data_10062 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Backbone 1H and 15N Chemical Shift Assignments for Nedd8 ; _BMRB_accession_number 10062 _BMRB_flat_file_name bmr10062.str _Entry_type original _Submission_date 2006-12-07 _Accession_date 2006-12-07 _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 Sakata Eri . . 2 Yamaguchi Yoshiki . . 3 Miyauchi Yasuhiro . . 4 Iwai Kazuhiro . . 5 Chiba Tomoki . . 6 Saeki Yasusi . . 7 Matsuda Noriyuki . . 8 Tanaka Keiji . . 9 Kato Koichi . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 72 "15N chemical shifts" 72 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2007-03-23 original author . stop_ _Original_release_date 2007-03-23 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Direct interactions between Nedd8 and ubiquitin E2 conjugating enzymes upregulate cullin-based E3 ligase activity ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17206147 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sakata Eri . . 2 Yamaguchi Yoshiki . . 3 Miyauchi Yasuhiro . . 4 Iwai Kazuhiro . . 5 Chiba Tomoki . . 6 Saeki Yasusi . . 7 Matsuda Noriyuki . . 8 Tanaka Keiji . . 9 Kato Koichi . . stop_ _Journal_abbreviation 'Nat. Struct. Mol. Biol.' _Journal_volume 14 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 167 _Page_last 168 _Year 2007 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Nedd8 monomer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Nedd8 monomer' $Nedd8_polypeptide stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state 'protein monomer' _System_paramagnetic no _System_thiol_state unknown _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Nedd8_polypeptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Nedd8 _Molecular_mass . _Mol_thiol_state unknown _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 96 _Mol_residue_sequence ; MGSSHHHHHHSSGLVPRGSH MLIKVKTLTGKEIEIDIEPT DKVERIKERVEEKEGIPPQQ QRLIYSGKQMNDEKTAADYK ILGGSVLHLVLALRGG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -19 MET 2 -18 GLY 3 -17 SER 4 -16 SER 5 -15 HIS 6 -14 HIS 7 -13 HIS 8 -12 HIS 9 -11 HIS 10 -10 HIS 11 -9 SER 12 -8 SER 13 -7 GLY 14 -6 LEU 15 -5 VAL 16 -4 PRO 17 -3 ARG 18 -2 GLY 19 -1 SER 20 0 HIS 21 1 MET 22 2 LEU 23 3 ILE 24 4 LYS 25 5 VAL 26 6 LYS 27 7 THR 28 8 LEU 29 9 THR 30 10 GLY 31 11 LYS 32 12 GLU 33 13 ILE 34 14 GLU 35 15 ILE 36 16 ASP 37 17 ILE 38 18 GLU 39 19 PRO 40 20 THR 41 21 ASP 42 22 LYS 43 23 VAL 44 24 GLU 45 25 ARG 46 26 ILE 47 27 LYS 48 28 GLU 49 29 ARG 50 30 VAL 51 31 GLU 52 32 GLU 53 33 LYS 54 34 GLU 55 35 GLY 56 36 ILE 57 37 PRO 58 38 PRO 59 39 GLN 60 40 GLN 61 41 GLN 62 42 ARG 63 43 LEU 64 44 ILE 65 45 TYR 66 46 SER 67 47 GLY 68 48 LYS 69 49 GLN 70 50 MET 71 51 ASN 72 52 ASP 73 53 GLU 74 54 LYS 75 55 THR 76 56 ALA 77 57 ALA 78 58 ASP 79 59 TYR 80 60 LYS 81 61 ILE 82 62 LEU 83 63 GLY 84 64 GLY 85 65 SER 86 66 VAL 87 67 LEU 88 68 HIS 89 69 LEU 90 70 VAL 91 71 LEU 92 72 ALA 93 73 LEU 94 74 ARG 95 75 GLY 96 76 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-07 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 1NDD "Structure Of Nedd8" 79.17 76 100.00 100.00 6.85e-45 PDB 1R4M "Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex" 79.17 76 100.00 100.00 6.85e-45 PDB 1R4N "Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex With Atp" 79.17 76 100.00 100.00 6.85e-45 PDB 1XT9 "Crystal Structure Of Den1 