data_16462 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of Sem-5 indicate cooperative conformational coupling ; _BMRB_accession_number 16462 _BMRB_flat_file_name bmr16462.str _Entry_type new _Submission_date 2009-08-19 _Accession_date 2009-08-19 _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 Ferreon Josephine C. . 2 Hilser Vincent J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count binding_constants 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-03-08 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of Sem-5 indicate cooperative conformational coupling' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 12717021 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ferreon Josephine C. . 2 Hilser Vincent J. . stop_ _Journal_abbreviation 'Protein Sci.' _Journal_volume 12 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 982 _Page_last 996 _Year 2003 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Sem-5 Sos peptide complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Sem-5 $Sem-5 'Sos peptide' $Sos_peptide stop_ _System_molecular_weight 15799.86 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Sem-5 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Sem-5 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 58 _Mol_residue_sequence ; ETKFVQALFDFNPQESGELA FKRGDVITLINKDDPNWWEG QLNNRRGIFPSNYVAPYN ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 155 GLU 2 156 THR 3 157 LYS 4 158 PHE 5 159 VAL 6 160 GLN 7 161 ALA 8 162 LEU 9 163 PHE 10 164 ASP 11 165 PHE 12 166 ASN 13 167 PRO 14 168 GLN 15 169 GLU 16 170 SER 17 171 GLY 18 172 GLU 19 173 LEU 20 174 ALA 21 175 PHE 22 176 LYS 23 177 ARG 24 178 GLY 25 179 ASP 26 180 VAL 27 181 ILE 28 182 THR 29 183 LEU 30 184 ILE 31 185 ASN 32 186 LYS 33 187 ASP 34 188 ASP 35 189 PRO 36 190 ASN 37 191 TRP 38 192 TRP 39 193 GLU 40 194 GLY 41 195 GLN 42 196 LEU 43 197 ASN 44 198 ASN 45 199 ARG 46 200 ARG 47 201 GLY 48 202 ILE 49 203 PHE 50 204 PRO 51 205 SER 52 206 ASN 53 207 TYR 54 208 VAL 55 209 ALA 56 210 PRO 57 211 TYR 58 212 ASN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-02-05 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 PDB 1K76 "Solution Structure Of The C-Terminal Sem-5 Sh3 Domain (Minimized Average Structure)" 100.00 62 100.00 100.00 3.07e-34 PDB 1KFZ "Solution Structure Of C-Terminal Sem-5 Sh3 Domain (Ensemble Of 16 Structures)" 100.00 62 100.00 100.00 3.07e-34 PDB 1SEM "Structural Determinants Of Peptide-Binding Orientation And Of Sequence Specificity In Sh3 Domains" 100.00 58 98.28 98.28 1.85e-33 PDB 2SEM "Sem5 Sh3 Domain Complexed With Peptoid Inhibitor" 100.00 60 98.28 98.28 1.54e-33 PDB 3SEM "Sem5 Sh3 Domain Complexed With Peptoid Inhibitor" 100.00 60 98.28 98.28 1.54e-33 stop_ save_ save_Sos_peptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Sos_peptide _Molecular_mass . _Mol_thiol_state 'not present' _Details 'X = ACE' _Residue_count 10 _Mol_residue_sequence XPPPVPPRRR loop_ _Residue_seq_code _Residue_label 1 ACE 2 PRO 3 PRO 4 PRO 5 VAL 6 PRO 7 PRO 8 ARG 9 ARG 10 ARG 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 PDB 1SEM '10-RESIDUE PROLINE-RICH PEPTIDE FROM MSOS' . . . . . stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_ACE _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'ACETYL GROUP' _BMRB_code . _PDB_code ACE _Standard_residue_derivative . _Molecular_mass 44.053 _Mol_paramagnetic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 12:48:52 2009 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? O O O . 0 . ? CH3 CH3 C . 0 . ? H H H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB C O ? ? SING C CH3 ? ? SING C H ? ? SING CH3 H1 ? ? SING CH3 H2 ? ? SING CH3 H3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Sem-5 'Caenorhabditis elegans' 6239 Eukaryota Metazoa . . $Sos_peptide . . . . . . 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 $Sem-5 'purified from the natural source' . . . . . $Sos_peptide 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'Peptide was titrated with a final concentration of about 2 times that of the protein' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $Sem-5 0.66 mM . . [U-15N] NaOAc 50 mM . . 'natural abundance' 'sodium chloride' 100 mM . . 'natural abundance' 'calcium chloride' 10 mM . . 'natural abundance' $Sos_peptide . mM 0 1.32 'natural abundance' D2O 10 % . . 'natural abundance' H2O 90 % . . 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Sem-5 0.66 mM [U-15N] NaOAc 50 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' 'calcium chloride' 10 mM 'natural abundance' $Sos_peptide 1.32 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Sem-5 0.66 mM [U-15N] NaOAc 50 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' 'calcium chloride' 10 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_Felix _Saveframe_category software _Name Felix _Version 98 loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task processing stop_ _Details . save_ save_Modelfree_4.01 _Saveframe_category software _Name Modelfree_4.01 _Version . loop_ _Vendor _Address _Electronic_address '(Columbia University. http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer)' . . stop_ loop_ _Task 'statistical tests' stop_ _Details . save_ save_Molmol _Saveframe_category software _Name Molmol _Version 2K.1 loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task visualization stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UnityPlus _Field_strength 400 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_3D_1H-15N_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_2 save_ save_3D_1H-15N_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_3 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 4.8 . pH pressure 1 . atm stop_ save_