data_11004 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Structure of Ebola fusion peptide in SDS micelles at pH 7 ; _BMRB_accession_number 11004 _BMRB_flat_file_name bmr11004.str _Entry_type new _Submission_date 2007-07-05 _Accession_date 2007-07-11 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Freitas Monica 'Santos de' . 2 Gaspar Luciane Pinto . 3 Lorenzoni Marcos . . 4 Almeida Fabio Ceneviva . 5 Tinoco Luzineide Wanderley . 6 Almeida Marcius Silva . 7 Maia Lenize Fernandes . 8 Degreve Leo . . 9 Valente 'Ana Paula' . . 10 Silva Jerson Lima . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 75 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-25 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_title ; Structure of the Ebola fusion peptide in a membrane-mimetic environment and the interaction with lipid rafts ; _Citation_status published _Citation_type journal _PubMed_ID 17545161 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Freitas Monica 'Santos de' . 2 Gaspar Luciane Pinto . 3 Lorenzoni Marcos . . 4 Almeida Fabio Ceneviva . 5 Tinoco Luzineide Wanderley . 6 Almeida Marcius Silva . 7 Maia Lenize Fernandes . 8 Degreve Leo . . 9 Valente 'Ana Paula' . . 10 Silva Jerson Lima . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 282 _Journal_issue 37 _Page_first 27306 _Page_last 27314 _Year 2007 save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Ebola fusion peptide' loop_ _Mol_system_component_name _Mol_label 'fusion peptide' $entity stop_ _System_physical_state native _System_oligomer_state ? _System_paramagnetic no loop_ _Biological_function 'Membrane fusion' stop_ save_ ######################## # Monomeric polymers # ######################## save_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 1576.854 _Mol_thiol_state 'not present' ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence GAAIGLAWIPYFGPAA loop_ _Residue_seq_code _Residue_label 1 GLY 2 ALA 3 ALA 4 ILE 5 GLY 6 LEU 7 ALA 8 TRP 9 ILE 10 PRO 11 TYR 12 PHE 13 GLY 14 PRO 15 ALA 16 ALA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-04-26 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 17638 Ebolavirus_Fusion_Loop_pH_5.5 100.00 54 100.00 100.00 4.35e-01 BMRB 17639 Ebolavirus_Fusion_Loop_pH_7.0 100.00 54 100.00 100.00 4.35e-01 BMRB 19383 entity 100.00 54 100.00 100.00 4.44e-01 PDB 2LCY "Nmr Structure Of The Complete Internal Fusion Loop From Ebolavirus Gp2 At Ph 5.5" 100.00 54 100.00 100.00 4.35e-01 PDB 2LCZ "Nmr Structure Of The Complete Internal Fusion Loop From Ebolavirus Gp2 At Ph 7.0" 100.00 54 100.00 100.00 4.35e-01 PDB 2MB1 "Nmr Structure Of The Complete Internal Fusion Loop Mutant I544a From Ebolavirus Gp2 At Ph 5.5" 100.00 54 100.00 100.00 4.44e-01 PDB 2RLJ "Nmr Structure Of Ebola Fusion Peptide In Sds Micelles At Ph 7" 100.00 16 100.00 100.00 1.34e+00 PDB 3CSY "Crystal Structure Of The Trimeric Prefusion Ebola Virus Glycoprotein In Complex With A Neutralizing Antibody From A Human Survi" 100.00 131 100.00 100.00 2.76e-01 GB AAA96744 "envelope glycoprotein [Zaire ebolavirus]" 100.00 676 100.00 100.00 5.94e-02 GB AAB37093 "virion spike glycoprotein [Tai Forest ebolavirus]" 100.00 676 100.00 100.00 9.29e-02 GB AAB37095 "virion spike glycoprotein [Zaire ebolavirus]" 100.00 676 100.00 100.00 7.54e-02 GB AAB81004 "glycoprotein [Zaire ebolavirus]" 100.00 676 100.00 100.00 6.00e-02 GB AAC54887 "virion spike glycoprotein [Zaire ebolavirus]" 100.00 676 100.00 100.00 6.00e-02 REF NP_066246 "spike glycoprotein [Zaire ebolavirus]" 100.00 676 100.00 100.00 6.00e-02 REF YP_003815426 "spike glycoprotein [Tai Forest ebolavirus]" 100.00 676 100.00 100.00 9.11e-02 REF YP_003815435 "spike glycoprotein [Bundibugyo virus]" 100.00 676 100.00 100.00 4.73e-02 SP O11457 "RecName: Full=Envelope glycoprotein; AltName: Full=GP1,2; Short=GP; Contains: RecName: Full=GP1; Contains: RecName: Full=GP2; C" 100.00 676 100.00 100.00 6.72e-02 SP P87666 "RecName: Full=Envelope glycoprotein; AltName: Full=GP1,2; Short=GP; Contains: RecName: Full=GP1; Contains: RecName: Full=GP2; C" 100.00 676 100.00 100.00 7.54e-02 SP P87671 "RecName: Full=Envelope glycoprotein; AltName: Full=GP1,2; Short=GP; Contains: RecName: Full=GP1; Contains: RecName: Full=GP2; C" 100.00 676 100.00 100.00 6.00e-02 SP Q05320 "RecName: Full=Envelope glycoprotein; AltName: Full=GP1,2; Short=GP; Contains: RecName: Full=GP1; Contains: RecName: Full=GP2; C" 100.00 676 100.00 100.00 6.00e-02 SP Q66810 "RecName: Full=Envelope glycoprotein; AltName: Full=GP1,2; Short=GP; Contains: RecName: Full=GP1; Contains: RecName: Full=GP2; C" 100.00 676 100.00 100.00 9.29e-02 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 'Ebola virus' 205488 Viruses . 