data_25082 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Fyn SH2 domain in complex with the natural inhibitory phosphotyrosine peptide ; _BMRB_accession_number 25082 _BMRB_flat_file_name bmr25082.str _Entry_type original _Submission_date 2014-07-09 _Accession_date 2014-07-09 _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 Huculeci Radu . . 2 Buts Lieven . . 3 Lenaerts Tom AJ . 4 'van Nuland' Nico . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 53 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-07-13 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 17368 'Fyn SH2 free state' 17369 'Fyn SH2 in complex with the high affinity inhibitory peptide' 25081 'Fyn SH2 domain bound to the natural inhibitory peptide' stop_ _Original_release_date 2015-07-13 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Dynamically coupled residues within the SH2 domain of FYN are key to unlock its activity ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Huculeci Radu . . 2 Cilia Elisa . . 3 Buts Lieven . . 4 Houben Klaartje . . 5 'van Nuland' Nico . . 6 Lenaerts Tom . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Fyn SH2 domain in complex with the natural inhibitory phosphotyrosine peptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Fyn SH2 domain' $entity_1 'natural inhibitory phosphotyrosine peptide' $entity_2 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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass 11690.439 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 122 _Mol_residue_sequence ; MGSSHHHHHHSSGLVPRGSH MEWYFGKLGRKDAERQLLSF GNPRGTFLIRESETTKGAYS LSIRDWDDMKGDHVKHYKIR KLDNGGYYITTRAQFETLQQ LVQHYSERAAGLCCRLVVPC HK ; loop_ _Residue_seq_code _Residue_label 1 MET 2 GLY 3 SER 4 SER 5 HIS 6 HIS 7 HIS 8 HIS 9 HIS 10 HIS 11 SER 12 SER 13 GLY 14 LEU 15 VAL 16 PRO 17 ARG 18 GLY 19 SER 20 HIS 21 MET 22 GLU 23 TRP 24 TYR 25 PHE 26 GLY 27 LYS 28 LEU 29 GLY 30 ARG 31 LYS 32 ASP 33 ALA 34 GLU 35 ARG 36 GLN 37 LEU 38 LEU 39 SER 40 PHE 41 GLY 42 ASN 43 PRO 44 ARG 45 GLY 46 THR 47 PHE 48 LEU 49 ILE 50 ARG 51 GLU 52 SER 53 GLU 54 THR 55 THR 56 LYS 57 GLY 58 ALA 59 TYR 60 SER 61 LEU 62 SER 63 ILE 64 ARG 65 ASP 66 TRP 67 ASP 68 ASP 69 MET 70 LYS 71 GLY 72 ASP 73 HIS 74 VAL 75 LYS 76 HIS 77 TYR 78 LYS 79 ILE 80 ARG 81 LYS 82 LEU 83 ASP 84 ASN 85 GLY 86 GLY 87 TYR 88 TYR 89 ILE 90 THR 91 THR 92 ARG 93 ALA 94 GLN 95 PHE 96 GLU 97 THR 98 LEU 99 GLN 100 GLN 101 LEU 102 VAL 103 GLN 104 HIS 105 TYR 106 SER 107 GLU 108 ARG 109 ALA 110 ALA 111 GLY 112 LEU 113 CYS 114 CYS 115 ARG 116 LEU 117 VAL 118 VAL 119 PRO 120 CYS 121 HIS 122 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-25 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 25081 FynSH2_bound 91.80 112 100.00 100.00 2.89e-77 PDB 1AOT "Nmr Structure Of The Fyn Sh2 Domain Complexed With A Phosphotyrosyl Peptide, Minimized Average Structure" 82.79 106 97.03 97.03 3.92e-66 PDB 1AOU "Nmr Structure Of The Fyn Sh2 Domain Complexed With A Phosphotyrosyl Peptide, 22 Structures" 82.79 106 97.03 97.03 3.92e-66 PDB 1G83 "Crystal Structure Of Fyn Sh3-Sh2" 81.15 165 96.97 96.97 7.17e-64 PDB 2MQI "Human Fyn Sh2 Free State" 81.97 100 100.00 100.00 5.96e-68 PDB 2MRJ "Structure Of Fyn Protein Sh2 Bound" 81.97 100 100.00 100.00 5.96e-68 PDB 2MRK "Fyn Sh2 Domain In Complex With The Natural Inhibitory Phosphotyrosine Peptide" 81.97 100 100.00 100.00 5.96e-68 PDB 4U17 "Swapped Dimer Of The Human Fyn-sh2 