SMTL ID : 5gin.1 (1 other biounit)

Crystal structure of box C/D RNP with 12 nt guide regions and 9 nt substrates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.31 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x C- C- A- U- G- A- G- U- G: substrate(Non-covalent)

C-C-A-U-G-A-G-U-G.1: 30 residues within 4Å: Chain A: E.301, K.302, F.305, R.309 Chain C: F.57, R.58, K.60, S.87, T.89, E.116, K.182, R.184, S.185, V.188, D.220, K.221, H.223 Chain D: N.155, E.159, H.179 Chain G: C.19, A.20, C.21, U.22, C.23, A.24, U.25, G.26, G.27 Ligands: SAH.3 Protein-ligand interaction information (PLIP) not available C-C-A-U-G-A-G-U-G.2: 32 residues within 4Å: Chain A: N.155, E.159, E.177, H.179 Chain D: E.301, K.302, F.305, R.309 Chain F: F.57, R.58, K.60, A.86, S.87, T.89, E.116, K.182, R.184, S.185, V.188, D.220, K.221, H.223 Chain H: C.19, A.20, C.21, U.22, C.23, A.24, U.25, G.26, G.27 Ligands: SAH.4 Protein-ligand interaction information (PLIP) not available

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.3: 19 residues within 4Å: Chain C: K.60, Y.82, G.84, A.85, A.86, T.89, T.90, E.108, F.109, S.110, A.132, D.133, A.134, D.153, I.154, A.155, Q.156 Chain G: U.25 Ligands: C-C-A-U-G-A-G-U-G.1 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:A.86 Hydrogen bonds: C:T.89, C:T.90, C:T.90, C:F.109, C:D.133, C:A.134, C:D.153, C:D.153, C:A.155, C:Q.156 pi-Stacking: C:F.109, C:F.109 SAH.4: 18 residues within 4Å: Chain F: Y.82, G.84, A.86, T.89, T.90, E.108, F.109, S.110, A.132, D.133, A.134, D.153, I.154, A.155, Q.156 Chain H: U.25 Ligands: C-C-A-U-G-A-G-U-G.2, C-C-A-U-G-A-G-U-G.2 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:A.86 Hydrogen bonds: F:T.89, F:T.90, F:F.109, F:D.133, F:A.134, F:D.153, F:D.153, F:A.155, F:Q.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Box C/D guide RNAs recognize a maximum of 10 nt of substrates. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-09-14

Peptides

C/D box methylation guide ribonucleoprotein complex aNOP56 subunit: AD
50S ribosomal protein L7Ae: BE
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

B
C

E
D

C
E

F
F

C/D box methylation guide ribonucleoprotein complex aNOP56 subunit

50S ribosomal protein L7Ae

Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

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