data_34214 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of EphA2-Sam stapled peptides (S13STshort) ; _BMRB_accession_number 34214 _BMRB_flat_file_name bmr34214.str _Entry_type original _Submission_date 2017-12-11 _Accession_date 2017-12-11 _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 Mercurio F. A. . 2 Leone M. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 99 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-08-14 update BMRB 'update entry citation' 2018-07-26 original author 'original release' stop_ _Original_release_date 2017-12-22 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Sam domain-based stapled peptides: Structural analysis and interaction studies with the Sam domains from the EphA2 receptor and the lipid phosphatase Ship2 ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30036816 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mercurio F. A. . 2 Pirone L. . . 3 'Di Natale' C. . . 4 Marasco D. . . 5 Pedone E. M. . 6 Leone M. . . stop_ _Journal_abbreviation 'Bioorg. Chem.' _Journal_volume 80 _Journal_issue . _Journal_ASTM BOCMBM _Journal_ISSN 0045-2068 _Journal_CSD 0368 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 602 _Page_last 610 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Ephrin type-A receptor 2 (E.C.2.7.10.1)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _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 1587.998 _Mol_thiol_state 'not present' _Details ; Fragment 951-963 of human EphA2 receptor (Uniprot entry P29317) with Q955 and A959 mutated in MK8 (=(S)-2-(4'-pentenyl) alanine). ; ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence ; XLPGHXKRIXYSLLX ; loop_ _Residue_seq_code _Residue_label 1 ACE 2 LEU 3 PRO 4 GLY 5 HIS 6 MK8 7 LYS 8 ARG 9 ILE 10 MK8 11 TYR 12 SER 13 LEU 14 LEU 15 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_MK8 _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 2-methyl-L-norleucine _BMRB_code MK8 _PDB_code MK8 _Standard_residue_derivative . _Molecular_mass 145.199 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? N N N . 0 . ? O O O . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CD CD C . 0 . ? CE CE C . 0 . ? CG CG C . 0 . ? CB1 CB1 C . 0 . ? OXT OXT O . 0 . ? HN HN H . 0 . ? HNA HNA H . 0 . ? HB HB H . 0 . ? HBA HBA H . 0 . ? HD HD H . 0 . ? HDA HDA H . 0 . ? HE HE H . 0 . ? HEA HEA H . 0 . ? HEB HEB H . 0 . ? HG HG H . 0 . ? HGA HGA H . 0 . ? HB1 HB1 H . 0 . ? HB1A HB1A H . 0 . ? HB1B HB1B H . 0 . ? HXT HXT 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 C CA ? ? SING C OXT ? ? SING N HN ? ? SING N HNA ? ? DOUB O C ? ? SING CA N ? ? SING CA CB ? ? SING CB HB ? ? SING CB HBA ? ? SING CD CG ? ? SING CD HD ? ? SING CD HDA ? ? SING CE CD ? ? SING CE HE ? ? SING CE HEA ? ? SING CE HEB ? ? SING CG CB ? ? SING CG HG ? ? SING CG HGA ? ? SING CB1 CA ? ? SING CB1 HB1 ? ? SING CB1 HB1A ? ? SING CB1 HB1B ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _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 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 HN1 ? ? SING N HN2 ? ? stop_ save_ save_chem_comp_ACE _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'ACETYL GROUP' _BMRB_code ACE _PDB_code ACE _Standard_residue_derivative . _Molecular_mass 44.053 _Mol_paramagnetic . _Details . 