data_4054 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Alpha-Helical Coiled Coil Trimerization Domain of Chicken Cartilage Matrix Protein (Reduced C5-C7 Disulfide Bonds) ; _BMRB_accession_number 4054 _BMRB_flat_file_name bmr4054.str _Entry_type original _Submission_date 1997-08-07 _Accession_date 1997-08-08 _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 Wiltscheck Ronald . . 2 Kammerer Richard A. . 3 Dames Sonja A. . 4 Schulthess Therese . . 5 Blommers Marcel J.J. . 6 Engel Jurgen . . 7 Alexandrescu Andrei T. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 164 "15N chemical shifts" 40 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 1998-02-25 reformat BMRB 'converted to NMR-STAR version 2.1' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Wiltscheck, R., Kammerer, R. A., Dames, S. A., Schulthess, T., Blommers, M. J.J., Engel, J., and Alexandrescu, A. T., "Heteronuclear NMR Assignments and Secondary Structure of the Coiled Coil Trimerization Domain from Cartilage Matrix Protein in Oxidized and Reduced Forms," Protein Sci. 6, 1734-1745 (1997). ; _Citation_title ; Heteronuclear NMR Assignments and Secondary Structure of the Coiled Coil Trimerization Domain from Cartilage Matrix Protein in Oxidized and Reduced Forms. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 97406913 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wiltscheck Ronald . . 2 Kammerer Richard A. . 3 Dames Sonja A. . 4 Schulthess Therese . . 5 Blommers Marcel J.J. . 6 Engel Jurgen . . 7 Alexandrescu Andrei T. . stop_ _Journal_abbreviation 'Protein Sci.' _Journal_name_full 'Protein Science' _Journal_volume 6 _Journal_issue 8 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1734 _Page_last 1745 _Year 1997 _Details . loop_ _Keyword alpha-helix 'coiled coil' 'disulfide bonds' flexibility 'heteronuclear NMR' hydrogen-exchange 'oligomerization domain' stop_ save_ ################################## # Molecular system description # ################################## save_CMPcc _Saveframe_category molecular_system _Mol_system_name 'Cartilage Matrix Protein' _Abbreviation_common CMPcc _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'subunit A' $CMPcc_reduced 'subunit B' $CMPcc_reduced 'subunit C' $CMPcc_reduced stop_ _System_molecular_weight . _System_physical_state reduced _System_oligomer_state trimer _System_paramagnetic no _System_thiol_state . loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'subunit A' 1 'subunit B' 1 'subunit C' stop_ _Database_query_date . _Details ; This molecule is a parallel homo-trimer!! However because of 3-fold symmetry (e.g. magnetic equivalence) the chemical shifts of each of the three monomer chains are equivalent. Cartilage matrix protein is a parallel trimeric coiled coil, linked by inter-monomer disulfide bonds between Cys 5 and Cys 7. The present entry gives NMR data for the protein when the C5-C7 disulfide bonds are broken by a 10-fold excess of DTT per monomer (1 mM protein, 32 mM DTT). ; save_ ######################## # Monomeric polymers # ######################## save_CMPcc_reduced _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Coiled Coil domain of Chicken Cartilage Matrix Protein' _Abbreviation_common CMPcc _Molecular_mass 