data_17459 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Identification of the Binding Site for Acidic Phospholipids on the PH Domain of Dynamin: Implications for Stimulation of GTPase Activity ; _BMRB_accession_number 17459 _BMRB_flat_file_name bmr17459.str _Entry_type original _Submission_date 2011-02-11 _Accession_date 2011-02-11 _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 Zheng Jie . . 2 Cahill Sean M. . 3 Lemmon Mark A. . 4 Fushman David . . 5 Schlessinger Joseph . . 6 Cowburn David . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count binding_constants 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-06-06 original author . stop_ _Original_release_date 2012-06-06 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Identification of the Binding Site for Acidic Phospholipids on the PH Domain of Dynamin: Implications for Stimulation of GTPase Activity' _Citation_status published _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 Zheng Jie . . 2 Cahill Sean M. . 3 Lemmon Mark A. . 4 Fushman David . . 5 Schlessinger Joseph . . 6 Cowburn David . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 255 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 14 _Page_last 21 _Year 1996 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'dynaminPHdomain/IBS complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label dynaminPHdomain $dynaminPHdomain IBS $IBS 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_dynaminPHdomain _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common dynaminPHdomain _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 125 _Mol_residue_sequence ; MKTSGNQDEILVIRKGWLTI NNIGIMKGGSKEYWFVLTAE NLSWYKDDEEKEKKYMLSVD NLKLRDVEKGFMSSKHIFAL FNTEQRNVYKDYRQLELACE TQEEVDSWKASFLRAGVYPE RVGDK ; loop_ _Residue_seq_code _Residue_label 1 MET 2 LYS 3 THR 4 SER 5 GLY 6 ASN 7 GLN 8 ASP 9 GLU 10 ILE 11 LEU 12 VAL 13 ILE 14 ARG 15 LYS 16 GLY 17 TRP 18 LEU 19 THR 20 ILE 21 ASN 22 ASN 23 ILE 24 GLY 25 ILE 26 MET 27 LYS 28 GLY 29 GLY 30 SER 31 LYS 32 GLU 33 TYR 34 TRP 35 PHE 36 VAL 37 LEU 38 THR 39 ALA 40 GLU 41 ASN 42 LEU 43 SER 44 TRP 45 TYR 46 LYS 47 ASP 48 ASP 49 GLU 50 GLU 51 LYS 52 GLU 53 LYS 54 LYS 55 TYR 56 MET 57 LEU 58 SER 59 VAL 60 ASP 61 ASN 62 LEU 63 LYS 64 LEU 65 ARG 66 ASP 67 VAL 68 GLU 69 LYS 70 GLY 71 PHE 72 MET 73 SER 74 SER 75 LYS 76 HIS 77 ILE 78 PHE 79 ALA 80 LEU 81 PHE 82 ASN 83 THR 84 GLU 85 GLN 86 ARG 87 ASN 88 VAL 89 TYR 90 LYS 91 ASP 92 TYR 93 ARG 94 GLN 95 LEU 96 GLU 97 LEU 98 ALA 99 CYS 100 GLU 101 THR 102 GLN 103 GLU 104 GLU 105 VAL 106 ASP 107 SER 108 TRP 109 LYS 110 ALA 111 SER 112 PHE 113 LEU 114 ARG 115 ALA 116 GLY 117 VAL 118 TYR 119 PRO 120 GLU 121 ARG 122 VAL 123 GLY 124 ASP 125 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-07-08 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 1DYN "Crystal Structure At 2.2 Angstroms Resolution Of The Pleckstrin Homology Domain From Human Dynamin" 100.00 125 100.00 100.00 1.79e-85 PDB 2DYN "Dynamin (Pleckstrin Homology Domain) (Dynph)" 96.80 122 100.00 100.00 2.41e-82 PDB 3SNH "Crystal Structure Of Nucleotide-free Human Dynamin1" 99.20 743 99.19 100.00 4.40e-80 PDB 3ZVR "Crystal Structure Of Dynamin" 99.20 772 100.00 100.00 1.22e-80 PDB 3ZYS "Human Dynamin 1 Deltaprd Polymer Stabilized With Gmppcp" 90.40 113 100.00 100.00 4.25e-76 PDB 4UUD "Human Dynamin 1 K44a Superconstricted Polymer Stabilized With Gtp" 99.20 864 100.00 100.00 8.74e-81 PDB 4UUK "Human Dynamin 1 K44a Superconstricted Polymer Stabilized With Gtp Strand 2" 99.20 864 100.00 100.00 8.74e-81 DBJ BAD90284 "mKIAA4093 protein [Mus musculus]" 99.20 871 100.00 100.00 5.88e-81 DBJ BAD92361 "dynamin 1 isoform 2 variant [Homo sapiens]" 99.20 600 100.00 100.00 1.60e-81 DBJ BAG53342 "unnamed protein product [Homo sapiens]" 99.20 396 100.00 100.00 1.14e-84 DBJ BAG58137 "unnamed protein product [Homo sapiens]" 99.20 790 100.00 100.00 1.57e-80 DBJ BAG59018 "unnamed protein product [Homo sapiens]" 99.20 851 100.00 100.00 1.28e-80 EMBL CAA38397 "D100 [Rattus norvegicus]" 99.20 851 100.00 100.00 1.78e-80 GB AAA02803 "dynamin [Homo