In Complex With Nedd8" 79.17 76 100.00 100.00 6.85e-45 PDB 2BKR "Nedd8 Nedp1 Complex" 79.17 77 100.00 100.00 6.45e-45 PDB 2KO3 "Nedd8 Solution Structure" 79.17 76 100.00 100.00 6.85e-45 PDB 2NVU "Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A Trapped Ubiquitin-Like Protein Activation Complex" 82.29 81 97.47 97.47 1.54e-45 PDB 4F8C "Structure Of The Cif:nedd8 Complex - Yersinia Pseudotuberculosis Cycle Inhibiting Factor In Complex With Human Nedd8" 79.17 88 100.00 100.00 4.94e-44 PDB 4FBJ "Structure Of The Cif:nedd8 Complex - Photorhabdus Luminescens Cycle Inhibiting Factor In Complex With Human Nedd8" 79.17 88 100.00 100.00 4.94e-44 PDB 4HCP "Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Nedd8" 81.25 78 97.44 98.72 3.06e-45 PDB 4P5O "Structure Of An Rbx1-ubc12~nedd8-cul1-dcn1 Complex: A Ring-e3- E2~ubiquitin-like Protein-substrate Intermediate Trapped In Acti" 82.29 81 97.47 97.47 1.54e-45 DBJ BAA01719 "ubiquitin like protein [Mus musculus]" 79.17 81 100.00 100.00 1.25e-44 DBJ BAA04889 "ubiquitin-like protein [Homo sapiens]" 79.17 81 100.00 100.00 1.18e-44 DBJ BAE27394 "unnamed protein product [Mus musculus]" 79.17 81 100.00 100.00 1.25e-44 DBJ BAE27660 "unnamed protein product [Mus musculus]" 79.17 81 100.00 100.00 1.25e-44 DBJ BAE34759 "unnamed protein product [Mus musculus]" 65.63 68 100.00 100.00 1.54e-35 EMBL CAF89342 "unnamed protein product, partial [Tetraodon nigroviridis]" 72.92 70 98.57 98.57 9.28e-40 EMBL CAF97715 "unnamed protein product, partial [Tetraodon nigroviridis]" 79.17 77 98.68 98.68 5.99e-44 EMBL CAG05755 "unnamed protein product [Tetraodon nigroviridis]" 79.17 86 98.68 98.68 1.98e-43 EMBL CAG28590 "NEDD8 [Homo sapiens]" 79.17 81 98.68 100.00 1.46e-44 EMBL CAJ82981 "neural precursor cell expressed, developmentally down-regulated 8 [Xenopus (Silurana) tropicalis]" 79.17 77 98.68 98.68 6.40e-44 GB AAC64189 "ubiquitin-like protein [Rattus norvegicus]" 79.17 81 100.00 100.00 1.25e-44 GB AAF73911 "NEDD8 [Bos taurus]" 79.17 81 100.00 100.00 1.18e-44 GB AAH04625 "Neural precursor cell expressed, developmentally down-regulated gene 8 [Mus musculus]" 79.17 81 100.00 100.00 1.25e-44 GB AAH55645 "Neural precursor cell expressed, developmentally down-regulated 8 [Danio rerio]" 79.17 89 98.68 98.68 1.19e-43 GB AAH76245 "Neural precursor cell expressed, developmentally down-regulated 8, like [Danio rerio]" 79.17 80 98.68 98.68 8.64e-44 REF NP_001002557 "neural precursor cell expressed, developmentally down-regulated 8, like [Danio rerio]" 79.17 80 98.68 98.68 8.64e-44 REF NP_001016973 "neural precursor cell expressed, developmentally down-regulated 8 [Xenopus (Silurana) tropicalis]" 79.17 77 98.68 98.68 6.40e-44 REF NP_001075681 "NEDD8 precursor [Oryctolagus cuniculus]" 79.17 81 100.00 100.00 1.18e-44 REF NP_001154087 "neural precursor cell expressed, developmentally down-regulated 8 [Oncorhynchus mykiss]" 79.17 88 98.68 98.68 8.06e-44 REF NP_001187300 "neural precursor cell expressed, developmentally down-regulated 8 [Ictalurus punctatus]" 79.17 89 97.37 97.37 1.86e-42 SP P29595 "RecName: Full=NEDD8; AltName: Full=Neddylin; AltName: Full=Neural precursor cell expressed developmentally down-regulated prote" 79.17 81 100.00 100.00 1.25e-44 SP P61282 "RecName: Full=NEDD8; AltName: Full=Neddylin; AltName: Full=Ubiquitin-like protein Nedd8; Flags: Precursor" 79.17 81 100.00 100.00 