5386 _Mol_thiol_state . _Details ; Molecule corresponds to the C-terminal domain (residues 451 to 492) of chicken cartilage matrix protein. The molecule is an alpha-helical coiled coil trimer with 3-fold symmetry. Because monomers have equivalent magnetic environments, NMR spectra contain resonances corresponding to the sequence of the monomers. The Swiss-Prot index for CMP is P05099. A separate BMRB deposit has been made for the chemical shifts of the oxidized (native) form of the protein. Inter-chain-disulfide between residue 9 and 11 is broken by 10 fold excess of DTT per monomer The protein contains 4 extra residues that are a cloning artefact. The following numbering scheme has been used: G(-4), S(-3), H(-2), M(-1), E(1), E(2). While the 2nd residue in the protein is Ser, and residue 3 His, these are not found in nature. The wild type protein begins EEAP..., and the extra four residues GSHM have been numbered using negative numbers from the C- to the N-terminus. ; ############################## # Polymer residue sequence # ############################## _Residue_count 47 _Mol_residue_sequence ; GSHMEEDPCECKSIVKFQTK VEELINTLQQKLEAVAKRIE ALENKII ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -4 GLY 2 -3 SER 3 -2 HIS 4 -1 MET 5 1 GLU 6 2 GLU 7 3 ASP 8 4 PRO 9 5 CYS 10 6 GLU 11 7 CYS 12 8 LYS 13 9 SER 14 10 ILE 15 11 VAL 16 12 LYS 17 13 PHE 18 14 GLN 19 15 THR 20 16 LYS 21 17 VAL 22 18 GLU 23 19 GLU 24 20 LEU 25 21 ILE 26 22 ASN 27 23 THR 28 24 LEU 29 25 GLN 30 26 GLN 31 27 LYS 32 28 LEU 33 29 GLU 34 30 ALA 35 31 VAL 36 32 ALA 37 33 LYS 38 34 ARG 39 35 ILE 40 36 GLU 41 37 ALA 42 38 LEU 43 39 GLU 44 40 ASN 45 41 LYS 46 42 ILE 47 43 ILE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-07-14 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 BMRB 4055 "Coiled Coil domain of Chicken Cartilage Matrix Protein" 100.00 47 100.00 100.00 1.19e-23 PDB 1AQ5 "High-Resolution Solution Nmr Structure Of The Trimeric Coiled-Coil Domain Of Chicken Cartilage Matrix Protein, 20 Structures" 100.00 47 100.00 100.00 1.19e-23 EMBL CAA30915 "cartilage matrix protein [Gallus gallus]" 93.62 493 97.73 100.00 3.41e-18 GB AAA48695 "cartilage matrix protein, partial [Gallus gallus]" 93.62 416 97.73 100.00 1.54e-18 REF NP_001025546 "cartilage matrix protein precursor [Gallus gallus]" 93.62 493 97.73 100.00 3.08e-18 SP P05099 "RecName: Full=Cartilage matrix protein; AltName: Full=Matrilin-1; Flags: Precursor" 93.62 493 97.73 100.00 3.41e-18 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Organ _Tissue $CMPcc_reduced chicken 9031 Eukaryota Metazoa Gallus gallus endoskeleton 'cartilage matrix' stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name _Details $CMPcc_reduced 'recombinant technology' 'E. coli' Escherichia coli BL21(DE3) plasmid pET-15b synthetic stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_CMPcc_reduced _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $CMPcc_reduced 1 mM [U-15N] DTT 32 mM . NaCl 150 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX600 _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save__1 _Saveframe_category NMR_applied_experiment _Sample_label $sample_CMPcc_reduced save_ ####################### # Sample conditions # ####################### save_experimental_conditions_CMPcc_reduced _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.8 0.1 pH pressure 1 . atm temperature 373 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_CMPcc_reduced _Saveframe_category chemical_shift_reference _Details ; DSS in water as described in Wishart D.S., Bigam C.G., Yao J., Abildgaard F., Dyson H.J., Oldfield E., Markley J.L., Sykes B.D. 