6D6Q

Human nuclear exosome-MTR4 RNA complex - overall reconstruction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.

Weick, E.M.Puno, M.R.Januszyk, K.Zinder, J.C.DiMattia, M.A.Lima, C.D.

(2018) Cell 173: 1663

  • DOI: 10.1016/j.cell.2018.05.041
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Sch ...

    The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4.


    Organizational Affiliation

    Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA. Electronic address: limac@mskcc.org.,Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP45
A
473Homo sapiensMutation(s): 0 
Gene Names: EXOSC9 (PMSCL1)
Find proteins for Q06265 (Homo sapiens)
Go to Gene View: EXOSC9
Go to UniProtKB:  Q06265
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP41
B
249Homo sapiensMutation(s): 0 
Gene Names: EXOSC4 (RRP41, SKI6)
Find proteins for Q9NPD3 (Homo sapiens)
Go to Gene View: EXOSC4
Go to UniProtKB:  Q9NPD3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP43
C
278Homo sapiensMutation(s): 0 
Gene Names: EXOSC8 (OIP2, RRP43)
Find proteins for Q96B26 (Homo sapiens)
Go to Gene View: EXOSC8
Go to UniProtKB:  Q96B26
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP46
D
237Homo sapiensMutation(s): 0 
Gene Names: EXOSC5 (CML28, RRP46)
Find proteins for Q9NQT4 (Homo sapiens)
Go to Gene View: EXOSC5
Go to UniProtKB:  Q9NQT4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP42
E
293Homo sapiensMutation(s): 0 
Gene Names: EXOSC7 (KIAA0116, RRP42)
Find proteins for Q15024 (Homo sapiens)
Go to Gene View: EXOSC7
Go to UniProtKB:  Q15024
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component MTR3
F
272Homo sapiensMutation(s): 0 
Gene Names: EXOSC6 (MTR3)
Find proteins for Q5RKV6 (Homo sapiens)
Go to Gene View: EXOSC6
Go to UniProtKB:  Q5RKV6
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP40
G
277Homo sapiensMutation(s): 0 
Gene Names: EXOSC3 (RRP40)
Find proteins for Q9NQT5 (Homo sapiens)
Go to Gene View: EXOSC3
Go to UniProtKB:  Q9NQT5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP4
H
296Homo sapiensMutation(s): 0 
Gene Names: EXOSC2 (RRP4)
Find proteins for Q13868 (Homo sapiens)
Go to Gene View: EXOSC2
Go to UniProtKB:  Q13868
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component CSL4
I
197Homo sapiensMutation(s): 0 
Gene Names: EXOSC1 (CSL4)
Find proteins for Q9Y3B2 (Homo sapiens)
Go to Gene View: EXOSC1
Go to UniProtKB:  Q9Y3B2
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Exosome component 10
J
761Homo sapiensMutation(s): 1 
Gene Names: EXOSC10 (PMSCL, PMSCL2, RRP6)
EC: 3.1.13.-
Find proteins for Q01780 (Homo sapiens)
Go to Gene View: EXOSC10
Go to UniProtKB:  Q01780
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP44
K
960Homo sapiensMutation(s): 2 
Gene Names: DIS3 (KIAA1008, RRP44)
EC: 3.1.13.-, 3.1.26.-
Find proteins for Q9Y2L1 (Homo sapiens)
Go to Gene View: DIS3
Go to UniProtKB:  Q9Y2L1
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
M-phase phosphoprotein 6
L
162Homo sapiensMutation(s): 0 
Gene Names: MPHOSPH6 (MPP6)
Find proteins for Q99547 (Homo sapiens)
Go to Gene View: MPHOSPH6
Go to UniProtKB:  Q99547
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Exosome RNA helicase MTR4
M
1045Homo sapiensMutation(s): 0 
Gene Names: MTREX (DOB1, KIAA0052, MTR4, SKIV2L2)
EC: 3.6.4.13
Find proteins for P42285 (Homo sapiens)
Go to UniProtKB:  P42285
Entity ID: 14
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')N16synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
DNA/RNA (62-MER)O62synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
M
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
K
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM118080
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-06-27
    Type: Data collection, Database references