Overview of exosome strucrure

Archeal exosome

Rrp41

Rrp42

Rrp4Csl4

Components of the core protein of exosome complex

Rrp45p

Archaeal exosome

Two RNase PH subunits: Rrp41 and Rrp42

Two S1 homologs subunit : Rrp4 and Csl4

Rrp42 Rrp41RNase PH RNase PH1 1275 248

19 18728 224

1 223

Rrp4

20 50 57 124 135 220

1 179

Cls4

9 47 58 122 145 165

All-β S1 KH

All-β S1 ZR

S. solfataricus

The archaeal exosome core is a hexameric ring structure with three catalytic subunits

41(mut):D182A

42(mut):E218A

NATURE STRUCTURAL & MOLECULAR BIOLOGY VOLUME 12 NUMBER 7 JULY 2005

Pink : phosphate binding site

Sequence alignment of Rrp41 and Rrp42

View of the S. solfataricus Rrp41-Rrp42 Exosome Core Bound to a Short Single-Stranded RNA

The RNA is bound with the 3’ end near the phosphate binding site and with the 5’ end toward the central channel.

Molecular Cell, Vol. 20, 473–481, November 11, 2005

Detailed view of the structure at the RNA binding site

Schematic of the interactions at the RNA binding site

RNA Binding Arginines Are Essential for Catalytic Activity

Structure of exosome bound A5, U8 and ADP

polyA5 + Pi polyA4 + ADP

Schematic of the reaction mechanism

How does the RNA reach the active site?

Archaeal exosome

Two RNase PH subunits: Rrp41 and Rrp42

Two S1 homologs subunit : Rrp4 and Csl4

Rrp42 Rrp41RNase PH RNase PH

Rrp4 Cls4

All-β S1 KH All-β S1 ZR

Molecular Cell, Vol. 20, 461–471, November 11, 2005

Archaeoglobus fulgidus

Molecular Cell, Vol. 20, 461–471, November 11, 2005

Structure of the nine subunit archaeal Rrp4- and Csl4- exosomes Archaeoglobus fulgidus

[A] top view

[B] side view

[C] top view

Detailed view of the interface of the N-terminal domain of Rrp4 (red), Cls4 (red) and the C-terminal helix of Rrp41 (blue)

Rrp4-Rrp41 Cls4-Rrp41

Archaeal exosome V.S. bacterial PNPase

PNPase

Archaeal exosomeRrp42 Rrp41

KH-S1Rrp4 (Csl4)

RNase PH RNase PH

RNase PH RNase PH

Align RNase PH domain of Rrp41, Rrp42 and PNPase

PNPase RNase PH RNase PH

Structure, Vol. 8, 1215–1226, November, 2000

The structure of S. antibioticus PNPase with the phosphate analog tungstate bound to the at the PNPase catalytic sites