data_25539 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Three dimensional structure of EPI-X4, a human albumin-derived peptide that regulates innate immunity through the CXCR4/CXCL12 chemotactic axis and antagonizes HIV-1 entry ; _BMRB_accession_number 25539 _BMRB_flat_file_name bmr25539.str _Entry_type original _Submission_date 2015-03-18 _Accession_date 2015-03-18 _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 Perez-Castells Javier . . 2 Canales Angeles . . 3 Jimenez-Barbero Jesus . . 4 Gimenez-Gallego Guillermo . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 100 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-08-29 update BMRB 'update entry citation' 2015-04-27 original author 'original release' stop_ _Original_release_date 2015-04-27 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Discovery and characterization of an endogenous CXCR4 antagonist ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25921529 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zirafi Onofrio . . 2 Kim Kyeong-ae . . 3 Standker Ludger . . 4 Mohr 'Katharina B.' . . 5 Sauter Daniel . . 6 Heigele Anke . . 7 Kluge 'Silvia F.' . . 8 Wiercinska Eliza . . 9 Chudziak Doreeh . . 10 Richter Rudolf . . 11 Moepps Barbara . . 12 Grieschik Peter . . 13 Vas Virg . . 14 Geiger Hartmut . . 15 Lamia Markus . . 16 Weil Tanja . . 17 Burster Timo . . 18 Zgraja Andreas . . 19 Daubeuf Francois . . 20 Forssard Nelly . . 21 Hachet-Haas Muriel . . 22 Heunisch Fabian . . 23 Reichetzeder Christoph . . 24 Galzi Jean-Luc . . 25 Perez-Castells Javier . . 26 Canales Angeles . . 27 Jimenez-Barbero Jesus . . 28 Gimenez-Gallego Guillermo . . 29 Scheneider Marion . . 30 Shorter James . . 31 Telendi Amalio . . 32 Hocher Berthold . . 33 Forssman 'Wolf Georg' . . 34 Kirchhoff Halvard . . 35 Munch Jan . . stop_ _Journal_abbreviation 'Cell Rep.' _Journal_volume 11 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 737 _Page_last 747 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'EPI-X4, a human albumin-derived peptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity $entity 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 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 1833.219 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence ; LVRYTKKVPQVSTPTL ; loop_ _Residue_seq_code _Residue_label 1 LEU 2 VAL 3 ARG 4 TYR 5 THR 6 LYS 7 LYS 8 VAL 9 PRO 10 GLN 11 VAL 12 SER 13 THR 14 PRO 15 THR 16 LEU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity 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 'purified from the natural source' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1 mM solution of albumin derived peptide was prepared in 10 mM Na-phosphate adjusted to a final pH of 7.0' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 1 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . 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 pH 7 . 