SMTL ID : 5gin.2 (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: 31 residues within 4Å: Chain A: C.19, A.20, C.21, U.22, C.23, A.24, U.25, G.26, G.27 Chain B: E.301, K.302, F.305, R.309 Chain D: V.38, Y.39, F.57, R.58, K.60, S.87, T.89, E.116, K.182, R.184, V.188, D.220, K.221, H.223 Chain F: N.155, E.159, H.179 Ligands: SAH.2 Protein-ligand interaction information (PLIP) not available C-C-A-U-G-A-G-U-G.3: 31 residues within 4Å: Chain B: N.155, E.159, H.179 Chain E: C.19, A.20, C.21, U.22, C.23, A.24, U.25, G.26, G.27 Chain F: E.301, K.302, F.305, R.309 Chain H: V.38, Y.39, F.57, R.58, K.60, S.87, T.89, E.116, K.182, R.184, V.188, D.220, K.221, H.223 Ligands: SAH.4 Protein-ligand interaction information (PLIP) not available

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

SAH.2: 17 residues within 4Å: Chain A: U.25 Chain D: R.58, Y.82, G.84, A.86, T.90, E.108, F.109, S.110, A.132, D.133, A.134, D.153, I.154, A.155, Q.156 Ligands: C-C-A-U-G-A-G-U-G.1 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:A.86 Hydrogen bonds: D:Y.82, D:T.90, D:T.90, D:F.109, D:D.133, D:D.133, D:A.134, D:D.153, D:D.153, D:A.155 SAH.4: 17 residues within 4Å: Chain E: U.25 Chain H: R.58, Y.82, G.84, A.86, T.90, E.108, F.109, S.110, A.132, D.133, A.134, D.153, I.154, A.155, Q.156 Ligands: C-C-A-U-G-A-G-U-G.3 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:A.86 Hydrogen bonds: H:T.90, H:T.90, H:F.109, H:D.133, H:A.134, H:D.153, H:A.155

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: BF
50S ribosomal protein L7Ae: CG
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
K

F
K

C
L

G
L

D
M

H
M

C/D box methylation guide ribonucleoprotein complex aNOP56 subunit

50S ribosomal protein L7Ae

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

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