptide termini-blocked by N-acetyl and C-amide groups, purchased from a company'
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
$NEMO_ZF-C417F 1 mM 'natural abundance'
$ZN 2 mM 'natural abundance'
TCEP 2 mM 'natural abundance'
stop_
save_
############################
# Computer software used #
############################
save_VNMR
_Saveframe_category software
_Name VNMR
_Version 6.1C
loop_
_Vendor
_Address
_Electronic_address
Varian . .
stop_
loop_
_Task
collection
stop_
_Details .
save_
save_NMRPipe
_Saveframe_category software
_Name NMRPipe
_Version 2.2
loop_
_Vendor
_Address
_Electronic_address
'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . .
stop_
loop_
_Task
processing
stop_
_Details .
save_
save_NMRView
_Saveframe_category software
_Name NMRView
_Version 5.03
loop_
_Vendor
_Address
_Electronic_address
'Johnson, One Moon Scientific' . .
stop_
loop_
_Task
'data analysis'
'peak picking'
'chemical shift assignment'
stop_
_Details .
save_
save_ARIA
_Saveframe_category software
_Name ARIA
_Version 1.2
loop_
_Vendor
_Address
_Electronic_address
'Linge, O'Donoghue and Nilges' . .
stop_
loop_
_Task
'structure solution'
refinement
stop_
_Details .
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_spectrometer_1
_Saveframe_category NMR_spectrometer
_Manufacturer Varian
_Model INOVA
_Field_strength 600
_Details 'Spectrometer equipped with a cryoprobe'
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_TOCSY_2
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H TOCSY'
_Sample_label $sample_1
save_
save_2D_purged-COSY_3
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D purged-COSY'
_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 298 . K
pH 6.6 . pH
pressure 1 . atm
'ionic strength' 0 . M
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
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Experiment_label
'2D 1H-1H NOESY'
'2D 1H-1H TOCSY'
'2D purged-COSY'
stop_
loop_
_Sample_label
$sample_1
stop_
_Sample_conditions_label $sample_conditions_1
_Chem_shift_reference_set_label $chemical_shift_reference_1
_Mol_system_component_name 'NEMO ZF-C417F'
_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 SER H H 8.134 0.005 1
2 1 1 SER HA H 4.406 0.005 1
3 1 1 SER HB2 H 3.712 0.005 2
4 1 1 SER HB3 H 3.804 0.005 2
5 2 2 SER H H 8.345 0.005 1
6 2 2 SER HA H 4.321 0.005 1
7 2 2 SER HB2 H 3.658 0.005 2
8 2 2 SER HB3 H 3.772 0.005 2
9 3 3 ASP H H 7.937 0.005 1
10 3 3 ASP HA H 4.259 0.005 1
11 3 3 ASP HB2 H 1.950 0.005 2
