data_4591 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the syndecan-4 whole cytoplasmic domain ; _BMRB_accession_number 4591 _BMRB_flat_file_name bmr4591.str _Entry_type original _Submission_date 2000-05-05 _Accession_date 2000-09-07 _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 Lee D. . . 2 Oh E. S. . 3 Woods A. . . 4 Couchman J. R. . 5 Lee W. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 181 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2001-03-06 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 4592 'complex state with PIP2' stop_ _Original_release_date 2001-03-06 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Structure of a Syndecan-4 Cytoplasmic Domain and Its Interaction with Phosphatidylinositol 4,5-Bisphosphate ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 98250752 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lee D. . . 2 Oh E. S. . 3 Woods A. . . 4 Couchman J. R. . 5 Lee W. . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'Journal of Biological Chemistry' _Journal_volume 273 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 13022 _Page_last 13029 _Year 1998 _Details . loop_ _Keyword 'symmetric-parallel-interwinded dimer' stop_ save_ ################################## # Molecular system description # ################################## save_system_Syndecan4 _Saveframe_category molecular_system _Mol_system_name 'syndecan-4 whole cytoplasmic domain' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Syndecan 4 monomer 1' $Syndecan4 'Syndecan 4 monomer 2' $Syndecan4 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state dimer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'Syndecan 4 monomer 1' 1 'Syndecan 4 monomer 2' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Syndecan4 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Syndecan 4' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; RMKKKDEGSYDLGKKPIYKK APTNEFYA ; loop_ _Residue_seq_code _Residue_label 1 ARG 2 MET 3 LYS 4 LYS 5 LYS 6 ASP 7 GLU 8 GLY 9 SER 10 TYR 11 ASP 12 LEU 13 GLY 14 LYS 15 LYS 16 PRO 17 ILE 18 TYR 19 LYS 20 LYS 21 ALA 22 PRO 23 THR 24 ASN 25 GLU 26 PHE 27 TYR 28 ALA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-09-01 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 4592 "Syndecan 4" 100.00 28 100.00 100.00 7.67e-10 PDB 1EJP "Solution Structure Of The Syndecan-4 Whole Cytoplasmic Domain" 100.00 28 100.00 100.00 7.67e-10 PDB 1EJQ "Solution Structure Of The Syndecan-4 Whole Cytoplasmic Domain In The Presence Of Phosphatidylinositol 4,5- Bisphosphate" 100.00 28 100.00 100.00 7.67e-10 PDB 1YBO "Crystal Structure Of The Pdz Tandem Of Human Syntenin With Syndecan Peptide" 60.71 17 100.00 100.00 7.71e-02 DBJ BAA02550 "ryudocan core protein precursor [Homo sapiens]" 100.00 198 100.00 100.00 6.57e-10 DBJ BAA19613 "ryudocan core protein [Homo sapiens]" 100.00 198 100.00 100.00 6.57e-10 DBJ BAA22135 "ryudocan core protein [Mus musculus]" 100.00 198 100.00 100.00 9.97e-10 DBJ BAA22136 "ryudocan core protein [Mus musculus]" 100.00 198 100.00 100.00 9.97e-10 DBJ BAD96415 "syndecan 4 precursor variant [Homo sapiens]" 100.00 198 100.00 100.00 4.56e-10 EMBL CAA47406 "amphiglycan [Homo sapiens]" 100.00 198 100.00 100.00 4.56e-10 EMBL CAG46842 "SDC4 [Homo sapiens]" 100.00 198 100.00 100.00 6.57e-10 EMBL CAG46871 "SDC4 [Homo sapiens]" 100.00 198 100.00 100.00 6.57e-10 EMBL CAH91121 "hypothetical protein [Pongo abelii]" 100.00 198 100.00 100.00 6.51e-10 GB AAA16479 "heparan sulfate proteoglycan [Gallus gallus]" 100.00 197 100.00 100.00 7.67e-10 GB AAA73167 "'anticoagulant active and inactive heparan sulfate proteoglycan coreprotein' [Rattus norvegicus]" 100.00 202 100.00 100.00 6.31e-10 GB AAB26725 "ryudocan [Rattus sp.]" 100.00 202 100.00 100.00 6.31e-10 GB AAH02312 "Sdc4 protein [Mus musculus]" 100.00 64 100.00 100.00 2.55e-10 GB AAH05679 "Syndecan 4 [Mus musculus]" 100.00 198 100.00 100.00 9.97e-10 REF NP_001007870 "syndecan-4 precursor [Gallus gallus]" 100.00 197 100.00 100.00 7.67e-10 REF NP_001127378 "syndecan-4 precursor [Pongo abelii]" 100.00 198 100.00 100.00 6.51e-10 REF NP_001162499 "syndecan-4 precursor [Papio anubis]" 100.00 198 100.00 100.00 5.45e-10 REF NP_001244363 "syndecan-4 precursor [Macaca mulatta]" 100.00 198 100.00 100.00 5.78e-10 REF NP_001269761 "syndecan-4 [Columba livia]" 100.00 195 100.00 100.00 8.56e-10 SP O35988 "RecName: Full=Syndecan-4; Short=SYND4; AltName: Full=Ryudocan core protein; Flags: Precursor" 100.00 198 100.00 100.00 9.97e-10 SP P31431 "RecName: Full=Syndecan-4; Short=SYND4; AltName: Full=Amphiglycan; AltName: Full=Ryudocan core protein; Flags: Precursor" 100.00 198 100.00 100.00 6.57e-10 SP P34901 "RecName: Full=Syndecan-4; Short=SYND4; AltName: Full=Ryudocan core protein; Flags: Precursor" 100.00 202 100.00 100.00 6.31e-10 SP P49416 "RecName: Full=Syndecan-4; Flags: Precursor" 100.00 197 100.00 100.00 7.67e-10 SP Q5RAT9 "RecName: Full=Syndecan-4; Short=SYND4; Flags: Precursor" 100.00 198 100.00 100.00 6.51e-10 TPG DAA22957 "TPA: syndecan 4-like [Bos taurus]" 100.00 199 100.00 100.00 6.74e-10 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Syndecan4 . . . . . . 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 $Syndecan4 . . . . . . 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $Syndecan4 . mM 2 4 . 'phosphate buffer' 50 mM . . . H2O 90 % . . . D2O 10 % . . . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $Syndecan4 . mM 2 4 . 'phosphate buffer' 50 mM . . . D2O 100 % . . . