7Y18 | pdb_00007y18

Crystal structure of ribosomal ITS2 pre-rRNA processing complex from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free: 
    0.318 (Depositor), 0.320 (DCC) 
  • R-Value Work: 
    0.278 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 
    0.280 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and mechanistic insights into ribosomal ITS2 RNA processing by nuclease-kinase machinery.

Chen, J.Chen, H.Li, S.Lin, X.Hu, R.Zhang, K.Liu, L.

(2024) Elife 12

  • DOI: https://doi.org/10.7554/eLife.86847
  • Primary Citation of Related Structures:  
    7Y16, 7Y17, 7Y18, 8J5Y, 8J60

  • PubMed Abstract: 

    Precursor ribosomal RNA (pre-rRNA) processing is a key step in ribosome biosynthesis and involves numerous RNases. A HEPN (higher eukaryote and prokaryote nucleotide binding) nuclease Las1 and a polynucleotide kinase Grc3 assemble into a tetramerase responsible for rRNA maturation. Here, we report the structures of full-length Saccharomyces cerevisiae and Cyberlindnera jadinii Las1-Grc3 complexes, and C. jadinii Las1. The Las1-Grc3 structures show that the central coiled-coil domain of Las1 facilitates pre-rRNA binding and cleavage, while the Grc3 C-terminal loop motif directly binds to the HEPN active center of Las1 and regulates pre-rRNA cleavage. Structural comparison between Las1 and Las1-Grc3 complex exhibits that Grc3 binding induces conformational rearrangements of catalytic residues associated with HEPN nuclease activation. Biochemical assays identify that Las1 processes pre-rRNA at the two specific sites (C2 and C2'), which greatly facilitates rRNA maturation. Our structures and specific pre-rRNA cleavage findings provide crucial insights into the mechanism and pathway of pre-rRNA processing in ribosome biosynthesis.


  • Organizational Affiliation
    • State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polynucleotide 5'-hydroxyl-kinase GRC3A,
D [auth B],
E
632Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GRC3YLL035W
EC: 2.7.1
UniProt
Find proteins for Q07845 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07845 
Go to UniProtKB:  Q07845
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07845
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LAS1B [auth C],
C [auth D],
F
502Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LAS1YKR063C
UniProt
Find proteins for P36146 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36146 
Go to UniProtKB:  P36146
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36146
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free:  0.318 (Depositor), 0.320 (DCC) 
  • R-Value Work:  0.278 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 0.280 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 233.556α = 90
b = 116.142β = 96.406
c = 159.311γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
Cootmodel building
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171286

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-01-17
    Changes: Database references