Domain" 86.07 105 100.00 100.00 6.48e-72 PDB 4U1P "Human Fyn-sh2 Domain In Complex With A Synthetic High-affinity Phospho-peptide" 100.00 122 100.00 100.00 4.71e-85 DBJ BAE33766 "unnamed protein product [Mus musculus]" 82.79 537 100.00 100.00 7.88e-65 DBJ BAG70107 "protein-tyrosine kinase fyn isoform a [Homo sapiens]" 82.79 537 100.00 100.00 7.40e-65 DBJ BAG70240 "protein-tyrosine kinase fyn isoform a [Homo sapiens]" 82.79 537 100.00 100.00 7.40e-65 DBJ BAI46902 "FYN oncogene related to SRC, FGR, YES [synthetic construct]" 82.79 537 100.00 100.00 7.40e-65 EMBL CAA36435 "fyn [Xenopus laevis]" 82.79 537 99.01 100.00 2.44e-64 GB AAA36615 "src-like tyrosine kinase (put.); putative [Homo sapiens]" 82.79 537 99.01 100.00 2.68e-64 GB AAA49719 "c-fyn protein [Xenopus laevis]" 82.79 537 99.01 100.00 2.44e-64 GB AAA82942 "proto-oncogene FYN [Rattus norvegicus]" 82.79 537 100.00 100.00 8.05e-65 GB AAC08285 "c-syn protooncogene [Homo sapiens]" 82.79 537 100.00 100.00 7.40e-65 GB AAH32496 "FYN oncogene related to SRC, FGR, YES [Homo sapiens]" 69.67 482 100.00 100.00 1.89e-51 REF NP_001071440 "tyrosine-protein kinase Fyn [Bos taurus]" 82.79 537 100.00 100.00 9.14e-65 REF NP_001073675 "tyrosine-protein kinase Fyn [Sus scrofa]" 82.79 537 100.00 100.00 8.05e-65 REF NP_001079077 "tyrosine-protein kinase Fyn [Xenopus laevis]" 82.79 537 99.01 100.00 2.44e-64 REF NP_001080120 "proto-oncogene tyrosine-protein kinase fyn [Xenopus laevis]" 82.79 537 98.02 99.01 1.13e-63 REF NP_001116365 "tyrosine-protein kinase Fyn isoform a [Mus musculus]" 82.79 537 100.00 100.00 7.88e-65 SP A0JNB0 "RecName: Full=Tyrosine-protein kinase Fyn; AltName: Full=Proto-oncogene c-Fyn; AltName: Full=p59-Fyn" 82.79 537 100.00 100.00 9.14e-65 SP A1Y2K1 "RecName: Full=Tyrosine-protein kinase Fyn; AltName: Full=Proto-oncogene c-Fyn; AltName: Full=p59-Fyn" 82.79 537 100.00 100.00 8.05e-65 SP P06241 "RecName: Full=Tyrosine-protein kinase Fyn; AltName: Full=Proto-oncogene Syn; AltName: Full=Proto-oncogene c-Fyn; AltName: Full=" 82.79 537 100.00 100.00 7.40e-65 SP P13406 "RecName: Full=Tyrosine-protein kinase Fyn; AltName: Full=Proto-oncogene c-Fyn; AltName: Full=p59-Fyn" 82.79 537 99.01 100.00 2.44e-64 SP P39688 "RecName: Full=Tyrosine-protein kinase Fyn; AltName: Full=Proto-oncogene c-Fyn; AltName: Full=p59-Fyn" 82.79 537 100.00 100.00 7.88e-65 TPG DAA26259 "TPA: proto-oncogene tyrosine-protein kinase Fyn [Bos taurus]" 82.79 537 100.00 100.00 9.14e-65 stop_ save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_2 _Molecular_mass 1254.209 _Mol_thiol_state 'not present' _Details . _Residue_count 10 _Mol_residue_sequence ; EPQYQPGENL ; loop_ _Residue_seq_code _Residue_label 1 GLU 2 PRO 3 GLN 4 PTR 5 GLN 6 PRO 7 GLY 8 GLU 9 ASN 10 LEU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_PTR _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common O-PHOSPHOTYROSINE _BMRB_code PTR _PDB_code PTR _Standard_residue_derivative . _Molecular_mass 261.168 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? CE1 CE1 C . 0 . ? CE2 CE2 C . 0 . ? CZ CZ C . 0 . ? OH OH O . 0 . ? P P P . 0 . ? O1P O1P O . 0 . ? O2P O2P O . 0 . ? O3P O3P O . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 H . 0 . ? HO2P HO2P H . 