sapiens]" 99.20 864 100.00 100.00 8.47e-81 GB AAA37318 "dynamin, partial [Mus musculus domesticus]" 99.20 743 98.39 98.39 2.82e-78 GB AAA37323 "dynamin, partial [Mus musculus]" 99.20 612 100.00 100.00 3.96e-81 GB AAH34679 "Dnm1 protein [Mus musculus]" 99.20 867 100.00 100.00 2.78e-80 GB AAH50279 "Dynamin 1 [Homo sapiens]" 99.20 851 100.00 100.00 1.42e-80 PIR B40671 "dynamin, internal form 2, short C-terminal form - human" 99.20 851 100.00 100.00 1.42e-80 PRF 1614348A "dynamin 1 D100 protein" 99.20 851 100.00 100.00 1.78e-80 REF NP_001005336 "dynamin-1 isoform 2 [Homo sapiens]" 99.20 851 100.00 100.00 1.42e-80 REF NP_001070288 "dynamin-1 [Bos taurus]" 99.20 856 99.19 99.19 8.88e-80 REF NP_001124521 "dynamin-1 [Canis lupus familiaris]" 99.20 864 99.19 99.19 4.44e-80 REF NP_001275666 "dynamin-1 isoform 3 [Homo sapiens]" 99.20 851 100.00 100.00 1.67e-80 REF NP_001275667 "dynamin-1 isoform 3 [Homo sapiens]" 99.20 851 100.00 100.00 1.67e-80 SP P21575 "RecName: Full=Dynamin-1; AltName: Full=B-dynamin; AltName: Full=D100; AltName: Full=Dynamin, brain" 99.20 864 100.00 100.00 1.51e-80 SP P39053 "RecName: Full=Dynamin-1" 99.20 867 100.00 100.00 2.78e-80 SP Q05193 "RecName: Full=Dynamin-1" 99.20 864 100.00 100.00 8.74e-81 SP Q08DF4 "RecName: Full=Dynamin-1" 99.20 856 99.19 99.19 8.88e-80 TPG DAA24145 "TPA: dynamin-1 [Bos taurus]" 99.20 856 99.19 99.19 8.88e-80 stop_ save_ ############# # Ligands # ############# save_IBS _Saveframe_category ligand _Mol_type non-polymer _Name_common "IBS (L-ALPHA-GLYCEROPHOSPHO-D-MYO-INOSITOL-4,5-BIS-PHOSPHATE)" _BMRB_code . _PDB_code IBS _Molecular_mass 492.158 _Mol_charge 0 _Mol_paramagnetic no _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Feb 16 15:04:47 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O1 O1 O . 0 . ? O2 O2 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . 0 . ? O5 O5 O . 0 . ? O6 O6 O . 0 . ? P1 P1 P . 0 . ? O11 O11 O . 0 . ? O12 O12 O . 0 . ? C21 C21 C . 0 . ? C24 C24 C . 0 . ? O29 O29 O . 0 . ? C25 C25 C . 0 . ? O26 O26 O . 0 . ? O13 O13 O . 0 . ? P4 P4 P . 0 . ? O41 O41 O . 0 . ? O42 O42 O . 0 . ? O43 O43 O . 0 . ? P5 P5 P . 0 . ? O51 O51 O . 0 . ? O52 O52 O . 0 . ? O53 O53 O . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? HO2 HO2 H . 0 . ? HO3 HO3 H . 0 . ? HO6 HO6 H . 0 . ? H211 H211 H . 0 . ? H212 H212 H . 0 . ? H25 H25 H . 0 . ? H251 H251 H . 0 . ? H26 H26 H . 0 . ? HO13 HO13 H . 0 . ? HO42 HO42 H . 0 . ? HO43 HO43 H . 0 . ? HO52 HO52 H . 0 . ? HO53 HO53 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 C1 C2 ? ? SING C1 C6 ? ? SING C1 O1 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 O2 ? ? SING C2 H2 ? ? SING C3 C4 ? ? SING C3 O3 ? ? SING C3 H3 ? ? SING C4 C5 ? ? SING C4 O4 ? ? SING C4 H4 ? ? SING C5 C6 ? ? SING C5 O5 ? ? SING C5 H5 ? ? SING C6 O6 ? ? SING C6 H6 ? ? SING O1 P1 ? ? SING O2 HO2 ? ? SING O3 HO3 ? ? SING O4 P4 ? ? SING O5 P5 ? ? SING O6 HO6 ? ? DOUB P1 O11 ? ? SING P1 O12 ? ? SING P1 O13 ? ? SING O12 C21 ? ? SING C21 C24 ? ? SING C21 H211 ? ? SING C21 H212 ? ? DOUB C24 O29 ? ? SING C24 C25 ? ? SING C25 O26 ? ? SING C25 H25 ? ? SING C25 H251 ? ? SING O26 H26 ? ? SING O13 HO13 ? ? DOUB P4 O41 ? ? SING P4 O42 ? ? SING P4 O43 ? ? SING O42 HO42 ? ? SING O43 HO43 ? ? DOUB P5 O51 ? ? SING P5 O52 ? ? SING P5 O53 ? ? SING O52 HO52 ? ? SING O53 HO53 ? ? stop_ _Mol_thiol_state 'not present' _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $dynaminPHdomain 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 $dynaminPHdomain 'recombinant technology' . Escherichia coli . ns 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 $dynaminPHdomain 1.9 mM . . [U-15N] $IBS . mM 0 13.74 'natural abundance' dithiothreitol 4 mM . . [U-2H] H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_InsightII _Saveframe_category software _Name InsightII _Version . loop_ _Vendor _Address _Electronic_address 'Biosym Technologies' . . stop_ loop_ _Task 'figure generation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 500 _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.2 . pH pressure 1 . atm temperature 298 . K stop_ save_