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J. Biomol. NMR 6, 135-140 (1995). ; 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 C 13 . ppm 0.000 . indirect . . . 0.251449528 DSS H 1 . ppm 0.000 . direct . . . . DSS N 15 . ppm 0.000 . indirect . . . 0.101329118 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_CMPcc_reduced _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_CMPcc_reduced stop_ _Sample_conditions_label $experimental_conditions_CMPcc_reduced _Chem_shift_reference_set_label $chem_shift_reference_CMPcc_reduced _Mol_system_component_name 'subunit A' _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 . 6 GLU HA H 4.29 . 1 2 . 7 ASP H H 8.26 . 1 3 . 7 ASP HA H 4.89 . 1 4 . 7 ASP HB2 H 2.78 . 2 5 . 7 ASP HB3 H 2.56 . 2 6 . 7 ASP N N 122.9 . 1 7 . 9 CYS H H 8.13 . 1 8 . 9 CYS HA H 4.35 . 1 9 . 9 CYS HB2 H 3.62 . 2 10 . 9 CYS N N 115.4 . 1 11 . 10 GLU H H 8.33 . 1 12 . 10 GLU HA H 4.29 . 1 13 . 10 GLU HB2 H 1.97 . 2 14 . 10 GLU HB3 H 2.11 . 2 15 . 10 GLU HG2 H 2.28 . 1 16 . 10 GLU N N 121.6 . 1 17 . 11 CYS H H 8.41 . 1 18 . 11 CYS HA H 4.40 . 1 19 . 11 CYS HB2 H 2.99 . 2 20 . 11 CYS HB3 H 3.83 . 2 21 . 11 CYS N N 118.0 . 1 22 . 12 LYS H H 8.25 . 1 23 . 12 LYS HA H 4.24 . 1 24 . 12 LYS N N 122.2 . 1 25 . 13 SER H H 8.20 . 1 26 . 13 SER HA H 4.11 . 1 27 . 13 SER HB2 H 2.99 . 2 28 . 13 SER N N 119.7 . 1 29 . 14 ILE H H 7.67 . 1 30 . 14 ILE HA H 3.80 . 1 31 . 14 ILE HB H 2.10 . 1 32 . 14 ILE N N 121.4 . 1 33 . 15 VAL H H 7.88 . 1 34 . 15 VAL HA H 4.12 . 1 35 . 15 VAL HB H 1.93 . 1 36 . 15 VAL HG1 H 1.02 . 2 37 . 15 VAL N N 121.2 . 1 38 . 16 LYS H H 8.01 . 1 39 . 16 LYS HA H 4.39 . 1 40 . 16 LYS N N 122.8 . 1 41 . 17 PHE H H 7.87 . 1 42 . 17 PHE HA H 4.17 . 1 43 . 17 PHE HB2 H 3.37 . 2 44 . 17 PHE HB3 H 3.16 . 2 45 . 17 PHE HD1 H 7.31 . 3 46 . 17 PHE N N 120.4 . 1 47 . 18 GLN H H 8.46 . 1 48 . 18 GLN HA H 3.59 . 1 49 . 18 GLN HB2 H 1.93 . 2 50 . 18 GLN N N 118.6 . 1 51 . 19 THR H H 7.95 . 1 52 . 19 THR HA H 4.01 . 1 53 . 19 THR HB H 4.22 . 1 54 . 19 THR HG2 H 1.26 . 1 55 . 19 THR N N 113.3 . 1 56 . 20 LYS H H 7.68 . 1 57 . 20 LYS HA H 4.12 . 1 58 . 20 LYS HB2 H 1.96 . 2 59 . 20 LYS N N 122.6 . 1 60 . 21 VAL H H 8.18 . 1 61 . 21 VAL HA H 3.52 . 1 62 . 21 VAL HB H 2.00 . 1 63 . 21 VAL HG1 H 0.88 . 2 64 . 21 VAL HG2 H 0.67 . 2 65 . 21 VAL N N 118.5 . 1 66 . 22 GLU H H 8.28 . 1 67 . 22 GLU HA H 3.84 . 1 68 . 22 GLU HB2 H 2.07 . 2 69 . 22 GLU N N 119.5 . 1 70 . 23 GLU H H 7.87 . 1 71 . 23 GLU HA H 4.12 . 1 72 . 23 GLU HB2 H 2.21 . 2 73 . 23 GLU HG2 H 2.46 . 1 74 . 23 GLU N N 119.4 . 1 75 . 24 LEU H H 8.13 . 1 76 . 24 LEU HA H 4.11 . 1 77 . 24 LEU HB2 H 1.44 . 2 78 . 24 LEU HD1 H 0.91 . 2 79 . 24 LEU N N 121.3 . 1 80 . 25 ILE H H 8.56 . 1 81 . 25 ILE HA H 3.62 . 1 82 . 25 ILE HB H 2.03 . 1 83 . 25 ILE HG12 H 1.05 . 2 84 . 25 ILE HD1 H 0.74 . 1 85 . 25 ILE N N 119.4 . 