data_17225 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Solution Structure and DNA-binding Properties of the Cold-shock Domain of the Human Y-box Protein YB-1 ; _BMRB_accession_number 17225 _BMRB_flat_file_name bmr17225.str _Entry_type new _Submission_date 2010-09-29 _Accession_date 2010-09-29 _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 Kloks Cathelijne P.A.M. . 2 Spronk Christian A.E.M. . 3 Lasonder Edwin . . 4 Hoffmann Astrid . . 5 Vuister Geerten W. . 6 Grzesiek Stephan . . 7 Hilbers Cornelis W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count binding_constants 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-11-10 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'The Solution Structure and DNA-binding Properties of the Cold-shock Domain of the Human Y-box Protein YB-1' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 11851341 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kloks Cathelijne P.A.M. . 2 Spronk Christian A.E.M. . 3 Lasonder Edwin . . 4 Hoffmann Astrid . . 5 Vuister Geerten W. . 6 Grzesiek Stephan . . 7 Hilbers Cornelis W. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of Molecular Biology' _Journal_volume 316 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 317 _Page_last 326 _Year 2002 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'CSD/ssDNA complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label CSD $CSD ssDNA $ssDNA 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_CSD _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common CSD _Molecular_mass . _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 79 _Mol_residue_sequence ; MKKVIATKVLGTVKWFNVRN GYGFINRNDTKEDVFVHQTA IKKNNPRKYLRSVGDGETVE FDVVEGEKGAEAANVTGPG ; loop_ _Residue_seq_code _Residue_label 1 MET 2 LYS 3 LYS 4 VAL 5 ILE 6 ALA 7 THR 8 LYS 9 VAL 10 LEU 11 GLY 12 THR 13 VAL 14 LYS 15 TRP 16 PHE 17 ASN 18 VAL 19 ARG 20 ASN 21 GLY 22 TYR 23 GLY 24 PHE 25 ILE 26 ASN 27 ARG 28 ASN 29 ASP 30 THR 31 LYS 32 GLU 33 ASP 34 VAL 35 PHE 36 VAL 37 HIS 38 GLN 39 THR 40 ALA 41 ILE 42 LYS 43 LYS 44 ASN 45 ASN 46 PRO 47 ARG 48 LYS 49 TYR 50 LEU 51 ARG 52 SER 53 VAL 54 GLY 55 ASP 56 GLY 57 GLU 58 THR 59 VAL 60 GLU 61 PHE 62 ASP 63 VAL 64 VAL 65 GLU 66 GLY 67 GLU 68 LYS 69 GLY 70 ALA 71 GLU 72 ALA 73 ALA 74 ASN 75 VAL 76 THR 77 GLY 78 PRO 79 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-09-30 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 4147 "Cold Shock domain" 100.00 79 100.00 100.00 2.29e-48 PDB 1H95 "Solution Structure Of The Single-Stranded Dna-Binding Cold Shock Domain (Csd) Of Human Y-Box Protein 1 (Yb1) Determined By Nmr " 100.00 79 100.00 100.00 2.29e-48 DBJ BAA02569 "DNA binding protein B [Rattus sp.]" 98.73 322 100.00 100.00 4.71e-47 DBJ BAA03376 "dbpA murine homologue [Mus musculus domesticus]" 97.47 308 98.70 100.00 9.06e-43 DBJ BAA05380 "unnamed protein product [Gallus gallus]" 98.73 326 100.00 100.00 7.18e-47 DBJ BAA19849 "Y box protein 1 [Carassius auratus]" 98.73 311 100.00 100.00 6.21e-47 DBJ BAC45236 "Y-box binding protein [Oryzias latipes]" 98.73 306 100.00 100.00 7.52e-47 EMBL CAA40847 "Y box-binbing protein [Mus musculus]" 98.73 321 100.00 100.00 4.09e-47 EMBL CAA42778 "YB3 [Xenopus laevis]" 98.73 305 100.00 100.00 6.89e-47 EMBL CAA51261 "cold shock domain protein A [Homo sapiens]" 97.47 372 98.70 100.00 5.77e-46 EMBL CAA64631 "DNA-binding protein [Homo sapiens]" 97.47 372 98.70 100.00 5.77e-46 EMBL CAB46826 "DNA binding protein [Canis lupus familiaris]" 78.48 96 98.39 100.00 1.24e-34 GB AAA02573 "YB-1 protein [Gallus gallus]" 98.73 321 100.00 100.00 5.40e-47 GB AAA20871 "similar to dbpB protein [Homo sapiens]" 98.73 324 100.00 100.00 5.31e-47 GB AAA21677 "transcription factor EF1(A) [Bos taurus]" 72.15 110 100.00 100.00 5.88e-33 GB AAA30497 "transcription factor EF1(A) [Bos taurus]" 98.73 324 100.00 100.00 5.31e-47 GB AAA35749 "DNA-binding protein A, partial [Homo sapiens]" 97.47 412 98.70 100.00 1.19e-42 PRF 2210343A "nicotinic acetylcholine receptor repressor" 97.47 361 98.70 100.00 7.12e-46 REF NP_001003127 "Y-box-binding protein 3 [Canis lupus familiaris]" 97.47 304 97.40 98.70 4.47e-46 REF NP_001016677 "nuclease-sensitive element-binding protein 1 [Xenopus (Silurana) tropicalis]" 98.73 306 100.00 100.00 7.77e-47 REF NP_001076254 "nuclease-sensitive element-binding protein 1 [Oryctolagus cuniculus]" 98.73 324 100.00 100.00 5.09e-47 REF NP_001079367 "nuclease-sensitive element-binding protein 1 [Xenopus laevis]" 97.47 303 100.00 100.00 3.03e-46 REF NP_001080330 "B box-binding protein [Xenopus laevis]" 98.73 305 100.00 100.00 6.89e-47 SP P16989 "RecName: Full=Y-box-binding protein 3; AltName: Full=Cold shock domain-containing protein A; AltName: Full=DNA-binding protein " 97.47 372 98.70 100.00 5.77e-46 SP P21573 "RecName: Full=Nuclease-sensitive element-binding protein 1; AltName: Full=Y-box transcription factor; AltName: Full=Y-box-bindi" 97.47 303 100.00 100.00 2.84e-46 SP P62960 "RecName: Full=Nuclease-sensitive element-binding protein 1; AltName: Full=CCAAT-binding transcription factor I subunit A; Short" 98.73 322 100.00 100.00 4.71e-47 SP P62961 "RecName: Full=Nuclease-sensitive element-binding protein 1; AltName: Full=CCAAT-binding transcription factor I subunit A; Short" 98.73 322 100.00 100.00 4.71e-47 SP P67808 "RecName: Full=Nuclease-sensitive element-binding protein 1; AltName: Full=CCAAT-binding transcription factor I subunit A; Short" 98.73 324 100.00 100.00 5.31e-47 TPG DAA29365 "TPA: cold shock domain protein A [Bos taurus]" 97.47 376 98.70 100.00 1.27e-42 TPG DAA30957 "TPA: nuclease-sensitive element-binding protein 1 [Bos taurus]" 98.73 324 100.00 100.00 5.31e-47 stop_ save_ save_ssDNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common ssDNA _Molecular_mass . _Mol_thiol_state 'not reported' _Details . _Residue_count 5 _Mol_residue_sequence ATTGG loop_ _Residue_seq_code _Residue_label 1 DA 2 DT 3 DT 4 DG 5 DG 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 $CSD Human 9606 Eukaryota Metazoa . . $ssDNA . . . . . . 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 $CSD 'recombinant technology' . . . . na $ssDNA '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $CSD 2.7 mg . . 'natural abundance' $ssDNA . equivalents 0 2 'natural abundance' H2O 95 % . . 'natural abundance' D2O 5 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_PIPP _Saveframe_category software _Name PIPP _Version . loop_ _Vendor _Address _Electronic_address 'Garrett, D. S., Powers, R., Gronenborn, A. M. & Clore, G. M.' . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UnityInova _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _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 temperature 298 . K pH 6.7 . pH pressure ambient . atm stop_ save_