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 2.5 loop_ _Task 'data collection' 'data processing' stop_ _Details Bruker save_ save_Sparky _Saveframe_category software _Name Sparky _Version 3.6 loop_ _Task 'data analysis' stop_ _Details 'James, T.' save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 3.851 loop_ _Task refinement stop_ _Details 'Brunger, A.T' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_DQF_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'DQF COSY' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'DQF COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.4 . n/a temperature 298 . K 'ionic strength' 50 . mM pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_ref_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_citation_label _Correction_value_citation_label . H 1 . ppm . . . . . . $entry_citation $entry_citation 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_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_ref_1 _Mol_system_component_name 'Syndecan 4 monomer 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 ARG H H 8.27 . . 2 . 1 ARG HA H 4.23 . . 3 . 1 ARG HB2 H 1.74 . . 4 . 1 ARG HB3 H 1.74 . . 5 . 1 ARG HG2 H 1.61 . . 6 . 1 ARG HG3 H 1.61 . . 7 . 1 ARG HD2 H 3.17 . . 8 . 1 ARG HD3 H 3.17 . . 9 . 1 ARG HE H 7.16 . . 10 . 2 MET H H 8.40 . . 11 . 2 MET HA H 4.41 . . 12 . 2 MET HB2 H 1.99 . . 13 . 2 MET HB3 H 1.99 . . 14 . 2 MET HG2 H 2.50 . . 15 . 2 MET HG3 H 2.50 . . 16 . 3 LYS H H 8.28 . . 17 . 3 LYS HA H 4.27 . . 18 . 3 LYS HB2 H 1.72 . . 19 . 3 LYS HB3 H 1.72 . . 20 . 3 LYS HG2 H 1.39 . . 21 . 3 LYS HG3 H 1.39 . . 22 . 3 LYS HD2 H 1.72 . . 23 . 3 LYS HD3 H 1.72 . . 24 . 3 LYS HE2 H 2.96 . . 25 . 3 LYS HE3 H 2.96 . . 26 . 4 LYS H H 8.42 . . 27 . 4 LYS HA H 4.19 . . 28 . 4 LYS HB2 H 1.70 . . 29 . 4 LYS HB3 H 1.70 . . 30 . 4 LYS HG2 H 1.36 . . 31 . 4 LYS HG3 H 1.36 . . 32 . 4 LYS HD2 H 1.69 . . 33 . 4 LYS HD3 H 1.69 . . 34 . 4 LYS HE2 H 2.89 . . 35 . 4 LYS HE3 H 2.89 . . 36 . 5 LYS H H 8.18 . . 37 . 5 LYS HA H 4.19 . . 38 . 5 LYS HB2 H 1.70 . . 39 . 5 LYS HB3 H 1.70 . . 40 . 5 LYS HG2 H 1.39 . . 41 . 5 LYS HG3 H 1.39 . . 42 . 6 ASP H H 8.37 . . 43 . 6 ASP HA H 4.58 . . 44 . 6 ASP HB2 H 2.65 . . 45 . 6 ASP HB3 H 2.65 . . 46 . 7 GLU H H 8.36 . . 47 . 7 GLU HA H 4.26 . . 48 . 7 GLU HB2 H 1.91 . . 49 . 7 GLU HB3 H 1.91 . . 50 . 7 GLU HG2 H 2.24 . . 51 . 7 GLU HG3 H 2.24 . . 52 . 8 GLY H H 8.45 . . 53 . 8 GLY HA2 H 3.93 . . 54 . 8 GLY HA3 H 3.93 . . 55 . 9 SER H H 8.03 . . 56 . 9 SER HA H 4.38 . . 57 . 9 SER HB2 H 3.74 . . 58 . 9 SER HB3 H 3.74 . . 59 . 10 TYR H H 8.16 . . 60 . 10 TYR HA H 4.56 . . 61 . 10 TYR HB2 H 2.97 . . 62 . 10 TYR HB3 H 2.94 . . 63 . 10 TYR HD1 H 7.07 . . 64 . 10 TYR HD2 H 7.07 . . 65 . 10 TYR HE1 H 6.79 . . 66 . 10 TYR HE2 H 6.79 . . 67 . 11 ASP H H 7.95 . . 68 . 11 ASP HA H 4.45 . . 69 . 11 ASP HB2 H 2.54 . . 70 . 11 ASP HB3 H 2.66 . . 71 . 12 LEU H H 8.13 . . 72 . 12 LEU HA H 4.25 . . 73 . 12 LEU HB2 H 1.60 . . 74 . 12 LEU HB3 H 1.60 . . 75 . 12 LEU HG H 1.60 . . 76 . 12 LEU HD1 H 0.83 . . 77 . 12 LEU HD2 H 0.90 . . 78 . 