SMTL ID : 9e3b.1

Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-4-mer

Ligands

4 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 26 residues within 4Å: Chain A: P.314, L.315, L.319, Y.324, F.327, K.333, Y.334, G.365, A.366, G.367, R.368, P.370, L.371, V.391, E.392, K.393, N.394, A.397, S.418, D.419, M.420, R.421, E.435, L.436, C.449 Chain N: R.121 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.327 Hydrogen bonds: A:Y.324, A:K.333, A:G.365, A:G.367, A:K.393, A:K.393, A:N.394, A:D.419, A:M.420, A:R.421, A:E.435, A:E.435 pi-Cation interactions: A:K.393 SFG.2: 25 residues within 4Å: Chain C: P.314, L.315, L.319, Y.324, F.327, K.333, Y.334, G.365, A.366, G.367, R.368, P.370, L.371, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, C.449 Chain M: R.121 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.327, C:F.327 Hydrogen bonds: C:Y.324, C:Y.324, C:K.333, C:G.365, C:K.393, C:K.393, C:D.419, C:M.420, C:R.421, C:E.435 pi-Cation interactions: C:K.393 SFG.3: 25 residues within 4Å: Chain G: P.314, L.315, L.319, Y.324, F.327, K.333, Y.334, G.365, A.366, G.367, R.368, P.370, L.371, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, C.449 Chain O: R.121 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:F.327 Hydrogen bonds: G:Y.324, G:K.333, G:Y.334, G:G.365, G:G.367, G:E.392, G:K.393, G:N.394, G:D.419, G:M.420, G:R.421 pi-Cation interactions: G:K.393 SFG.4: 25 residues within 4Å: Chain J: P.314, L.315, L.319, Y.324, F.327, K.333, Y.334, G.365, A.366, G.367, R.368, P.370, L.371, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, C.449 Chain P: R.121 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:F.327 Hydrogen bonds: J:Y.324, J:K.333, J:Y.334, J:G.365, J:G.367, J:K.393, J:K.393, J:N.394, J:D.419, J:M.420, J:R.421 pi-Cation interactions: J:K.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, C.Y. et al., Substrate adaptors are flexible tethering modules that enhance substrate methylation by the arginine methyltransferase PRMT5. J.Biol.Chem. (2025)

Release Date

2025-02-19

Peptides

Protein arginine N-methyltransferase 5: ACGJ
Methylosome protein WDR77: BEHK
Methylosome subunit pICln: DFIL
Small nuclear ribonucleoprotein Sm D1: MNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

G
G

J
J

B
B

E
E

H
H

K
K

D
D

F
F

I
I

L
L

M
M

N
N

O
O

P
P

Protein arginine N-methyltransferase 5

Methylosome protein WDR77

Methylosome subunit pICln

Small nuclear ribonucleoprotein Sm D1

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