7S7B

Human Nuclear exosome targeting (NEXT) complex homodimer bound to RNA (substrate 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.06 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

Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex.

Puno, M.R.Lima, C.D.

(2022) Cell 185: 2132-2147.e26

  • DOI: https://doi.org/10.1016/j.cell.2022.04.016
  • Primary Citation of Related Structures:  
    7S7B, 7S7C

  • PubMed Abstract: 

    RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined cryogenic electron microscopy structures of human nuclear exosome targeting (NEXT) complexes bound to RNA that reveal mechanistic insights to substrate recognition and early steps that precede RNA handover to the exosome. The structures illuminate ZCCHC8 as a scaffold, mediating homodimerization while embracing the MTR4 helicase and flexibly anchoring RBM7 to the helicase core. All three subunits collaborate to bind the RNA, with RBM7 and ZCCHC8 surveying sequences upstream of the 3' end to facilitate RNA capture by MTR4. ZCCHC8 obscures MTR4 surfaces important for RNA binding and extrusion as well as MPP6-dependent recruitment and docking onto the RNA exosome core, interactions that contribute to RNA surveillance by coordinating RNA capture, translocation, and extrusion from the helicase to the exosome for decay.


  • Organizational Affiliation

    Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome RNA helicase MTR4
A, E
1,045Homo sapiensMutation(s): 0 
Gene Names: MTREXDOB1KIAA0052MTR4SKIV2L2
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P42285 (Homo sapiens)
Explore P42285 
Go to UniProtKB:  P42285
PHAROS:  P42285
GTEx:  ENSG00000039123 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42285
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger CCHC domain-containing protein 8,Zinc finger CCHC domain-containing protein 8
B, F
618Homo sapiensMutation(s): 0 
Gene Names: ZCCHC8
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NZY4 (Homo sapiens)
Explore Q6NZY4 
Go to UniProtKB:  Q6NZY4
PHAROS:  Q6NZY4
GTEx:  ENSG00000033030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NZY4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 7
C, G
83Homo sapiensMutation(s): 0 
Gene Names: RBM7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y580 (Homo sapiens)
Explore Q9Y580 
Go to UniProtKB:  Q9Y580
PHAROS:  Q9Y580
GTEx:  ENSG00000076053 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y580
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (46-MER)
D, H
46synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118080

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-06-22
    Changes: Database references