13 GLY H H 8.41 . . 79 . 13 GLY HA2 H 3.89 . . 80 . 13 GLY HA3 H 3.89 . . 81 . 14 LYS H H 7.89 . . 82 . 14 LYS HA H 4.29 . . 83 . 14 LYS HB2 H 1.75 . . 84 . 14 LYS HB3 H 1.75 . . 85 . 14 LYS HG2 H 1.34 . . 86 . 14 LYS HG3 H 1.34 . . 87 . 14 LYS HD2 H 1.65 . . 88 . 14 LYS HD3 H 1.65 . . 89 . 14 LYS HE2 H 2.94 . . 90 . 14 LYS HE3 H 2.94 . . 91 . 15 LYS H H 8.18 . . 92 . 15 LYS HA H 4.56 . . 93 . 15 LYS HB2 H 1.70 . . 94 . 15 LYS HB3 H 1.70 . . 95 . 15 LYS HG2 H 1.39 . . 96 . 15 LYS HG3 H 1.39 . . 97 . 15 LYS HD2 H 1.69 . . 98 . 15 LYS HD3 H 1.69 . . 99 . 16 PRO HA H 4.33 . . 100 . 16 PRO HB2 H 2.12 . . 101 . 16 PRO HB3 H 1.68 . . 102 . 16 PRO HG2 H 1.95 . . 103 . 16 PRO HG3 H 1.95 . . 104 . 16 PRO HD2 H 3.52 . . 105 . 16 PRO HD3 H 3.75 . . 106 . 17 ILE H H 8.06 . . 107 . 17 ILE HA H 4.05 . . 108 . 17 ILE HB H 1.70 . . 109 . 17 ILE HG12 H 1.06 . . 110 . 17 ILE HG13 H 1.06 . . 111 . 17 ILE HG2 H 1.06 . . 112 . 17 ILE HD1 H 0.78 . . 113 . 18 TYR H H 8.19 . . 114 . 18 TYR HA H 4.56 . . 115 . 18 TYR HB2 H 2.85 . . 116 . 18 TYR HB3 H 2.94 . . 117 . 18 TYR HD1 H 7.07 . . 118 . 18 TYR HD2 H 7.07 . . 119 . 18 TYR HE1 H 6.79 . . 120 . 18 TYR HE2 H 6.79 . . 121 . 19 LYS H H 8.37 . . 122 . 19 LYS HA H 4.27 . . 123 . 19 LYS HB2 H 1.74 . . 124 . 19 LYS HB3 H 1.74 . . 125 . 19 LYS HG2 H 1.39 . . 126 . 19 LYS HG3 H 1.39 . . 127 . 19 LYS HD2 H 1.69 . . 128 . 19 LYS HD3 H 1.69 . . 129 . 19 LYS HE2 H 2.68 . . 130 . 19 LYS HE3 H 2.68 . . 131 . 20 LYS H H 8.13 . . 132 . 20 LYS HA H 4.26 . . 133 . 20 LYS HB2 H 1.62 . . 134 . 20 LYS HB3 H 1.62 . . 135 . 20 LYS HG2 H 1.32 . . 136 . 20 LYS HG3 H 1.32 . . 137 . 20 LYS HD2 H 1.62 . . 138 . 20 LYS HD3 H 1.62 . . 139 . 21 ALA H H 8.33 . . 140 . 21 ALA HA H 4.54 . . 141 . 21 ALA HB H 1.31 . . 142 . 22 PRO HA H 4.41 . . 143 . 22 PRO HB2 H 2.25 . . 144 . 22 PRO HB3 H 1.89 . . 145 . 22 PRO HG2 H 1.98 . . 146 . 22 PRO HG3 H 1.98 . . 147 . 22 PRO HD2 H 3.58 . . 148 . 22 PRO HD3 H 3.70 . . 149 . 23 THR H H 8.13 . . 150 . 23 THR HA H 4.27 . . 151 . 23 THR HB H 4.27 . . 152 . 23 THR HG2 H 1.16 . . 153 . 24 ASN H H 8.39 . . 154 . 24 ASN HA H 4.66 . . 155 . 24 ASN HB2 H 2.75 . . 156 . 24 ASN HB3 H 2.75 . . 157 . 25 GLU H H 8.31 . . 158 . 25 GLU HA H 4.16 . . 159 . 25 GLU HB2 H 1.78 . . 160 . 25 GLU HB3 H 1.78 . . 161 . 25 GLU HG2 H 2.06 . . 162 . 25 GLU HG3 H 2.06 . . 163 . 26 PHE H H 8.13 . . 164 . 26 PHE HA H 4.25 . . 165 . 26 PHE HB2 H 2.87 . . 166 . 26 PHE HB3 H 3.03 . . 167 . 26 PHE HD1 H 6.79 . . 168 . 26 PHE HD2 H 6.79 . . 169 . 26 PHE HE1 H 7.10 . . 170 . 26 PHE HE2 H 7.10 . . 171 . 27 TYR H H 7.94 . . 172 . 27 TYR HA H 4.53 . . 173 . 27 TYR HB2 H 2.91 . . 174 . 27 TYR HB3 H 2.91 . . 175 . 27 TYR HD1 H 7.27 . . 176 . 27 TYR HD2 H 7.27 . . 177 . 27 TYR HE1 H 7.12 . . 178 . 27 TYR HE2 H 7.12 . . 179 . 28 ALA H H 7.67 . . 180 . 28 ALA HA H 4.11 . . 181 . 28 ALA HB H 1.29 . . stop_ save_