data_11358 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assigned chemical shifts of the zf-CW domain with H3 peptide ; _BMRB_accession_number 11358 _BMRB_flat_file_name bmr11358.str _Entry_type original _Submission_date 2010-09-07 _Accession_date 2010-09-07 _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 He F. . . 2 Muto Y. . . 3 Inoue M. . . 4 Kigawa T. . . 5 Shirouzu M. . . 6 Terada T. . . 7 Yokoyama S. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 56 "15N chemical shifts" 56 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-01-04 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 11359 'Assigned chemical shifts of the zf-CW domain with H3 dimethyl K4 peptide' 11360 'Assigned chemical shifts of the zf-CW domain with H3 trimethyl K4 peptide' 11361 'Assigned chemical shifts of the zf-CW domain with H4 trimethyl K20 peptide' 11362 'Assigned chemical shifts of the zf-CW domain in zinc finger CW-type PWWP domain protein 1' stop_ _Original_release_date 2011-01-04 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural insight into the zinc finger CW domain as a histone modification reader.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20826339 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 He Fahu . . 2 Umehara Takashi . . 3 Saito Kohei . . 4 Harada Takushi . . 5 Watanabe Satoru . . 6 Yabuki Takashi . . 7 Kigawa Takanori . . 8 Takahashi Mari . . 9 Kuwasako Kanako . . 10 Tsuda Kengo . . 11 Matsuda Takayoshi . . 12 Aoki Masaaki . . 13 Seki Eiko . . 14 Kobayashi Naohiro . . 15 Guntert Peter . . 16 Yokoyama Shigeyuki . . 17 Muto Yutaka . . stop_ _Journal_abbreviation Structure _Journal_name_full 'Structure (London, England : 1993)' _Journal_volume 18 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1127 _Page_last 1139 _Year 2010 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Zinc finger CW-type PWWP domain protein 1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'zf-CW domain' $entity_1 'ZINC ION' $ZN 'H3 peptide' $entity_3 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_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'zf-CW domain' _Molecular_mass . _Mol_thiol_state 'free and other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 69 _Mol_residue_sequence ; GSSGSSGEISGFGQCLVWVQ CSFPNCGKWRRLCGNIDPSV LPDNWSCDQNTDVQYNRCDI PEETWTGLE ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 SER 3 SER 4 GLY 5 SER 6 SER 7 GLY 8 GLU 9 ILE 10 SER 11 GLY 12 PHE 13 GLY 14 GLN 15 CYS 16 LEU 17 VAL 18 TRP 19 VAL 20 GLN 21 CYS 22 SER 23 PHE 24 PRO 25 ASN 26 CYS 27 GLY 28 LYS 29 TRP 30 ARG 31 ARG 32 LEU 33 CYS 34 GLY 35 ASN 36 ILE 37 ASP 38 PRO 39 SER 40 VAL 41 LEU 42 PRO 43 ASP 44 ASN 45 TRP 46 SER 47 CYS 48 ASP 49 GLN 50 ASN 51 THR 52 ASP 53 VAL 54 GLN 55 TYR 56 ASN 57 ARG 58 CYS 59 ASP 60 ILE 61 PRO 62 GLU 63 GLU 64 THR 65 TRP 66 THR 67 GLY 68 LEU 69 GLU 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 BMRB 11115 "zf-CW domain" 100.00 69 100.00 100.00 1.23e-41 BMRB 11359 "zf-CW domain" 100.00 69 