data_18148 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; VEGFR2-Integrin B3 interaction ; _BMRB_accession_number 18148 _BMRB_flat_file_name bmr18148.str _Entry_type original _Submission_date 2011-12-18 _Accession_date 2011-12-18 _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 Deshmukh Lalit . . 2 Vinogradova Olga . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 48 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-03-02 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Integrin (3) Crosstalk with VEGFR Accommodating Tyrosine Phosphorylation as a Regulatory Switch.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22363548 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 West Xiaoxia Z. . 2 Meller Nahum . . 3 Malinin Nikolay L. . 4 Deshmukh Lalit . . 5 Meller Julia . . 6 Mahabeleshwar Ganapati H. . 7 Weber Malory E. . 8 Kerr Bethany A. . 9 Vinogradova Olga . . 10 Byzova Tatiana V. . stop_ _Journal_abbreviation 'PLoS ONE' _Journal_name_full 'PloS one' _Journal_volume 7 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2012 _Details . loop_ _Keyword VEGFR Integrin 'Tyrosine Phosphorylation' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name VEGFR-2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label VEGFR-2 $cytoplasmic_tail_of_VEGFR-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_cytoplasmic_tail_of_VEGFR-2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common cytoplasmic_tail_of_VEGFR-2 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence LRTVKRANGGELKTGYLSIV loop_ _Residue_seq_code _Residue_label 1 LEU 2 ARG 3 THR 4 VAL 5 LYS 6 ARG 7 ALA 8 ASN 9 GLY 10 GLY 11 GLU 12 LEU 13 LYS 14 THR 15 GLY 16 TYR 17 LEU 18 SER 19 ILE 20 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-04-23 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 4AGC "Crystal Structure Of Vegfr2 (Juxtamembrane And Kinase Domains) In Complex With Axitinib (Ag-013736) (N-Methyl-2-( 3-((E)-2-Pyri" 95.00 353 100.00 100.00 5.71e-03 PDB 4AGD "Crystal Structure Of Vegfr2 (Juxtamembrane And Kinase Domains) In Complex With Sunitinib (Su11248) (N-2- Diethylaminoethyl)-5-(" 95.00 353 100.00 100.00 5.71e-03 PDB 4ASD "Crystal Structure Of Vegfr2 (Juxtamembrane And Kinase Domains) In Complex With Sorafenib (Bay 43-9006)" 95.00 353 100.00 100.00 5.71e-03 PDB 4ASE "Crystal Structure Of Vegfr2 (Juxtamembrane And Kinase Domains) In Complex With Tivozanib (Av-951)" 95.00 353 100.00 100.00 5.71e-03 DBJ BAD93138 "kinase insert domain receptor (a type III receptor tyrosine kinase) variant [Homo sapiens]" 100.00 1451 100.00 100.00 2.60e-03 EMBL CAO79613 "Vascular Endothelial Growth Factor Receptor 2 [Spalax judaei]" 100.00 1316 100.00 100.00 2.56e-03 GB AAB88005 "KDR/flk-1 protein [Homo sapiens]" 100.00 1356 100.00 100.00 2.57e-03 GB AAC16450 "vascular endothelial growth factor receptor 2 [Homo sapiens]" 100.00 1356 100.00 100.00 2.57e-03 GB AAI31823 "Kinase insert domain receptor (a type III receptor tyrosine kinase) [Homo sapiens]" 100.00 1356 100.00 100.00 2.57e-03 GB ABB82619 "VEGFR2 [Canis lupus familiaris]" 100.00 1355 100.00 100.00 2.57e-03 GB ACF37106 "vascular endothelial growth factor receptor 2 [Sus scrofa]" 100.00 648 100.00 100.00 2.35e-03 REF NP_001041489 "vascular endothelial growth factor receptor 2 precursor [Canis lupus familiaris]" 100.00 1355 100.00 