SMTL ID : 4ifd.1

Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

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

Ligands

10 x BR: BROMIDE ION(Non-covalent)

BR.1: 1 residues within 4Å: Chain A: T.223 Ligand excluded by PLIP BR.2: 4 residues within 4Å: Chain A: R.70, P.71, F.72, E.73 Ligand excluded by PLIP BR.4: 2 residues within 4Å: Chain E: W.219, P.258 Ligand excluded by PLIP BR.5: 4 residues within 4Å: Chain C: Y.130 Chain F: L.9, L.10, G.11 Ligand excluded by PLIP BR.8: 2 residues within 4Å: Chain H: K.133, Q.134 Ligand excluded by PLIP BR.12: 4 residues within 4Å: Chain I: S.221, A.257, R.258, K.296 Ligand excluded by PLIP BR.13: 3 residues within 4Å: Chain J: Y.276, P.295, R.296 Ligand excluded by PLIP BR.14: 3 residues within 4Å: Chain J: F.497, P.607, M.608 Ligand excluded by PLIP BR.15: 1 residues within 4Å: Chain J: R.139 Ligand excluded by PLIP BR.16: 3 residues within 4Å: Chain J: Y.620, R.649, S.650 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain C: I.53, E.54, N.55, F.391, I.393 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.53, C:N.55, C:N.55 GOL.6: 4 residues within 4Å: Chain A: D.25 Chain G: R.211, Q.232, E.235 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.232, G:E.235 GOL.9: 7 residues within 4Å: Chain H: Y.106, A.107, S.206, S.207, I.209, R.211, V.229 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:A.107, H:S.206, H:I.209, H:R.211, H:R.211 GOL.10: 5 residues within 4Å: Chain H: R.117, D.129, F.201, Q.203, Y.232 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.117, H:Q.203 GOL.11: 6 residues within 4Å: Chain B: M.115 Chain H: G.72, H.73, G.74, T.75, S.85 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:G.74, H:S.85, B:S.155

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 8 residues within 4Å: Chain G: D.154, G.155, K.199, C.200, E.201, E.202, L.203, T.206 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.155

1 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 4 residues within 4Å: Chain J: D.545, D.554 Chain L: U.44, U.45 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:D.545, J:D.554, J:D.554

1 x ZN: ZINC ION(Non-covalent)

ZN.18: 4 residues within 4Å: Chain J: C.49, C.54, C.57, H.186 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.49, J:C.54, J:C.57, J:H.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Makino, D.L. et al., Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. Nature (2013)

Release Date

2013-02-06

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
Exosome complex exonuclease RRP6: 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

Exosome complex exonuclease RRP6

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