12 3 3 ASP HB3 H 2.112 0.005 2
13 4 4 PHE H H 8.156 0.005 1
14 4 4 PHE HA H 4.641 0.005 1
15 4 4 PHE HB2 H 2.950 0.005 2
16 4 4 PHE HB3 H 2.950 0.005 2
17 4 4 PHE HD1 H 6.979 0.005 3
18 4 4 PHE HD2 H 6.979 0.005 3
19 4 4 PHE HE1 H 7.281 0.005 3
20 4 4 PHE HE2 H 7.281 0.005 3
21 5 5 CYS H H 7.819 0.005 1
22 5 5 CYS HA H 4.941 0.005 1
23 5 5 CYS HB2 H 2.688 0.005 2
24 5 5 CYS HB3 H 2.688 0.005 2
25 6 6 CYS H H 9.000 0.005 1
26 6 6 CYS HA H 4.563 0.005 1
27 6 6 CYS HB2 H 2.655 0.005 2
28 6 6 CYS HB3 H 3.228 0.005 2
29 7 7 PRO HA H 4.537 0.005 1
30 7 7 PRO HB2 H 2.137 0.005 2
31 7 7 PRO HB3 H 2.374 0.005 2
32 7 7 PRO HD2 H 4.049 0.005 2
33 7 7 PRO HD3 H 4.210 0.005 2
34 7 7 PRO HG2 H 2.021 0.005 2
35 7 7 PRO HG3 H 2.021 0.005 2
36 8 8 LYS H H 9.199 0.005 1
37 8 8 LYS HA H 4.404 0.005 1
38 8 8 LYS HB2 H 1.788 0.005 2
39 8 8 LYS HB3 H 1.788 0.005 2
40 8 8 LYS HD2 H 1.575 0.005 2
41 8 8 LYS HD3 H 1.575 0.005 2
42 8 8 LYS HE2 H 2.897 0.005 2
43 8 8 LYS HE3 H 2.897 0.005 2
44 8 8 LYS HG2 H 1.329 0.005 2
45 8 8 LYS HG3 H 1.329 0.005 2
46 9 9 CYS H H 8.029 0.005 1
47 9 9 CYS HA H 5.023 0.005 1
48 9 9 CYS HB2 H 2.260 0.005 2
49 9 9 CYS HB3 H 3.232 0.005 2
50 10 10 GLN H H 8.029 0.005 1
51 10 10 GLN HA H 4.169 0.005 1
52 10 10 GLN HB2 H 1.849 0.005 2
53 10 10 GLN HB3 H 2.013 0.005 2
54 11 11 TYR H H 8.666 0.005 1
55 11 11 TYR HA H 4.165 0.005 1
56 11 11 TYR HB2 H 1.871 0.005 2
57 11 11 TYR HB3 H 2.968 0.005 2
58 11 11 TYR HD1 H 6.302 0.005 3
59 11 11 TYR HD2 H 6.302 0.005 3
60 11 11 TYR HE1 H 6.437 0.005 3
61 11 11 TYR HE2 H 6.437 0.005 3
62 12 12 GLN H H 7.652 0.005 1
63 12 12 GLN HA H 4.338 0.005 1
64 12 12 GLN HB2 H 1.644 0.005 2
65 12 12 GLN HB3 H 1.740 0.005 2
66 12 12 GLN HG2 H 2.137 0.005 2
67 12 12 GLN HG3 H 2.198 0.005 2
68 13 13 ALA H H 8.154 0.005 1
69 13 13 ALA HA H 4.317 0.005 1
70 13 13 ALA HB H 1.442 0.005 1
71 14 14 PRO HA H 4.439 0.005 1
72 14 14 PRO HB2 H 2.086 0.005 2
73 14 14 PRO HB3 H 2.241 0.005 2
74 14 14 PRO HD2 H 3.622 0.005 2
75 14 14 PRO HD3 H 3.723 0.005 2
76 14 14 PRO HG2 H 1.957 0.005 2
77 14 14 PRO HG3 H 1.957 0.005 2
78 15 15 ASP H H 6.954 0.005 1
79 15 15 ASP HA H 3.613 0.005 1
80 15 15 ASP HB2 H 2.713 0.005 2
81 15 15 ASP HB3 H 2.713 0.005 2
82 16 16 MET H H 8.091 0.005 1
83 16 16 MET HA H 3.911 0.005 1
84 16 16 MET HB2 H 1.915 0.005 2
85 16 16 MET HB3 H 1.915 0.005 2
86 16 16 MET HG2 H 2.546 0.005 2
87 16 16 MET HG3 H 2.546 0.005 2
88 17 17 ASP H H 8.247 0.005 1
89 17 17 ASP HA H 4.254 0.005 1