0 . ? HO3P HO3P 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 SING N CA ? ? SING N H ? ? SING N HN2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 CE1 ? ? SING CD1 HD1 ? ? DOUB CD2 CE2 ? ? SING CD2 HD2 ? ? DOUB CE1 CZ ? ? SING CE1 HE1 ? ? SING CE2 CZ ? ? SING CE2 HE2 ? ? SING CZ OH ? ? SING OH P ? ? DOUB P O1P ? ? SING P O2P ? ? SING P O3P ? ? SING O2P HO2P ? ? SING O3P HO3P ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 Human 9606 Eukaryota Metazoa Homo sapiens $entity_2 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 $entity_1 'recombinant technology' . . . . pET15b 'The SH2 domain from human p59fyn is represented by residues149-248.' $entity_2 'chemical synthesis' . . . . NA 'The natural inhibitory peptide is a 10 residues phosphotyrosine segment from the C-terminal region of the Fyn kinase.' 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 $entity_1 0.93 mM '[U-99% 13C; U-99% 15N]' $entity_2 1.2 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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_CCPNMR _Saveframe_category software _Name CCPNMR _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_HADDOCK _Saveframe_category software _Name HADDOCK _Version . loop_ _Vendor _Address _Electronic_address 'Alexandre Bonvin' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_600 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Varian NMR Systems' _Field_strength 600 _Details . save_ save_800 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Varian NMR Systems' _Field_strength 800 _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_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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 'ionic strength' 0 . M pH 6.50 . pH pressure 1 . atm temperature 298 . K 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' 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 'natural inhibitory phosphotyrosine peptide' _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 GLU H H 8.286 0.001 1 2 1 1 GLU HA H 4.500 0.001 1 3 1 1 GLU HB2 H 1.984 0.009 2 4 1 1 GLU HB3 H 1.820 0.001 2 5 1 1 GLU HG2 H 2.275 0.011 2 6 1 1 GLU HG3 H 2.256 0.008 2 7 2 2 PRO HA H 4.357 0.001 1 8 2 2 PRO HB2 H 1.831 0.004 2 9 2 2 PRO HB3 H 2.151 0.003 2 10 2 2 PRO HG2 H 1.984 0.004 1 11 2 2 PRO HG3 H 1.984 0.004 1 12 2 2 PRO HD2 H 3.670 0.002 2 13 2 2 PRO HD3 H 3.783 0.003 2 14 3 3 GLN H H 8.519 0.004 1 15 3 3 GLN HA H 4.206 0.004 1 16 3 3 GLN HB2 H 1.932 0.008 1 17 3 3 GLN HB3 H 1.932 0.008 1 18 3 3 GLN HG2 H 2.297 0.001 2 19 3 3 GLN HG3 H 2.228 0.004 2 20 3 3 GLN HE21 H 7.511 0.000 1 21 3 3 GLN HE22 H 6.820 0.001 1 22 4 4 PTR H H 7.003 0.002 1 23 4 4 PTR HB2 H 2.968 0.000 1 24 4 4 PTR HB3 H 2.968 0.000 1 25 5 5 GLN HE21 H 7.073 0.002 1 26 5 5 GLN HE22 H 7.596 0.001 1 27 6 6 PRO HA H 4.491 0.000 1 28 6 6 PRO HB2 H 2.063 0.000 2 29 6 6 PRO HB3 H 2.371 0.000 2 30 6 6 PRO HD2 H 3.629 0.000 1 31 6 6 PRO HD3 H 3.629 0.000 1 32 7 7 GLY H H 8.716 0.001 1 33 7 7 GLY HA2 H 3.893 0.002 1 34 7 7 GLY HA3 H 3.893 0.002 1 35 8 8 GLU H H 8.178 0.002 1 36 8 8 GLU HA H 4.266 0.000 1 37 8 8 GLU HB2 H 2.065 0.001 2 38 8 8 GLU HB3 H 1.983 0.003 2 39 8 8 GLU HG2 H 2.306 0.007 1 40 8 8 GLU HG3 H 2.306 0.007 1 41 9 9 ASN H H 8.512 0.015 1 42 9 9 ASN HA H 4.196 0.005 1 43 9 9 ASN HB2 H 2.725 0.003 2 44 9 9 ASN HB3 H 2.893 0.003 2 45 9 9 ASN HD21 H 7.618 0.000 1 46 9 9 ASN HD22 H 6.915 0.001 1 47 10 10 LEU H H 8.285 0.009 1 48 10 10 LEU HA H 4.265 0.001 1 49 10 10 LEU HB2 H 1.647 0.001 2 50 10 10 LEU HB3 H 1.572 0.002 2 51 10 10 LEU HG H 1.572 0.002 1 52 10 10 LEU HD1 H 0.908 0.001 2 53 10 10 LEU HD2 H 0.846 0.001 2 stop_ save_