100.00 100.00 1.23e-41 BMRB 11360 "zf-CW domain" 100.00 69 100.00 100.00 1.23e-41 BMRB 11361 "zf-CW domain" 100.00 69 100.00 100.00 1.23e-41 BMRB 11362 "zf-CW domain" 100.00 69 100.00 100.00 1.23e-41 PDB 2E61 "Solution Structure Of The Zf-Cw Domain In Zinc Finger Cw-Type Pwwp Domain Protein 1" 100.00 69 100.00 100.00 1.23e-41 PDB 2RR4 "Complex Structure Of The Zf-Cw Domain And The H3k4me3 Peptide" 100.00 69 100.00 100.00 1.23e-41 DBJ BAA91424 "unnamed protein product [Homo sapiens]" 92.75 403 98.44 98.44 4.76e-38 DBJ BAC04028 "unnamed protein product [Homo sapiens]" 94.20 468 96.92 96.92 1.14e-36 DBJ BAG62414 "unnamed protein product [Homo sapiens]" 92.75 524 98.44 98.44 2.96e-38 DBJ BAG63489 "unnamed protein product [Homo sapiens]" 92.75 609 98.44 98.44 2.07e-38 EMBL CAB66669 "hypothetical protein [Homo sapiens]" 92.75 494 98.44 98.44 2.00e-38 GB AAH02725 "ZCWPW1 protein [Homo sapiens]" 92.75 477 98.44 98.44 2.98e-38 GB AIC60275 "ZCWPW1, partial [synthetic construct]" 92.75 477 98.44 98.44 2.98e-38 GB EAW76538 "zinc finger, CW type with PWWP domain 1, isoform CRA_a [Homo sapiens]" 92.75 649 98.44 98.44 2.10e-38 GB EAW76539 "zinc finger, CW type with PWWP domain 1, isoform CRA_b, partial [Homo sapiens]" 91.30 598 100.00 100.00 1.75e-38 GB EAW76540 "zinc finger, CW type with PWWP domain 1, isoform CRA_c [Homo sapiens]" 92.75 524 98.44 98.44 2.96e-38 REF NP_001244937 "zinc finger CW-type PWWP domain protein 1 isoform 2 [Homo sapiens]" 92.75 524 98.44 98.44 2.96e-38 REF NP_060454 "zinc finger CW-type PWWP domain protein 1 isoform 1 [Homo sapiens]" 92.75 648 98.44 98.44 1.98e-38 REF XP_002803268 "PREDICTED: zinc finger CW-type PWWP domain protein 1-like [Macaca mulatta]" 91.30 577 98.41 98.41 2.12e-37 REF XP_003318693 "PREDICTED: zinc finger CW-type PWWP domain protein 1 isoform X4 [Pan troglodytes]" 91.30 648 100.00 100.00 2.00e-38 REF XP_003318694 "PREDICTED: zinc finger CW-type PWWP domain protein 1 isoform X11 [Pan troglodytes]" 92.75 524 98.44 98.44 3.33e-38 SP Q9H0M4 "RecName: Full=Zinc finger CW-type PWWP domain protein 1" 92.75 648 98.44 98.44 1.98e-38 stop_ save_ save_entity_3 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'H3 peptide' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 20 _Mol_residue_sequence ; ARTKQTARKSTGGKAPRKQL ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 ARG 3 THR 4 LYS 5 GLN 6 THR 7 ALA 8 ARG 9 LYS 10 SER 11 THR 12 GLY 13 GLY 14 LYS 15 ALA 16 PRO 17 ARG 18 LYS 19 GLN 20 LEU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type non-polymer _Name_common "ZN (ZINC ION)" _BMRB_code . _PDB_code ZN _Molecular_mass 65.409 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 16:52:42 2009 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons ZN ZN ZN . 