Entry Database : PDB / ID : 6a6j Structure visualization Downloads & linksTitle Crystal structure of Zebra fish Y-box protein1 (YB-1) Cold-shock domain in complex with 6mer m5C RNA ComponentsRNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3')Zebra fish Y-box protein1 (YB-1) DetailsKeywords RNA BINDING PROTEIN/RNA / OB-fold / RNA BINDING PROTEIN-RNA complexFunction / homology Function and homology informationFunction Domain/homology Component
negative regulation of mRNA processing / mRNA Splicing - Major Pathway / : / establishment of RNA localization / : / tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / negative regulation of striated muscle cell differentiation / miRNA transport ... negative regulation of mRNA processing / mRNA Splicing - Major Pathway / : / establishment of RNA localization / : / tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / negative regulation of striated muscle cell differentiation / miRNA transport / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / : / CRD-mediated mRNA stabilization / Noncanonical activation of NOTCH3 / RNA transport / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / histone pre-mRNA 3'end processing complex / embryonic morphogenesis / positive regulation of cytoplasmic translation / U12-type spliceosomal complex / mRNA stabilization / cellular response to interleukin-7 / miRNA binding / mRNA Splicing - Minor Pathway / negative regulation of cellular senescence / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of cell division / epidermis development / negative regulation of translational initiation / mRNA Splicing - Major Pathway / RNA splicing / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / P-body / mRNA processing / cytoplasmic stress granule / Interferon gamma signaling / sequence-specific double-stranded DNA binding / GTPase binding / single-stranded DNA binding / regulation of gene expression / double-stranded DNA binding / in utero embryonic development / nucleic acid binding / negative regulation of translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / mRNA binding / synapse / chromatin binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold ... Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta Similarity search - Domain/homologyBiological species Danio rerio (zebrafish)Homo sapiens (human)Method X-RAY DIFFRACTION / SYNCHROTRON / Resolution : 2.255 Å DetailsAuthors Zhang, M.M. / Wu, B.X. / Huang, Y. / Ma, J.B. CitationJournal : Mol.Cell / Year : 2019Title : RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay.Authors: Yang, Y. / Wang, L. / Han, X. / Yang, W.L. / Zhang, M. / Ma, H.L. / Sun, B.F. / Li, A. / Xia, J. / Chen, J. / Heng, J. / Wu, B. / Chen, Y.S. / Xu, J.W. / Yang, X. / Yao, H. / Sun, J. / Lyu, ... Authors : Yang, Y. / Wang, L. / Han, X. / Yang, W.L. / Zhang, M. / Ma, H.L. / Sun, B.F. / Li, A. / Xia, J. / Chen, J. / Heng, J. / Wu, B. / Chen, Y.S. / Xu, J.W. / Yang, X. / Yao, H. / Sun, J. / Lyu, C. / Wang, H.L. / Huang, Y. / Sun, Y.P. / Zhao, Y.L. / Meng, A. / Ma, J. / Liu, F. / Yang, Y.G. History Deposition Jun 28, 2018 Deposition site : PDBJ / Processing site : PDBJRevision 1.0 Jun 19, 2019 Provider : repository / Type : Initial releaseRevision 1.1 Jun 26, 2019 Group : Data collection / Database references ... Data collection / Database references / Source and taxonomy / Structure summary Category : entity / entity_name_com ... entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq Item : _entity.pdbx_description / _entity.pdbx_fragment ... _entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession Revision 1.2 Aug 14, 2019 Group : Data collection / Database references / Structure summaryCategory : audit_author / citation / citation_authorItem : _audit_author.name / _citation.country ... _audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year Revision 1.3 Aug 21, 2019 Group : Data collection / Database references / Category : citation / citation_authorItem : _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.nameRevision 1.4 Oct 2, 2019 Group : Data collection / Database references / Category : citationItem : _citation.journal_volume / _citation.page_first / _citation.page_lastRevision 1.5 Mar 27, 2024 Group : Data collection / Database references / Derived calculationsCategory : chem_comp_atom / chem_comp_bond ... chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type Item : _database_2.pdbx_DOI / _database_2.pdbx_database_accession ... _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
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