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 TSP H 1 'methylene protons' ppm 0 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 _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 entity _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 LEU HA H 4.046 0.010 1 2 1 1 LEU HB2 H 1.920 0.030 1 3 1 1 LEU HB3 H 1.920 0.030 1 4 1 1 LEU HD1 H 0.773 0.020 1 5 1 1 LEU HD2 H 0.896 0.020 1 6 2 2 VAL H H 8.400 0.020 1 7 2 2 VAL HA H 4.243 0.030 1 8 2 2 VAL HB H 1.967 0.020 1 9 2 2 VAL HG1 H 0.876 0.020 1 10 2 2 VAL HG2 H 0.876 0.020 1 11 3 3 ARG H H 8.389 0.020 1 12 3 3 ARG HA H 4.292 0.010 1 13 3 3 ARG HB2 H 1.638 0.010 1 14 3 3 ARG HB3 H 1.697 0.010 1 15 3 3 ARG HG2 H 1.446 0.040 1 16 3 3 ARG HG3 H 1.537 0.020 1 17 3 3 ARG HD2 H 3.123 0.020 1 18 3 3 ARG HD3 H 3.123 0.020 1 19 4 4 TYR H H 8.389 0.010 1 20 4 4 TYR HA H 4.640 0.010 1 21 4 4 TYR HB2 H 2.902 0.020 1 22 4 4 TYR HB3 H 3.024 0.020 1 23 4 4 TYR HD1 H 7.096 0.020 1 24 4 4 TYR HD2 H 7.096 0.020 1 25 4 4 TYR HE1 H 6.774 0.020 1 26 4 4 TYR HE2 H 6.774 0.020 1 27 5 5 THR H H 8.181 0.020 1 28 5 5 THR HA H 4.601 0.020 1 29 5 5 THR HB H 4.134 0.020 1 30 5 5 THR HG2 H 1.217 0.010 1 31 6 6 LYS H H 8.449 0.020 1 32 6 6 LYS HA H 4.240 0.020 1 33 6 6 LYS HB2 H 1.700 0.030 1 34 6 6 LYS HB3 H 1.790 0.030 1 35 6 6 LYS HG2 H 1.374 0.020 1 36 6 6 LYS HG3 H 1.374 0.020 1 37 6 6 LYS HD2 H 1.419 0.020 1 38 6 6 LYS HD3 H 1.419 0.020 1 39 6 6 LYS HE2 H 2.972 0.020 1 40 6 6 LYS HE3 H 2.972 0.020 1 41 7 7 LYS H H 8.356 0.020 1 42 7 7 LYS HA H 4.292 0.020 1 43 7 7 LYS HB2 H 1.690 0.030 1 44 7 7 LYS HB3 H 1.755 0.030 1 45 7 7 LYS HG2 H 1.329 0.030 1 46 7 7 LYS HG3 H 1.329 0.030 1 47 7 7 LYS HD2 H 1.398 0.020 1 48 7 7 LYS HD3 H 1.398 0.020 1 49 7 7 LYS HE2 H 2.961 0.020 1 50 7 7 LYS HE3 H 2.961 0.020 1 51 8 8 VAL H H 8.202 0.020 1 52 8 8 VAL HA H 4.405 0.010 1 53 8 8 VAL HB H 2.068 0.010 1 54 8 8 VAL HG1 H 0.906 0.020 1 55 8 8 VAL HG2 H 0.940 0.020 1 56 9 9 PRO HA H 4.358 0.020 1 57 9 9 PRO HB2 H 1.856 0.020 1 58 9 9 PRO HB3 H 2.263 0.020 1 59 9 9 PRO HG2 H 1.951 0.010 1 60 9 9 PRO HG3 H 2.035 0.010 1 61 9 9 PRO HD2 H 3.669 0.010 1 62 9 9 PRO HD3 H 3.833 0.010 1 63 10 10 GLN H H 8.428 0.020 1 64 10 10 GLN HA H 4.319 0.020 1 65 10 10 GLN HB2 H 1.954 0.020 1 66 10 10 GLN HB3 H 2.049 0.020 1 67 10 10 GLN HG2 H 2.353 0.020 1 68 10 10 GLN HG3 H 2.353 0.020 1 69 10 10 GLN HE21 H 7.518 0.020 1 70 10 10 GLN HE22 H 6.871 0.020 1 71 11 11 VAL H H 8.214 0.020 1 72 11 11 VAL HA H 4.170 0.020 1 73 11 11 VAL HB H 2.069 0.020 1 74 11 11 VAL HG1 H 0.910 0.020 1 75 11 11 VAL HG2 H 0.910 0.020 1 76 12 12 SER H H 8.435 0.020 1 77 12 12 SER HA H 4.508 0.020 1 78 12 12 SER HB2 H 3.829 0.020 1 79 12 12 SER HB3 H 3.829 0.020 1 80 13 13 THR H H 8.187 0.020 1 81 13 13 THR HA H 4.263 0.020 1 82 13 13 THR HB H 4.087 0.020 1 83 13 13 THR HG2 H 1.129 0.020 1 84 14 14 PRO HA H 4.465 0.020 1 85 14 14 PRO HB2 H 2.055 0.020 1 86 14 14 PRO HB3 H 2.287 0.020 1 87 14 14 PRO HG2 H 1.910 0.030 1 88 14 14 PRO HG3 H 1.983 0.030 1 89 14 14 PRO HD2 H 3.704 0.030 1 90 14 14 PRO HD3 H 3.826 0.030 1 91 15 15 THR H H 8.265 0.020 1 92 15 15 THR HA H 4.291 0.010 1 93 15 15 THR HB H 4.186 0.010 1 94 15 15 THR HG2 H 1.204 0.020 1 95 16 16 LEU H H 7.904 0.010 1 96 16 16 LEU HA H 4.200 0.010 1 97 16 16 LEU HB2 H 1.556 0.020 1 98 16 16 LEU HB3 H 1.556 0.020 1 99 16 16 LEU HD1 H 0.866 0.020 1 100 16 16 LEU HD2 H 0.866 0.020 1 stop_ save_