2 . ? stop_ _Mol_thiol_state . _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 $entity_1 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_type _Vector_name $entity_1 'cell free synthesis' 'E. coli' Escherichia coli . plasmid P060116-12 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 20mM d-Tris-HCl(pH {7.0);} 300uM {H3 peptide;} 100mM {NaCl;} 1mM {d-DTT;} 0.02% {NaN3;} 50uM ZnCl2+1mM {IDA;} 10% D2O, 90% H2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 . mM . $entity_3 300 uM . d-Tris-HCl 20 mM 'natural abundance' NaCl 100 mM 'natural abundance' d-DTT 1 mM 'natural abundance' NaN3 0.02 % 'natural abundance' ZnCl2 50 uM 'natural abundance' IDA 1 mM 'natural abundance' H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 2.6 loop_ _Vendor _Address _Electronic_address Bruker . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 20031121 loop_ _Vendor _Address _Electronic_address 'Delaglio, F.' . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version 5.0.4 loop_ _Vendor _Address _Electronic_address 'Johnson, B.A.' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_Kujira _Saveframe_category software _Name Kujira _Version 0.9819 loop_ _Vendor _Address _Electronic_address 'Kobayashi, N.' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, P.' . . stop_ loop_ _Task refinement '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_ ############################# # NMR applied experiments # ############################# save_3D_15N-separated_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N-separated NOESY' _Sample_label $sample_1 save_ save_3D_13C-separated_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 13C-separated NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 120 0.1 mM pH 7.0 0.05 pH pressure 1 0.001 atm temperature 298 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_reference_1 _Saveframe_category chemical_shift_reference _Details ; Chemical shift reference of 1H was based on the proton of water (4.784ppm at 298K) and then those of 15N and 13C were calculated based on their gyromagnetic ratios. ; 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 C 13 'methyl protons' ppm 0.0 . indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.0 . indirect . . . 1.0 DSS N 15 'methyl protons' ppm 0.0 . 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_chemical_shift_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $XWINNMR $NMRPipe $NMRView $Kujira $CYANA stop_ loop_ _Experiment_label '3D 15N-separated NOESY' '3D 13C-separated NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $reference_1 _Mol_system_component_name 'zf-CW domain' _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 7 7 GLY H H 8.361 0.030 1 2 7 7 GLY N N 110.568 0.300 1 3 8 8 GLU H H 8.200 0.030 1 4 8 8 GLU N N 120.685 0.300 1 5 9 9 ILE H H 8.211 0.030 1 6 9 9 ILE N N 121.788 0.300 1 7 10 10 SER H H 8.338 0.030 1 8 10 10 SER N N 119.701 0.300 1 9 11 11 GLY H H 8.307 0.030 1 10 11 11 GLY N N 110.754 0.300 1 11 12 12 PHE H H 8.123 0.030 1 12 12 12 PHE N N 119.884 0.300 1 13 13 13 GLY H H 8.368 0.030 1 14 13 13 GLY N N 110.316 0.300 1 15 14 14 GLN H H 8.188 0.030 1 16 14 14 GLN N N 119.396 0.300 1 17 17 17 VAL H H 8.374 0.030 1 18 17 17 VAL N N 122.650 0.300 1 19 18 18 TRP H H 9.491 