1.18e-44 SP Q15843 "RecName: Full=NEDD8; AltName: Full=Neddylin; AltName: Full=Neural precursor cell expressed developmentally down-regulated prote" 79.17 81 100.00 100.00 1.18e-44 SP Q4PLJ0 "RecName: Full=NEDD8; AltName: Full=Neddylin; AltName: Full=Ubiquitin-like protein Nedd8; Flags: Precursor" 79.17 81 100.00 100.00 1.18e-44 SP Q71UE8 "RecName: Full=NEDD8; AltName: Full=Neddylin; AltName: Full=Ubiquitin-like protein NEDD8; Flags: Precursor" 79.17 81 100.00 100.00 1.25e-44 TPG DAA25711 "TPA: NEDD8 precursor [Bos taurus]" 78.13 75 100.00 100.00 4.01e-44 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Fraction $Nedd8_polypeptide human 9606 Eukaryota Metazoa Homo sapiens no 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 $Nedd8_polypeptide 'recombinant technology' . . . . . 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 $Nedd8_polypeptide 1 mM '[U-98% 13C; U-98% 15N]' MES 50 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX500 _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-15N_HSQC _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N HSQC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_HNCA _Saveframe_category NMR_applied_experiment _Experiment_name HNCA _BMRB_pulse_sequence_accession_number . _Details . save_ save_HN(CO)CA _Saveframe_category NMR_applied_experiment _Experiment_name HN(CO)CA _BMRB_pulse_sequence_accession_number . _Details . save_ save_HNCO _Saveframe_category NMR_applied_experiment _Experiment_name HNCO _BMRB_pulse_sequence_accession_number . _Details . save_ save_HN(CA)CO _Saveframe_category NMR_applied_experiment _Experiment_name HN(CA)CO _BMRB_pulse_sequence_accession_number . _Details . save_ save_CBCA(CO)NH _Saveframe_category NMR_applied_experiment _Experiment_name CBCA(CO)NH _BMRB_pulse_sequence_accession_number . _Details . save_ save_CBCANH _Saveframe_category NMR_applied_experiment _Experiment_name CBCANH _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.0 0.1 pH temperature 303 1 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 DSS H 1 'methyl protons' ppm 0.05 external indirect . . . 1.0 DSS N 15 'methyl protons' ppm 0.5 external indirect . . . 0.101329118 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_Nedd8 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '1H-15N HSQC' HNCA HN(CO)CA HNCO HN(CA)CO CBCA(CO)NH CBCANH stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_condition_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Nedd8 monomer' _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 21 MET H H 9.18 0.05 1 2 1 21 MET N N 122.0 0.5 1 3 2 22 LEU H H 8.50 0.05 1 4 2 22 LEU N N 124.9 0.5 1 5 3 23 ILE H H 9.00 0.05 1 6 3 23 ILE N N 121.3 0.5 1 7 4 24 LYS H H 8.55 0.05 1 8 4 24 LYS N N 119.4 0.5 1 9 5 25 VAL H H 9.04 0.05 1 10 5 25 VAL N N 122.5 0.5 1 11 6 26 LYS H H 9.03 0.05 1 12 6 26 LYS N N 129.2 0.5 1 13 7 27 THR H H 8.85 0.05 1 14 7 27 THR N N 117.8 0.5 1 15 8 28 LEU H H 9.06 0.05 1 16 8 28 LEU N N 122.0 0.5 1 17 9 29 THR H H 7.66 0.05 1 18 9 29 THR N N 106.9 0.5 1 19 10 30 GLY H H 7.90 0.05 1 20 10 30 GLY N N 110.6 0.5 1 21 11 31 LYS H H 7.23 0.05 1 22 11 31 LYS N N 122.9 0.5 1 23 12 32 GLU H H 8.62 0.05 1 24 12 32 GLU N N 125.0 0.5 1 25 13 33 ILE H H 9.12 0.05 1 26 13 33 ILE N N 124.9 0.5 1 27 14 34 GLU H H 8.68 0.05 1 28 14 34 GLU N N 127.1 0.5 1 29 15 35 ILE H H 8.73 0.05 1 30 15 35 ILE N N 123.3 