SMTL ID : 9c7a.1

Crystal structure of R149W neurodevelopmental disease-associated U2AF2 variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x U- U- DU- U- U- BRU- C- C: DNA/RNA (5'-R(P*UP*U)-D(P*U)-R(P*UP*U)-D(P*(BRU))-R(P*CP*C)-3')

U-U-DU-U-U-BRU-C-C.1: 43 residues within 4Å: Chain A: Q.10, R.13, Y.15, N.18, N.55, K.58, N.59, F.60, F.62, K.88, R.90, R.91, P.92, H.93, D.94, T.115, V.116, V.117, D.119, K.123, F.125, G.127, G.128, N.152, V.154, K.155, S.157, K.163, Y.165, F.167, K.191, K.192, L.193, L.194, Q.196, R.197, A.198, V.200, G.201, A.202, K.203 Ligands: NA.3, NA.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.91, A:H.93 Water bridges: A:K.58, A:R.90, A:D.94 Salt bridges: A:K.58 pi-Stacking: A:Y.15, A:H.93

1 x GOL: GLYCEROL

GOL.2: 3 residues within 4Å: Chain A: M.75, R.90, V.116 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.90, A:R.90

2 x NA: SODIUM ION

NA.3: 5 residues within 4Å: Chain A: N.18, N.59, K.155, G.160 Ligands: U-U-DU-U-U-BRU-C-C.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.59, A:N.59 Water bridges: A:Q.85 NA.4: 5 residues within 4Å: Chain A: K.58, N.59, S.157, A.158 Ligands: U-U-DU-U-U-BRU-C-C.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.59, A:A.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maji, D. et al., Recurrent Neurodevelopmentally Associated Variants of the Pre-mRNA Splicing Factor U2AF2 Alter RNA Binding Affinities and Interactions. Biochemistry (2024)

Release Date

2024-10-02

Peptides

Splicing factor U2AF 65 kDa subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Splicing factor U2AF 65 kDa subunit