data_5501 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Solution Structure of Human Hepcidin, a Peptide-Hormone with Antimicrobial Activity that is Involved in Iron Uptake and Hereditary Hemochromatosis ; _BMRB_accession_number 5501 _BMRB_flat_file_name bmr5501.str _Entry_type original _Submission_date 2002-08-14 _Accession_date 2002-08-14 _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 Hunter H. N. . 2 Fulton D. B. . 3 Ganz T. . . 4 Vogel H. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 112 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2003-02-20 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 5502 'shorter Hepcidin' stop_ _Original_release_date 2002-08-14 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; The Solution Structure of Human Hepcidin, a Peptide Hormone with Antimicrobial Activity that is Involved in Iron Uptake and Hereditary Hemochromatosis ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22241871 _PubMed_ID 12138110 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hunter H. N. . 2 Fulton D. B. . 3 Ganz T. . . 4 Vogel H. J. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 277 _Journal_issue 40 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 37597 _Page_last 37603 _Year 2002 _Details . loop_ _Keyword beta-sheet 'hairpin loop' strand-loop-strand stop_ save_ ################################## # Molecular system description # ################################## save_system_Hepcidin _Saveframe_category molecular_system _Mol_system_name Hepcidin _Abbreviation_common hepicidin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Hepcidin-25 $Hepcidin_25 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Hepcidin_25 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common hepicidin _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; DTHFPICIFCCGCCHRSKCG MCCKT ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 60 ASP 2 61 THR 3 62 HIS 4 65 PHE 5 66 PRO 6 67 ILE 7 68 CYS 8 69 ILE 9 70 PHE 10 71 CYS 11 72 CYS 12 73 GLY 13 74 CYS 14 75 CYS 15 76 HIS 16 77 ARG 17 78 SER 18 79 LYS 19 80 CYS 20 81 GLY 21 82 MET 22 83 CYS 23 84 CYS 24 85 LYS 25 86 THR stop_ _Sequence_homology_query_date 2008-08-19 _Sequence_homology_query_revised_last_date 2008-08-19 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 5502 hepicidin 80.00 20 100.00 100.00 8.75e-02 PDB 1M4E 'Solution Structure Of Hepcidin-20' 80.00 20 100.00 100.00 8.75e-02 PDB 1M4F 'Solution Structure Of Hepcidin-25' 100.00 25 100.00 100.00 2.88e-05 EMBL CAC09419 'liver-expressed antimicrobial peptide [Homo sapiens]' 100.00 84 100.00 100.00 1.19e-06 GenBank AAG23966 'prohepcidin [Homo sapiens]' 100.00 84 100.00 100.00 1.19e-06 GenBank AAH20612 'Hepcidin antimicrobial peptide [Homo sapiens]' 100.00 84 100.00 100.00 1.19e-06 GenBank AAK14912 'putative liver tumor regressor [Homo sapiens]' 100.00 84 100.00 100.00 1.16e-06 GenBank AAQ89032 'LEAP-1 [Homo sapiens]' 100.00 84 100.00 100.00 1.19e-06 GenBank ABF47098 'hepcidin antimicrobial peptide [Homo sapiens]' 100.00 84 100.00 100.00 1.19e-06 REF NP_001103163 'hepcidin antimicrobial peptide [Pan troglodytes]' 100.00 84 100.00 100.00 1.05e-06 REF NP_066998 'hepcidin antimicrobial peptide preproprotein [Homo sapiens]' 100.00 84 100.00 100.00 1.19e-06 SWISS-PROT P81172 ; Hepcidin precursor (Liver-expressed antimicrobial peptide) (LEAP-1) (Putative liver tumor regressor) (PLTR) [Contains: Hepcidin-25 (Hepc25); Hepcidin-20 (Hepc20)] ; 100.00 84 100.00 100.00 1.19e-06 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Hepcidin_25 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 $Hepcidin_25 '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 $Hepcidin_25 1.6 mM [U-15N]-Gly,Phe,Ile 'phosphate buffer' 40 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 2.6 loop_ _Task collection stop_ _Details Bruker save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Task 'structure solution' stop_ _Details 'Brunger et al' save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 3.4 loop_ _Task processing stop_ _Details 'Delaglio, F.