SMTL ID : 5k36.1

Structure of an eleven component nuclear RNA exosome complex bound to RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

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

Ligands

10 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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.106, A:R.113, A:R.114, B:R.100 SO4.5: 5 residues within 4Å: Chain B: K.84, R.90, K.92 Chain E: Q.81, D.83 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Salt bridges: B:K.84, B:R.90, B:K.92 Hydrogen bonds: E:Q.81 SO4.7: 6 residues within 4Å: Chain D: Q.47, I.80, T.81, R.82, H.83, N.130 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.82, D:H.83, D:N.130 Salt bridges: D:H.83 SO4.8: 3 residues within 4Å: Chain E: K.244, P.245, H.246 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.246 Salt bridges: E:K.244 SO4.9: 4 residues within 4Å: Chain C: R.177 Chain F: S.21, N.22, T.23 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:N.22, F:N.22, F:T.23, F:T.23 Salt bridges: C:R.177 SO4.10: 3 residues within 4Å: Chain A: 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 SO4.12: 9 residues within 4Å: Chain I: R.215, S.216, T.217, T.251, A.252, R.253, N.254, W.276, K.291 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:S.216, I:T.217, I:N.254 Salt bridges: I:K.291 SO4.14: 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 SO4.15: 1 residues within 4Å: Chain K: R.52 1 PLIP interactions: 1 interactions with chain K Salt bridges: K:R.52 SO4.18: 5 residues within 4Å: Chain A: R.303, E.304 Chain K: Y.597, R.602 Chain L: A.17 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain K Hydrogen bonds: A:E.304 Salt bridges: A:R.303, K:R.602

7 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.36, A:K.274, A:K.274, A:Q.278 GOL.3: 9 residues within 4Å: Chain A: G.122, C.124, I.125, K.164, I.167, V.169 Chain K: Q.404, S.454, V.470 5 PLIP interactions: 3 interactions with chain K, 2 interactions with chain A Hydrogen bonds: K:Q.404, K:S.454, K:S.454, A:K.164 Water bridges: A:K.164 GOL.4: 4 residues within 4Å: Chain A: K.130, E.172, Q.173, I.174 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.130, A:I.174, C:T.99 GOL.6: 7 residues within 4Å: Chain B: F.159, D.160, V.194 Chain H: G.62, Y.78, L.80, Y.85 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:Y.78, H:Y.85, B:D.160 GOL.11: 7 residues within 4Å: Chain B: I.120, S.157 Chain H: G.74, H.75, G.76, T.77, S.87 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:G.76, H:T.77, H:S.87, H:S.87, B:S.157 GOL.16: 5 residues within 4Å: Chain K: F.287, L.309, R.311, A.312, W.458 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:F.287, K:Q.306, K:R.311, K:A.312 GOL.17: 7 residues within 4Å: Chain K: R.690, L.696, E.730, G.835, L.836 Chain L: U.13, A.14 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:R.690, K:R.690, K:G.835

1 x ZN: ZINC ION(Non-covalent)

ZN.13: 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

Zinder, J.C. et al., Nuclear RNA Exosome at 3.1 angstrom Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3. Mol.Cell (2016)

Release Date

2016-11-02

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

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 RRP6

Exosome complex exonuclease DIS3

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