'Ebola-like viruses' 'Ebola virus sp.' 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 'chemical synthesis' . . . . ? 'The Ebola fusion domain was purchased from Genemed' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelle loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 2 mM 'natural abundance' SDS 400 mM 'natural abundance' 'potassium phosphate' 15 mM 'natural abundance' D2O 10 % . H2O 90 % . stop_ save_ ############################ # Computer software used # ############################ save_NMRDraw _Saveframe_category software _Name NMRDraw loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ save_ save_NMRView _Saveframe_category software _Name NMRView loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ save_ save_CNSSOLVE _Saveframe_category software _Name CNSSOLVE loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ save_ save_ProcheckNMR _Saveframe_category software _Name ProcheckNMR loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task 'data analysis' stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 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 loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7 . pH pressure 1 . atm 'ionic strength' 0.015 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference 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 ? ? ? 1.0 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts 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 'fusion peptide' 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 GLY HA2 H 4.005 . 2 2 1 1 GLY HA3 H 3.936 . 2 3 2 2 ALA H H 8.532 . 1 4 2 2 ALA HA H 4.409 . 1 5 2 2 ALA HB H 1.477 . 1 6 3 3 ALA H H 8.316 . 1 7 3 3 ALA HA H 4.392 . 1 8 3 3 ALA HB H 1.472 . 1 9 4 4 ILE H H 7.733 . 1 10 4 4 ILE HA H 4.190 . 1 11 4 4 ILE HB H 1.982 . 1 12 4 4 ILE HG12 H 1.593 . 1 13 4 4 ILE HD1 H 1.011 . 1 14 4 4 ILE HG2 H 1.270 . 1 15 5 5 GLY H H 7.961 . 1 16 5 5 GLY HA2 H 4.064 . 2 17 5 5 GLY HA3 H 3.988 . 2 18 6 6 LEU H H 7.868 . 1 19 6 6 LEU HA H 4.298 . 1 20 6 6 LEU HB2 H 1.672 . 2 21 6 6 LEU HB3 H 1.600 . 2 22 6 6 LEU HG H 1.500 . 1 23 6 6 LEU HD1 H 0.899 . 2 24 7 7 ALA H H 8.153 . 1 25 7 7 ALA HA H 4.184 . 1 26 7 7 ALA HB H 1.437 . 1 27 8 8 TRP H H 7.415 . 1 28 8 8 TRP HA H 4.551 . 1 29 8 8 TRP HB2 H 3.512 . 2 30 8 8 TRP HB3 H 3.299 . 2 31 8 8 TRP HD1 H 7.394 . 1 32 8 8 TRP HE1 H 9.970 . 1 33 8 8 TRP HZ2 H 7.422 . 1 34 8 8 TRP HH2 H 7.137 . 1 35 8 8 TRP HZ3 H 7.039 . 1 36 8 8 TRP HE3 H 7.549 . 1 37 9 9 ILE H H 7.179 . 1 38 9 9 ILE HA H 4.068 . 1 39 9 9 ILE HB H 1.833 . 1 40 9 9 ILE HG12 H 0.956 . 1 41 9 9 ILE HG13 H 0.887 . 1 42 9 9 ILE HD1 H 0.622 . 1 43 9 9 ILE HG2 H 0.773 . 1 44 10 10 PRO HA H 4.372 . 1 45 10 10 PRO HB2 H 2.464 . 2 46 10 10 PRO HB3 H 2.267 . 2 47 10 10 PRO HG2 H 1.997 . 2 48 10 10 PRO HG3 H 1.789 . 2 49 10 10 PRO HD2 H 3.986 . 2 50 10 10 PRO HD3 H 3.583 . 2 51 11 11 TYR H H 7.562 . 1 52 11 11 TYR HA H 4.208 . 1 53 11 11 TYR HB2 H 2.801 . 2 54 11 11 TYR HB3 H 2.826 . 2 55 11 11 TYR HD1 H 6.776 . 3 56 12 12 PHE H H 7.992 . 1 57 12 12 PHE HA H 4.647 . 1 58 12 12 PHE HB2 H 2.924 . 2 59 12 12 PHE HB3 H 3.309 . 2 60 12 12 PHE HD1 H 7.373 . 3 61 12 12 PHE HE1 H 7.245 . 3 62 13 13 GLY H H 7.735 . 1 63 13 13 GLY HA2 H 4.079 . 2 64 14 14 PRO HA H 4.490 . 1 65 14 14 PRO HB2 H 2.349 . 2 66 14 14 PRO HB3 H 2.061 . 2 67 14 14 PRO HG2 H 1.999 . 2 68 14 14 PRO HD2 H 4.082 . 2 69 14 14 PRO HD3 H 3.647 . 2 70 15 15 ALA H H 8.386 . 1 71 15 15 ALA HA H 4.362 . 1 72 15 15 ALA HB H 1.437 . 1 73 16 16 ALA H H 7.901 . 1 74 16 16 ALA HA H 4.132 . 1 75 16 16 ALA HB H 1.360 . 1 stop_ save_