SMTL ID : 5vzj.1

STRUCTURE OF A TWELVE COMPONENT MPP6-NUCLEAR RNA EXOSOME COMPLEX BOUND TO RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

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

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: R.106, R.113, R.114 Chain B: R.100 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.100, A:R.106, A:R.113, A:R.114 Water bridges: A:R.114 SO4.3: 3 residues within 4Å: Chain B: E.98, R.99, R.100 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.98, B:R.99, B:R.100 Salt bridges: B:R.100 SO4.4: 6 residues within 4Å: Chain A: F.14 Chain G: D.156, G.157, C.202, L.205, T.208 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.157, G:T.208 SO4.5: 4 residues within 4Å: Chain A: Y.23, G.27 Chain G: R.213, E.237 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:E.237 Salt bridges: G:R.213 SO4.7: 3 residues within 4Å: Chain K: R.201, R.204, Q.222 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:Q.222, K:Q.222 Salt bridges: K:R.201, K:R.204

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: F.33, R.34, D.35, V.36, K.274, Q.278 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.34, A:V.36, A:K.274, A:K.274, A:Q.278 GOL.8: 5 residues within 4Å: Chain K: F.287, L.309, R.311, A.312, W.458 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:F.287, K:A.312

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain K: C.49, C.54, C.57, H.186 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.49, K:C.54, K:C.57, K:H.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wasmuth, E.V. et al., Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase. Elife (2017)

Release Date

2017-08-02

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 RRP6: J
Exosome complex exonuclease DIS3: K
M-phase phosphoprotein 6 homolog: L

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

L
L

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 RRP6

Exosome complex exonuclease DIS3

M-phase phosphoprotein 6 homolog

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