90 17 17 ASP HB2 H 2.528 0.005 2
91 17 17 ASP HB3 H 2.528 0.005 2
92 18 18 THR H H 8.601 0.005 1
93 18 18 THR HA H 3.935 0.005 1
94 18 18 THR HB H 3.935 0.005 1
95 18 18 THR HG2 H 1.419 0.005 1
96 19 19 LEU H H 7.694 0.005 1
97 19 19 LEU HA H 4.168 0.005 1
98 19 19 LEU HB2 H 1.439 0.005 2
99 19 19 LEU HB3 H 2.244 0.005 2
100 19 19 LEU HD1 H 0.904 0.005 4
101 19 19 LEU HD2 H 0.968 0.005 4
102 19 19 LEU HG H 1.722 0.005 1
103 20 20 GLN H H 8.361 0.005 1
104 20 20 GLN HA H 4.057 0.005 1
105 20 20 GLN HB2 H 2.141 0.005 2
106 20 20 GLN HB3 H 2.218 0.005 2
107 20 20 GLN HG2 H 2.483 0.005 2
108 20 20 GLN HG3 H 2.483 0.005 2
109 21 21 ILE H H 7.488 0.005 1
110 21 21 ILE HA H 3.736 0.005 1
111 21 21 ILE HB H 1.933 0.005 1
112 21 21 ILE HD1 H 0.825 0.005 1
113 21 21 ILE HG12 H 1.176 0.005 4
114 21 21 ILE HG13 H 1.722 0.005 4
115 21 21 ILE HG2 H 0.905 0.005 4
116 22 22 HIS H H 7.683 0.005 1
117 22 22 HIS HA H 4.190 0.005 1
118 22 22 HIS HB2 H 3.024 0.005 2
119 22 22 HIS HB3 H 3.780 0.005 2
120 22 22 HIS HD2 H 6.993 0.005 1
121 22 22 HIS HE1 H 7.531 0.005 1
122 23 23 VAL H H 8.692 0.005 1
123 23 23 VAL HA H 3.790 0.005 1
124 23 23 VAL HB H 2.242 0.005 1
125 23 23 VAL HG1 H 1.108 0.005 4
126 23 23 VAL HG2 H 1.235 0.005 4
127 24 24 MET H H 7.739 0.005 1
128 24 24 MET HA H 4.307 0.005 1
129 24 24 MET HB2 H 2.120 0.005 2
130 24 24 MET HB3 H 2.120 0.005 2
131 24 24 MET HG2 H 2.610 0.005 2
132 24 24 MET HG3 H 2.726 0.005 2
133 25 25 GLU H H 8.209 0.005 1
134 25 25 GLU HA H 4.158 0.005 1
135 25 25 GLU HB2 H 1.854 0.005 2
136 25 25 GLU HB3 H 2.018 0.005 2
137 25 25 GLU HG2 H 2.256 0.005 2
138 25 25 GLU HG3 H 2.256 0.005 2
139 26 26 PHE H H 8.075 0.005 1
140 26 26 PHE HA H 4.379 0.005 1
141 26 26 PHE HB2 H 2.954 0.005 2
142 26 26 PHE HB3 H 2.954 0.005 2
143 26 26 PHE HD1 H 7.028 0.005 3
144 26 26 PHE HD2 H 7.028 0.005 3
145 26 26 PHE HE1 H 7.247 0.005 3
146 26 26 PHE HE2 H 7.247 0.005 3
147 27 27 ILE H H 7.687 0.005 1
148 27 27 ILE HA H 3.935 0.005 1
149 27 27 ILE HB H 1.733 0.005 1
150 27 27 ILE HD1 H 0.780 0.005 1
151 27 27 ILE HG12 H 1.069 0.005 4
152 27 27 ILE HG13 H 1.381 0.005 4
153 27 27 ILE HG2 H 0.780 0.005 4
154 28 28 GLU H H 7.859 0.005 1
155 28 28 GLU HA H 4.007 0.005 1
156 28 28 GLU HB2 H 1.846 0.005 2
157 28 28 GLU HB3 H 1.956 0.005 2
158 28 28 GLU HG2 H 2.142 0.005 2
159 28 28 GLU HG3 H 2.142 0.005 2
stop_
loop_
_Atom_shift_assign_ID_ambiguity
100
'100,100,101,101,101'
'113,114,115,115,115'
'125,125,125,126,126,126'
'151,152,153,153,153'
stop_
save_