PDBsum entry 4r3h

RNA binding protein

PDB id: 4r3h

Contents

Protein chains

157 a.a.

Ligands

UNX ×11

SO4

Waters ×158

PDB id:

4r3h

Name:

RNA binding protein

Title:

The crystal structure of an apo RNA binding protein

Structure:

Yth domain-containing protein 1. Chain: a, b. Synonym: putative splicing factor yt521, yt521-b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ythdc1, kiaa1966, yt521. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.193 R-free: 0.240

Authors:

C.Xu,K.Liu,W.Tempel,Y.Li,C.Bountra,C.H.Arrowsmith,A.M.Edwards,J.Min, Structural Genomics Consortium (Sgc)

Key ref:

C.Xu et al. (2014). Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. Nat Chem Biol, 10, 927-929. PubMed id: 25242552 DOI: 10.1038/nchembio.1654

Date:

15-Aug-14 Release date: 17-Sep-14

Protein chains

Q96MU7  (YTDC1_HUMAN) -  YTH domain-containing protein 1 from Homo sapiens

Seq: 727 a.a.

Struc: 157 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/nchembio.1654

Nat Chem Biol 10:927-929 (2014)

PubMed id: 25242552

Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain.

C.Xu, X.Wang, K.Liu, I.A.Roundtree, W.Tempel, Y.Li, Z.Lu, C.He, J.Min.

ABSTRACT

N(6)-methyladenosine (m(6)A) is the most abundant internal modification of nearly all eukaryotic mRNAs and has recently been reported to be recognized by the YTH domain family proteins. Here we present the crystal structures of the YTH domain of YTHDC1, a member of the YTH domain family, and its complex with an m(6)A-containing RNA. Our structural studies, together with transcriptome-wide identification of YTHDC1-binding sites and biochemical experiments, not only reveal the specific mode of m(6)A-YTH binding but also explain the preferential recognition of the GG(m(6)A)C sequences by YTHDC1.