SMTL ID : 6a6j.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

monomer

Ligands

1 x C- A- U- 5MC- U: RNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3')(Non-covalent)

C-A-U-5MC-U.1: 15 residues within 4Å: Chain A: W.16, N.18, N.21, Y.23, F.25, D.34, F.36, H.38, T.40, E.68, K.69, G.70, A.71, E.72 Ligands: ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.18, A:N.21, A:Y.23 pi-Stacking: A:W.16, A:W.16

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: E.68, E.72 Ligands: C-A-U-5MC-U.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.68, A:E.68, A:E.72, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay. Mol.Cell (2019)

Release Date

2019-06-19

Peptides

Zebra fish Y-box protein1 (YB-1): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Zebra fish Y-box protein1 (YB-1)

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