7Z4Y

Human NEXT dimer - overall reconstruction of the core complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome.

Gerlach, P.Garland, W.Lingaraju, M.Salerno-Kochan, A.Bonneau, F.Basquin, J.Jensen, T.H.Conti, E.

(2022) Mol Cell 82: 2505

  • DOI: https://doi.org/10.1016/j.molcel.2022.04.011
  • Primary Citation of Related Structures:  
    7Z4Y, 7Z4Z, 7Z52

  • PubMed Abstract: 

    In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting (NEXT) complex plays a central role in directing non-functional transcripts to exosome-mediated degradation, but the structural and molecular mechanisms remain enigmatic. Here, we elucidated the architecture of the human NEXT complex, showing that it exists as a dimer of MTR4-ZCCHC8-RBM7 heterotrimers. Dimerization preconfigures the major MTR4-binding region of ZCCHC8 and arranges the two MTR4 helicases opposite to each other, with each protomer able to function on many types of RNAs. In the inactive state of the complex, the 3' end of an RNA substrate is enclosed in the MTR4 helicase channel by a ZCCHC8 C-terminal gatekeeping domain. The architecture of a NEXT-exosome assembly points to the molecular and regulatory mechanisms with which the NEXT complex guides RNA substrates to the exosome.


  • Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany. Electronic address: p.gerlach@imol.edu.pl.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger CCHC domain-containing protein 8
A, C
301Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome RNA helicase MTR4
B, D
1,046Homo 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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
European CommissionEuropean UnionERC-2016-ADG 740329 EXORICO
German Research Foundation (DFG)GermanySFB/TRR 237
German Research Foundation (DFG)GermanySFB 1035

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references
  • Version 1.2: 2024-07-17
    Changes: Data collection