0.5 1 31 16 36 ASP H H 8.27 0.05 1 32 16 36 ASP N N 126.1 0.5 1 33 17 37 ILE H H 8.92 0.05 1 34 17 37 ILE N N 118.7 0.5 1 35 18 38 GLU H H 8.37 0.05 1 36 18 38 GLU N N 120.0 0.5 1 37 20 40 THR H H 6.75 0.05 1 38 20 40 THR N N 99.8 0.5 1 39 21 41 ASP H H 7.83 0.05 1 40 21 41 ASP N N 124.1 0.5 1 41 22 42 LYS H H 8.52 0.05 1 42 22 42 LYS N N 120.7 0.5 1 43 23 43 VAL H H 9.23 0.05 1 44 23 43 VAL N N 126.6 0.5 1 45 24 44 GLU H H 8.61 0.05 1 46 24 44 GLU N N 118.9 0.5 1 47 25 45 ARG H H 7.44 0.05 1 48 25 45 ARG N N 119.7 0.5 1 49 26 46 ILE H H 7.81 0.05 1 50 26 46 ILE N N 121.3 0.5 1 51 27 47 LYS H H 7.78 0.05 1 52 27 47 LYS N N 117.9 0.5 1 53 28 48 GLU H H 7.84 0.05 1 54 28 48 GLU N N 121.8 0.5 1 55 29 49 ARG H H 8.10 0.05 1 56 29 49 ARG N N 121.3 0.5 1 57 30 50 VAL H H 8.31 0.05 1 58 30 50 VAL N N 122.1 0.5 1 59 32 52 GLU H H 7.95 0.05 1 60 32 52 GLU N N 120.1 0.5 1 61 33 53 LYS H H 7.30 0.05 1 62 33 53 LYS N N 116.0 0.5 1 63 34 54 GLU H H 8.66 0.05 1 64 34 54 GLU N N 116.3 0.5 1 65 35 55 GLY H H 8.64 0.05 1 66 35 55 GLY N N 109.7 0.5 1 67 36 56 ILE H H 6.27 0.05 1 68 36 56 ILE N N 121.1 0.5 1 69 39 59 GLN H H 8.90 0.05 1 70 39 59 GLN N N 115.6 0.5 1 71 40 60 GLN H H 7.92 0.05 1 72 40 60 GLN N N 117.5 0.5 1 73 41 61 GLN H H 7.62 0.05 1 74 41 61 GLN N N 119.1 0.5 1 75 42 62 ARG H H 8.67 0.05 1 76 42 62 ARG N N 123.6 0.5 1 77 43 63 LEU H H 8.49 0.05 1 78 43 63 LEU N N 124.0 0.5 1 79 44 64 ILE H H 9.23 0.05 1 80 44 64 ILE N N 124.6 0.5 1 81 45 65 TYR H H 8.78 0.05 1 82 45 65 TYR N N 126.4 0.5 1 83 46 66 SER H H 9.07 0.05 1 84 46 66 SER N N 126.8 0.5 1 85 47 67 GLY H H 8.38 0.05 1 86 47 67 GLY N N 104.5 0.5 1 87 48 68 LYS H H 7.80 0.05 1 88 48 68 LYS N N 121.9 0.5 1 89 49 69 GLN H H 8.78 0.05 1 90 49 69 GLN N N 124.5 0.5 1 91 50 70 MET H H 8.62 0.05 1 92 50 70 MET N N 126.5 0.5 1 93 51 71 ASN H H 8.60 0.05 1 94 51 71 ASN N N 123.9 0.5 1 95 52 72 ASP H H 8.50 0.05 1 96 52 72 ASP N N 124.3 0.5 1 97 53 73 GLU H H 8.77 0.05 1 98 53 73 GLU N N 115.2 0.5 1 99 54 74 LYS H H 7.56 0.05 1 100 54 74 LYS N N 121.4 0.5 1 101 55 75 THR H H 9.19 0.05 1 102 55 75 THR N N 109.5 0.5 1 103 56 76 ALA H H 8.33 0.05 1 104 56 76 ALA N N 122.2 0.5 1 105 57 77 ALA H H 8.45 0.05 1 106 57 77 ALA N N 120.8 0.5 1 107 58 78 ASP H H 7.93 0.05 1 108 58 78 ASP N N 121.4 0.5 1 109 59 79 TYR H H 7.37 0.05 1 110 59 79 TYR N N 116.9 0.5 1 111 60 80 LYS H H 8.00 0.05 1 112 60 80 LYS N N 116.5 0.5 1 113 61 81 ILE H H 7.11 0.05 1 114 61 81 ILE N N 119.1 0.5 1 115 62 82 LEU H H 7.21 0.05 1 116 62 82 LEU N N 125.8 0.5 1 117 63 83 GLY H H 8.68 0.05 1 118 63 83 GLY N N 108.5 0.5 1 119 64 84 GLY H H 9.27 0.05 1 120 64 84 GLY N N 114.4 0.5 1 121 65 85 SER H H 8.13 0.05 1 122 65 85 SER N N 118.6 0.5 1 123 66 86 VAL H H 8.44 0.05 1 124 66 86 VAL N N 122.1 0.5 1 125 67 87 LEU H H 9.24 0.05 1 126 67 87 LEU N N 128.8 0.5 1 127 68 88 HIS H H 9.14 0.05 1 128 68 88 HIS N N 120.5 0.5 1 129 69 89 LEU H H 8.27 0.05 1 130 69 89 LEU N N 125.3 0.5 1 131 70 90 VAL H H 9.09 0.05 1 132 70 90 VAL N N 126.9 0.5 1 133 71 91 LEU H H 8.18 0.05 1 134 71 91 LEU N N 124.3 0.5 1 135 72 92 ALA H H 8.58 0.05 1 136 72 92 ALA N N 127.7 0.5 1 137 73 93 LEU H H 8.18 0.05 1 138 73 93 LEU N N 122.7 0.5 1 139 74 94 ARG H H 8.39 0.05 1 140 74 94 ARG N N 122.6 0.5 1 141 75 95 GLY H H 8.44 0.05 1 142 75 95 GLY N N 111.9 0.5 1 143 76 96 GLY H H 7.92 0.05 1 144 76 96 GLY N N 116.1 0.5 1 stop_ save_