0.030 1 20 18 18 TRP N N 130.419 0.300 1 21 19 19 VAL H H 9.391 0.030 1 22 19 19 VAL N N 120.558 0.300 1 23 20 20 GLN H H 7.841 0.030 1 24 20 20 GLN N N 127.344 0.300 1 25 21 21 CYS H H 8.949 0.030 1 26 21 21 CYS N N 129.741 0.300 1 27 22 22 SER H H 8.817 0.030 1 28 22 22 SER N N 122.917 0.300 1 29 23 23 PHE H H 8.944 0.030 1 30 23 23 PHE N N 127.478 0.300 1 31 25 25 ASN H H 8.308 0.030 1 32 25 25 ASN N N 112.974 0.300 1 33 26 26 CYS H H 7.981 0.030 1 34 26 26 CYS N N 123.496 0.300 1 35 27 27 GLY H H 7.262 0.030 1 36 27 27 GLY N N 104.231 0.300 1 37 28 28 LYS H H 8.765 0.030 1 38 28 28 LYS N N 123.356 0.300 1 39 29 29 TRP H H 9.430 0.030 1 40 29 29 TRP N N 121.800 0.300 1 41 30 30 ARG H H 9.940 0.030 1 42 30 30 ARG N N 122.335 0.300 1 43 31 31 ARG H H 8.345 0.030 1 44 31 31 ARG N N 126.073 0.300 1 45 32 32 LEU H H 8.586 0.030 1 46 32 32 LEU N N 127.627 0.300 1 47 33 33 CYS H H 8.373 0.030 1 48 33 33 CYS N N 122.071 0.300 1 49 34 34 GLY H H 8.418 0.030 1 50 34 34 GLY N N 110.003 0.300 1 51 36 36 ILE H H 7.447 0.030 1 52 36 36 ILE N N 120.675 0.300 1 53 37 37 ASP H H 8.255 0.030 1 54 37 37 ASP N N 126.450 0.300 1 55 39 39 SER H H 8.496 0.030 1 56 39 39 SER N N 113.783 0.300 1 57 40 40 VAL H H 7.475 0.030 1 58 40 40 VAL N N 114.936 0.300 1 59 41 41 LEU H H 7.263 0.030 1 60 41 41 LEU N N 123.834 0.300 1 61 43 43 ASP H H 8.703 0.030 1 62 43 43 ASP N N 120.362 0.300 1 63 44 44 ASN H H 8.152 0.030 1 64 44 44 ASN N N 116.145 0.300 1 65 45 45 TRP H H 7.904 0.030 1 66 45 45 TRP N N 121.391 0.300 1 67 46 46 SER H H 5.990 0.030 1 68 46 46 SER N N 121.435 0.300 1 69 47 47 CYS H H 8.595 0.030 1 70 47 47 CYS N N 119.635 0.300 1 71 48 48 ASP H H 8.034 0.030 1 72 48 48 ASP N N 111.409 0.300 1 73 49 49 GLN H H 7.797 0.030 1 74 49 49 GLN N N 117.416 0.300 1 75 50 50 ASN H H 8.023 0.030 1 76 50 50 ASN N N 121.590 0.300 1 77 51 51 THR H H 8.408 0.030 1 78 51 51 THR N N 117.267 0.300 1 79 52 52 ASP H H 7.381 0.030 1 80 52 52 ASP N N 121.817 0.300 1 81 53 53 VAL H H 7.945 0.030 1 82 53 53 VAL N N 121.451 0.300 1 83 54 54 GLN H H 8.071 0.030 1 84 54 54 GLN N N 116.862 0.300 1 85 55 55 TYR H H 7.312 0.030 1 86 55 55 TYR N N 113.967 0.300 1 87 56 56 ASN H H 7.126 0.030 1 88 56 56 ASN N N 118.668 0.300 1 89 57 57 ARG H H 6.891 0.030 1 90 57 57 ARG N N 112.786 0.300 1 91 58 58 CYS H H 8.495 0.030 1 92 58 58 CYS N N 122.651 0.300 1 93 59 59 ASP H H 7.743 0.030 1 94 59 59 ASP N N 110.884 0.300 1 95 60 60 ILE H H 7.308 0.030 1 96 60 60 ILE N N 124.120 0.300 1 97 62 62 GLU H H 8.776 0.030 1 98 62 62 GLU N N 121.873 0.300 1 99 63 63 GLU H H 9.187 0.030 1 100 63 63 GLU N N 127.694 0.300 1 101 64 64 THR H H 8.353 0.030 1 102 64 64 THR N N 118.246 0.300 1 103 65 65 TRP H H 8.330 0.030 1 104 65 65 TRP N N 125.502 0.300 1 105 66 66 THR H H 8.049 0.030 1 106 66 66 THR N N 116.570 0.300 1 107 67 67 GLY H H 7.371 0.030 1 108 67 67 GLY N N 110.029 0.300 1 109 68 68 LEU H H 7.799 0.030 1 110 68 68 LEU N N 121.228 0.300 1 111 69 69 GLU H H 7.913 0.030 1 112 69 69 GLU N N 126.141 0.300 1 stop_ save_