100.00 2.57e-03 REF NP_001103470 "vascular endothelial growth factor receptor 2 precursor [Bos taurus]" 100.00 1356 100.00 100.00 2.57e-03 REF NP_001182599 "vascular endothelial growth factor receptor 2 precursor [Oryctolagus cuniculus]" 100.00 1356 100.00 100.00 2.57e-03 REF NP_001265494 "vascular endothelial growth factor receptor 2 precursor [Ovis aries]" 100.00 1356 100.00 100.00 2.57e-03 REF NP_002244 "vascular endothelial growth factor receptor 2 precursor [Homo sapiens]" 100.00 1356 100.00 100.00 2.57e-03 SP P35968 "RecName: Full=Vascular endothelial growth factor receptor 2; Short=VEGFR-2; AltName: Full=Fetal liver kinase 1; Short=FLK-1; Al" 100.00 1356 100.00 100.00 2.57e-03 TPG DAA28658 "TPA: kinase insert domain receptor [Bos taurus]" 100.00 1356 100.00 100.00 2.57e-03 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $cytoplasmic_tail_of_VEGFR-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 $cytoplasmic_tail_of_VEGFR-2 'chemical synthesis' . . . . . 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 $cytoplasmic_tail_of_VEGFR-2 1 mM 'natural abundance' D2O 5 % 'natural abundance' H20 95 % 'natural abundance' DSS 1 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' 'sodium phosphate' 25 mM 'natural abundance' 'GST-tagged B3 integrin tail' 20 uM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.24 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details 'equipped with triple resonance 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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 6.1 . pH pressure 1 . atm 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 internal direct . . . 1 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 TOCSY' '2D 1H-1H NOESY' 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 VEGFR-2 _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 3 3 THR H H 8.358 0.020 1 2 3 3 THR HA H 4.343 0.002 1 3 3 3 THR HB H 4.112 0.020 1 4 3 3 THR HG2 H 1.159 0.004 1 5 4 4 VAL H H 8.278 0.001 1 6 4 4 VAL HA H 4.119 0.004 1 7 4 4 VAL HB H 2.025 0.005 1 8 5 5 LYS H H 8.426 0.001 1 9 5 5 LYS HA H 4.305 0.002 1 10 7 7 ALA H H 8.480 0.001 1 11 7 7 ALA HA H 4.303 0.020 1 12 7 7 ALA HB H 1.360 0.020 1 13 8 8 ASN H H 8.517 0.020 1 14 8 8 ASN HA H 4.678 0.020 1 15 8 8 ASN HD21 H 6.916 0.020 1 16 8 8 ASN HD22 H 7.629 0.002 1 17 9 9 GLY H H 8.448 0.020 1 18 10 10 GLY H H 8.281 0.020 1 19 11 11 GLU H H 8.395 0.001 1 20 11 11 GLU HA H 4.236 0.003 1 21 12 12 LEU H H 8.281 0.001 1 22 12 12 LEU HA H 4.325 0.010 1 23 13 13 LYS H H 8.364 0.006 1 24 13 13 LYS HA H 4.379 0.001 1 25 14 14 THR H H 8.065 0.002 1 26 14 14 THR HA H 4.295 0.004 1 27 14 14 THR HB H 4.160 0.008 1 28 14 14 THR HG2 H 1.169 0.001 1 29 15 15 GLY H H 8.395 0.000 1 30 16 16 TYR H H 8.025 0.001 1 31 16 16 TYR HA H 4.526 0.007 1 32 16 16 TYR HD1 H 7.078 0.001 3 33 16 16 TYR HD2 H 7.078 0.001 3 34 16 16 TYR HE1 H 6.812 0.003 3 35 16 16 TYR HE2 H 6.812 0.003 3 36 17 17 LEU H H 8.103 0.001 1 37 17 17 LEU HA H 4.312 0.003 1 38 17 17 LEU HG H 1.439 0.005 1 39 18 18 SER H H 8.166 0.001 1 40 18 18 SER HA H 4.427 0.001 1 41 19 19 ILE H H 8.126 0.001 1 42 19 19 ILE HA H 4.218 0.003 1 43 19 19 ILE HB H 1.882 0.004 1 44 19 19 ILE HG2 H 0.876 0.002 1 45 19 19 ILE HD1 H 0.841 0.001 1 46 20 20 VAL H H 7.676 0.002 1 47 20 20 VAL HA H 4.025 0.003 1 48 20 20 VAL HB H 2.034 0.004 1 stop_ save_