SMTL ID : 5jea.1

Structure of a cytoplasmic 11-subunit RNA exosome complex including Ski7, bound to RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

7 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 8 residues within 4Å: Chain A: F.30, D.31, F.198, S.219, T.260, K.263, C.264, E.267 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.30, A:D.31, A:T.260 MPD.2: 4 residues within 4Å: Chain A: D.26, Q.32, R.34, D.35 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.26, A:R.34 Hydrogen bonds: A:D.35 MPD.5: 6 residues within 4Å: Chain C: K.368, I.369, I.374 Chain D: V.177, N.179, V.180 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.177, C:K.368, C:I.374 MPD.6: 7 residues within 4Å: Chain C: D.157, H.161 Chain D: E.106, F.107, S.108, L.109, D.184 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.106, D:F.107, D:S.108, D:L.109 Hydrophobic interactions: C:D.157 MPD.8: 2 residues within 4Å: Chain G: G.150, L.154 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.154 MPD.9: 10 residues within 4Å: Chain D: C.85, A.129 Chain G: G.26, P.27, G.28, I.29, Y.30, V.41, N.42, Y.63 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: G:V.41, D:A.129 Hydrogen bonds: G:G.28, G:Y.63, G:Y.63 MPD.10: 5 residues within 4Å: Chain B: E.29, S.30, S.31, E.46 Chain J: K.15 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain B Hydrogen bonds: J:K.15, B:E.46

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 7 residues within 4Å: Chain B: Y.160, I.161, S.162, V.192, V.193, G.194, R.228 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.162, B:V.192 NA.4: 1 residues within 4Å: Chain B: N.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.23 NA.7: 8 residues within 4Å: Chain F: I.83, T.88, Q.90, G.91, T.92, Y.130, K.132, S.133 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.88, F:Q.90, F:T.92, F:S.133 NA.12: 2 residues within 4Å: Chain J: F.499, M.610 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:M.610

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain J: C.51, C.56, C.59, H.188 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.51, J:C.56, J:C.59, J:H.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kowalinski, E. et al., Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex. Mol.Cell (2016)

Release Date

2016-07-13

Peptides

Exosome complex component RRP45: A
Exosome complex component SKI6: B
Exosome complex component RRP43: C
Exosome complex component RRP46: D
Exosome complex component RRP42: E
Exosome complex component MTR3: F
Exosome complex component RRP40: G
Exosome complex component RRP4: H
Exosome complex component CSL4: I
Exosome complex exonuclease DIS3: J
Superkiller protein 7,Endolysin: K

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

Exosome complex component RRP45

Exosome complex component SKI6

Exosome complex component RRP43

Exosome complex component RRP46

Exosome complex component RRP42

Exosome complex component MTR3

Exosome complex component RRP40

Exosome complex component RRP4

Exosome complex component CSL4

Exosome complex exonuclease DIS3

Superkiller protein 7,Endolysin

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