1 86 . 26 ASN H H 8.33 . 1 87 . 26 ASN HA H 4.50 . 1 88 . 26 ASN HB2 H 2.99 . 2 89 . 26 ASN HB3 H 2.88 . 2 90 . 26 ASN N N 119.5 . 1 91 . 27 THR H H 8.23 . 1 92 . 27 THR HA H 4.01 . 1 93 . 27 THR HB H 4.39 . 1 94 . 27 THR HG2 H 1.30 . 1 95 . 27 THR N N 116.8 . 1 96 . 28 LEU H H 8.03 . 1 97 . 28 LEU HA H 4.01 . 1 98 . 28 LEU HB2 H 2.04 . 2 99 . 28 LEU HB3 H 1.44 . 2 100 . 28 LEU HG H 1.93 . 1 101 . 28 LEU HD1 H 0.91 . 2 102 . 28 LEU N N 122.9 . 1 103 . 29 GLN H H 8.72 . 1 104 . 29 GLN HA H 3.90 . 1 105 . 29 GLN HB2 H 2.24 . 2 106 . 29 GLN HG2 H 2.50 . 2 107 . 29 GLN HG3 H 2.35 . 2 108 . 29 GLN N N 118.6 . 1 109 . 30 GLN H H 8.01 . 1 110 . 30 GLN HA H 4.11 . 1 111 . 30 GLN HB2 H 2.25 . 2 112 . 30 GLN HG2 H 2.64 . 2 113 . 30 GLN HG3 H 2.46 . 2 114 . 30 GLN N N 118.7 . 1 115 . 31 LYS H H 8.16 . 1 116 . 31 LYS HA H 4.15 . 1 117 . 31 LYS HB2 H 2.14 . 2 118 . 31 LYS HB3 H 2.03 . 2 119 . 31 LYS N N 121.1 . 1 120 . 32 LEU H H 8.55 . 1 121 . 32 LEU HA H 4.05 . 1 122 . 32 LEU HB2 H 1.93 . 2 123 . 32 LEU HB3 H 1.72 . 2 124 . 32 LEU HD1 H 0.91 . 1 125 . 32 LEU N N 121.5 . 1 126 . 33 GLU H H 8.12 . 1 127 . 33 GLU HA H 4.08 . 1 128 . 33 GLU HB2 H 2.15 . 2 129 . 33 GLU HG2 H 2.43 . 1 130 . 33 GLU HG3 H 2.32 . 2 131 . 33 GLU N N 119.8 . 1 132 . 34 ALA H H 7.71 . 1 133 . 34 ALA HA H 4.19 . 1 134 . 34 ALA HB H 1.58 . 1 135 . 34 ALA N N 121.4 . 1 136 . 35 VAL H H 8.08 . 1 137 . 35 VAL HA H 3.73 . 1 138 . 35 VAL HB H 2.32 . 1 139 . 35 VAL HG1 H 1.09 . 2 140 . 35 VAL HG2 H 0.91 . 2 141 . 35 VAL N N 118.0 . 1 142 . 36 ALA H H 8.47 . 1 143 . 36 ALA HA H 3.97 . 1 144 . 36 ALA HB H 1.54 . 1 145 . 36 ALA N N 123.5 . 1 146 . 37 LYS H H 7.90 . 1 147 . 37 LYS HA H 4.12 . 1 148 . 37 LYS HB2 H 1.97 . 2 149 . 37 LYS N N 117.7 . 1 150 . 38 ARG H H 7.65 . 1 151 . 38 ARG HA H 4.15 . 1 152 . 38 ARG HB2 H 2.04 . 2 153 . 38 ARG N N 120.4 . 1 154 . 39 ILE H H 8.11 . 1 155 . 39 ILE HA H 3.73 . 1 156 . 39 ILE HB H 1.93 . 1 157 . 39 ILE HG12 H 1.76 . 2 158 . 39 ILE HG2 H 0.91 . 1 159 . 39 ILE HD1 H 0.88 . 1 160 . 39 ILE N N 120.2 . 1 161 . 40 GLU H H 7.97 . 1 162 . 40 GLU HA H 4.11 . 1 163 . 40 GLU HB2 H 2.14 . 2 164 . 40 GLU N N 121.8 . 1 165 . 41 ALA H H 7.53 . 1 166 . 41 ALA HA H 4.18 . 1 167 . 41 ALA HB H 1.51 . 1 168 . 41 ALA N N 119.2 . 1 169 . 42 LEU H H 7.43 . 1 170 . 42 LEU HA H 4.08 . 1 171 . 42 LEU HB2 H 2.04 . 2 172 . 42 LEU HB3 H 1.47 . 2 173 . 42 LEU HD1 H 0.88 . 2 174 . 42 LEU N N 118.2 . 1 175 . 43 GLU H H 8.52 . 1 176 . 43 GLU HA H 3.87 . 1 177 . 43 GLU HB2 H 2.32 . 2 178 . 43 GLU HB3 H 1.97 . 2 179 . 43 GLU HG2 H 2.53 . 1 180 . 43 GLU HG3 H 2.25 . 2 181 . 43 GLU N N 118.6 . 1 182 . 44 ASN H H 7.63 . 1 183 . 44 ASN HA H 4.64 . 1 184 . 44 ASN HB2 H 2.85 . 2 185 . 44 ASN N N 113.8 . 1 186 . 45 LYS H H 7.56 . 1 187 . 45 LYS HA H 4.36 . 1 188 . 45 LYS HB2 H 1.93 . 2 189 . 45 LYS HG2 H 1.51 . 2 190 . 45 LYS HD2 H 1.65 . 2 191 . 45 LYS N N 118.3 . 1 192 . 46 ILE H H 7.51 . 1 193 . 46 ILE HA H 4.26 . 1 194 . 46 ILE HB H 1.93 . 1 195 . 46 ILE HG12 H 1.26 . 2 196 . 46 ILE HG2 H 0.91 . 1 197 . 46 ILE N N 118.3 . 1 198 . 47 ILE H H 7.41 . 1 199 . 47 ILE HA H 4.05 . 1 200 . 47 ILE HB H 1.86 . 1 201 . 47 ILE HG12 H 1.48 . 2 202 . 47 ILE HG13 H 1.19 . 2 203 . 47 ILE HG2 H 0.91 . 1 204 . 47 ILE N N 127.6 . 1 stop_ save_