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 $entity_1 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '400 uM S13STshort, trifluoroethanol/water' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 400 uM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name VNMRJ _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_4 _Saveframe_category software _Name Chimera _Version 1.10.1 loop_ _Vendor _Address _Electronic_address 'Pettersen et al.' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details 'Cold probe' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-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 pH 7.4 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 TSP H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 1 ACE H1 H 2.06 0.01 1 2 2 2 LEU H H 7.83 0.01 1 3 2 2 LEU HA H 4.59 0.01 1 4 2 2 LEU HB2 H 1.73 0.01 2 5 2 2 LEU HB3 H 1.61 0.01 2 6 2 2 LEU HG H 1.73 0.01 1 7 2 2 LEU HD1 H 0.97 0.01 1 8 2 2 LEU HD2 H 0.97 0.01 1 9 3 3 PRO HA H 4.42 0.01 1 10 3 3 PRO HB2 H 2.39 0.01 2 11 3 3 PRO HB3 H 1.92 0.01 2 12 3 3 PRO HG2 H 2.14 0.01 2 13 3 3 PRO HG3 H 2.07 0.01 2 14 3 3 PRO HD2 H 3.62 0.01 1 15 3 3 PRO HD3 H 3.62 0.01 1 16 4 4 GLY H H 8.09 0.01 1 17 4 4 GLY HA2 H 3.93 0.01 1 18 4 4 GLY HA3 H 3.93 0.01 1 19 5 5 HIS H H 7.93 0.01 1 20 5 5 HIS HA H 4.47 0.01 1 21 5 5 HIS HB2 H 3.18 0.01 1 22 5 5 HIS HB3 H 3.18 0.01 1 23 5 5 HIS HD2 H 6.89 0.01 1 24 5 5 HIS HE1 H 7.65 0.01 1 25 6 6 MK8 HB H 1.94 0.01 2 26 6 6 MK8 HB1 H 1.42 0.01 1 27 6 6 MK8 HB1A H 1.42 0.01 1 28 6 6 MK8 HB1B H 1.42 0.01 1 29 6 6 MK8 HBA H 2.02 0.01 2 30 6 6 MK8 HD H 2.06 0.01 2 31 6 6 MK8 HDA H 1.71 0.01 2 32 6 6 MK8 HE H 5.37 0.01 1 33 6 6 MK8 HG H 1.20 0.01 1 34 6 6 MK8 HGA H 1.20 0.01 1 35 6 6 MK8 HN H 7.83 0.01 1 36 7 7 LYS H H 8.09 0.01 1 37 7 7 LYS HA H 3.92 0.01 1 38 7 7 LYS HB2 H 1.90 0.01 2 39 7 7 LYS HB3 H 1.82 0.01 2 40 7 7 LYS HG2 H 1.66 0.01 2 41 7 7 LYS HG3 H 1.39 0.01 2 42 7 7 LYS HD2 H 1.75 0.01 1 43 7 7 LYS HD3 H 1.75 0.01 1 44 7 7 LYS HE2 H 2.94 0.01 1 45 7 7 LYS HE3 H 2.94 0.01 1 46 8 8 ARG H H 7.67 0.01 1 47 8 8 ARG HA H 4.07 0.01 1 48 8 8 ARG HB2 H 2.04 0.01 2 49 8 8 ARG HB3 H 2.02 0.01 2 50 8 8 ARG HG2 H 1.87 0.01 2 51 8 8 ARG HG3 H 1.71 0.01 2 52 8 8 ARG HD2 H 3.26 0.01 1 53 8 8 ARG HD3 H 3.26 0.01 1 54 9 9 ILE H H 7.52 0.01 1 55 9 9 ILE HA H 3.76 0.01 1 56 9 9 ILE HB H 2.15 0.01 1 57 9 9 ILE HG12 H 1.52 0.01 2 58 9 9 ILE HG13 H 1.19 0.01 2 59 9 9 ILE HG2 H 0.91 0.01 1 60 9 9 ILE HD1 H 0.80 0.01 1 61 10 10 MK8 HB H 2.05 0.01 2 62 10 10 MK8 HB1 H 1.50 0.01 1 63 10 10 MK8 HB1A H 1.50 0.01 1 64 10 10 MK8 HB1B H 1.50 0.01 1 65 10 10 MK8 HBA H 1.51 0.01 2 66 10 10 MK8 HD H 2.07 0.01 2 67 10 10 MK8 HDA H 1.67 0.01 2 68 10 10 MK8 HE H 5.48 0.01 1 69 10 10 MK8 HG H 1.49 0.01 2 70 10 10 MK8 HGA H 1.43 0.01 2 71 10 10 MK8 HN H 8.43 0.01 1 72 11 11 TYR H H 8.65 0.01 1 73 11 11 TYR HA H 4.22 0.01 1 74 11 11 TYR HB2 H 3.26 0.01 2 75 11 11 TYR HB3 H 3.11 0.01 2 76 11 11 TYR HD1 H 7.15 0.01 3 77 11 11 TYR HD2 H 7.15 0.01 3 78 11 11 TYR HE1 H 6.82 0.01 3 79 11 11 TYR HE2 H 6.82 0.01 3 80 12 12 SER H H 7.95 0.01 1 81 12 12 SER HA H 4.29 0.01 1 82 12 12 SER HB2 H 4.23 0.01 2 83 12 12 SER HB3 H 4.04 0.01 2 84 13 13 LEU H H 7.90 0.01 1 85 13 13 LEU HA H 4.42 0.01 1 86 13 13 LEU HB2 H 1.87 0.01 2 87 13 13 LEU HB3 H 1.60 0.01 2 88 13 13 LEU HG H 1.81 0.01 1 89 13 13 LEU HD1 H 0.88 0.01 1 90 13 13 LEU HD2 H 0.88 0.01 1 91 14 14 LEU H H 8.12 0.01 1 92 14 14 LEU HA H 4.28 0.01 1 93 14 14 LEU HB2 H 1.81 0.01 2 94 14 14 LEU HB3 H 1.56 0.01 2 95 14 14 LEU HG H 1.82 0.01 1 96 14 14 LEU HD1 H 0.89 0.01 1 97 14 14 LEU HD2 H 0.89 0.01 1 98 15 15 NH2 HN1 H 7.17 0.01 2 99 15 15 NH2 HN2 H 6.71 0.01 2 stop_ save_