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_Diffusion_experiment_3 _Saveframe_category NMR_applied_experiment _Experiment_name 'Diffusion experiment' _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.5 0.2 n/a pressure 1 . atm temperature 298 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 0.0 internal direct . . . 1.0 dioxane H 1 'methylene protons' ppm 3.75 internal . cylindrical . parallel . 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D TOCSY' 'Diffusion experiment' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name Hepcidin-25 _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 ASP HA H 4.626 0.002 1 2 . 1 ASP HB2 H 3.122 0.002 2 3 . 1 ASP HB3 H 3.034 0.002 2 4 . 2 THR HA H 4.234 0.002 1 5 . 2 THR HB H 4.177 0.002 1 6 . 2 THR HG2 H 1.132 0.002 1 7 . 3 HIS HA H 4.631 0.002 1 8 . 3 HIS HB2 H 3.117 0.002 2 9 . 3 HIS HB3 H 3.036 0.002 2 10 . 3 HIS HD2 H 7.192 0.002 1 11 . 3 HIS HE1 H 8.552 0.002 1 12 . 4 PHE HA H 4.906 0.002 1 13 . 4 PHE HB2 H 3.186 0.002 2 14 . 4 PHE HB3 H 2.880 0.002 2 15 . 4 PHE HD1 H 7.293 0.002 1 16 . 4 PHE HE1 H 7.356 0.002 3 17 . 4 PHE HZ H 7.332 0.002 1 18 . 4 PHE HE2 H 7.369 0.002 3 19 . 4 PHE HD2 H 7.293 0.002 1 20 . 5 PRO HA H 4.501 0.002 1 21 . 5 PRO HB2 H 2.202 0.002 2 22 . 5 PRO HB3 H 2.038 0.002 2 23 . 5 PRO HG2 H 1.983 0.002 2 24 . 5 PRO HG3 H 1.885 0.002 2 25 . 5 PRO HD2 H 3.769 0.002 2 26 . 5 PRO HD3 H 3.612 0.002 2 27 . 6 ILE HA H 4.251 0.002 1 28 . 6 ILE HB H 1.894 0.002 1 29 . 6 ILE HG12 H 1.631 0.002 2 30 . 6 ILE HG13 H 1.251 0.002 2 31 . 6 ILE HD1 H 0.908 0.002 1 32 . 6 ILE HG2 H 0.946 0.002 1 33 . 7 CYS HA H 5.478 0.002 1 34 . 7 CYS HB2 H 2.625 0.002 2 35 . 7 CYS HB3 H 3.154 0.002 2 36 . 8 ILE HA H 4.596 0.002 1 37 . 8 ILE HB H 1.862 0.002 1 38 . 8 ILE HG12 H 1.358 0.002 2 39 . 8 ILE HG13 H 1.136 0.002 2 40 . 8 ILE HD1 H 0.861 0.002 1 41 . 8 ILE HG2 H 0.905 0.002 1 42 . 9 PHE HA H 4.779 0.002 1 43 . 9 PHE HB2 H 3.001 0.002 1 44 . 9 PHE HB3 H 3.001 0.002 1 45 . 9 PHE HD1 H 7.092 0.002 1 46 . 9 PHE HE1 H 7.279 0.002 1 47 . 9 PHE HZ H 7.214 0.002 1 48 . 9 PHE HE2 H 7.279 0.002 1 49 . 9 PHE HD2 H 7.092 0.002 1 50 . 10 CYS HA H 4.829 0.002 1 51 . 10 CYS HB2 H 3.453 0.002 2 52 . 10 CYS HB3 H 3.053 0.002 2 53 . 11 CYS HA H 4.918 0.002 1 54 . 11 CYS HB2 H 3.008 0.002 2 55 . 11 CYS HB3 H 2.946 0.002 2 56 . 12 GLY HA2 H 4.060 0.002 1 57 . 12 GLY HA3 H 4.060 0.002 1 58 . 13 CYS HA H 4.928 0.002 1 59 . 13 CYS HB2 H 3.388 0.002 2 60 . 13 CYS HB3 H 3.241 0.002 2 61 . 14 CYS HB2 H 3.240 0.002 2 62 . 14 CYS HB3 H 3.114 0.002 2 63 . 15 HIS HD2 H 7.209 0.002 1 64 . 15 HIS HE1 H 8.588 0.002 1 65 . 16 ARG HA H 4.520 0.002 1 66 . 16 ARG HB2 H 1.849 0.002 2 67 . 16 ARG HB3 H 1.885 0.002 2 68 . 16 ARG HG2 H 1.678 0.002 2 69 . 16 ARG HG3 H 1.616 0.002 2 70 . 16 ARG HD2 H 3.169 0.002 1 71 . 16 ARG HD3 H 3.169 0.002 1 72 . 17 SER HA H 4.365 0.002 1 73 . 17 SER HB2 H 3.924 0.002 1 74 . 17 SER HB3 H 3.924 0.002 1 75 . 18 LYS HA H 4.452 0.002 1 76 . 18 LYS HB2 H 1.937 0.002 1 77 . 18 LYS HB3 H 1.937 0.002 1 78 . 18 LYS HG2 H 1.852 0.002 2 79 . 18 LYS HG3 H 1.496 0.002 2 80 . 18 LYS HD2 H 1.852 0.002 1 81 . 18 LYS HD3 H 1.852 0.002 1 82 . 18 LYS HE2 H 2.984 0.002 1 83 . 18 LYS HE3 H 2.984 0.002 1 84 . 19 CYS HA H 5.269 0.002 1 85 . 19 CYS HB2 H 3.180 0.002 2 86 . 19 CYS HB3 H 2.750 0.002 2 87 . 20 GLY HA2 H 4.031 0.002 2 88 . 20 GLY HA3 H 3.838 0.002 2 89 . 21 MET HA H 4.937 0.002 1 90 . 21 MET HB2 H 1.839 0.002 2 91 . 21 MET HB3 H 2.090 0.002 2 92 . 21 MET HG2 H 2.640 0.002 1 93 . 21 MET HG3 H 2.640 0.002 1 94 . 21 MET HE H 2.088 0.002 1 95 . 22 CYS HA H 5.074 0.002 1 96 . 22 CYS HB2 H 3.114 0.002 2 97 . 22 CYS HB3 H 3.009 0.002 2 98 . 23 CYS HA H 5.523 0.002 1 99 . 23 CYS HB2 H 3.016 0.002 2 100 . 23 CYS HB3 H 2.866 0.002 2 101 . 24 LYS HA H 4.562 0.002 1 102 . 24 LYS HB2 H 1.873 0.002 2 103 . 24 LYS HB3 H 1.659 0.002 2 104 . 24 LYS HG2 H 1.628 0.002 2 105 . 24 LYS HG3 H 1.396 0.002 2 106 . 24 LYS HD2 H 1.873 0.002 2 107 . 24 LYS HD3 H 1.771 0.002 2 108 . 24 LYS HE2 H 2.936 0.002 1 109 . 24 LYS HE3 H 2.936 0.002 1 110 . 25 THR HA H 4.236 0.002 1 111 . 25 THR HB H 4.027 0.002 1 112 . 25 THR HG2 H 1.071 0.002 1 stop_ save_