Crystal structure of Zebra fish Y-box protein1 (YB-1) Cold-shock domain in complex with 6mer m5C RNA

Summary for 6A6J

DescriptorZebra fish Y-box protein1 (YB-1), RNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3'), ZINC ION, ... (4 entities in total)
Functional Keywordsob-fold, rna binding protein-rna complex, rna binding protein/rna
Biological sourceDanio rerio (Zebrafish)
Total number of polymer chains4
Total molecular weight24039.73
Zhang, M.M.,Wu, B.X.,Huang, Y.,Ma, J.B. (deposition date: 2018-06-28, release date: 2019-06-19, Last modification date: 2019-10-02)
Primary citation
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.
RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay.
Mol.Cell, 75:1188-1202.e11, 2019
PubMed: 31399345 (PDB entries with the same primary citation)
DOI: 10.1016/j.molcel.2019.06.033
MImport into Mendeley
Experimental method

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliersRNA backbone 0.27390 1.4% 3.2% 0.26MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution