9DUN | pdb_00009dun

Human LAS1L-NOL9 complex

  • Classification: RNA BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2024-10-03 Released: 2025-04-30 
  • Deposition Author(s): Huang, J., Tong, L.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 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

Molecular insights into the overall architecture of human rixosome.

Huang, J.Tong, L.

(2025) Nat Commun 16: 3288-3288

  • DOI: https://doi.org/10.1038/s41467-025-58732-3
  • Primary Citation of Related Structures:  
    9DUM, 9DUN, 9DUO

  • PubMed Abstract: 

    Rixosome is a conserved, multi-subunit protein complex that has critical roles in ribosome biogenesis and silencing of Polycomb target genes. The subunits of human rixosome include PELP1, WDR18, TEX10, LAS1L and NOL9, with LAS1L providing the endoribonuclease activity and NOL9 the RNA 5' kinase activity. We report here cryo-EM structures of the human PELP1-WDR18-TEX10 and LAS1L-NOL9 complexes and a lower-resolution model of the human PELP1-WDR18-LAS1L complex. The structures reveal the overall organization of the human rixosome core scaffold of PELP1-WDR18-TEX10-LAS1L and indicate how the LAS1L-NOL9 endonuclease/kinase catalytic module is recruited to this core scaffold. Each TEX10 molecule has two regions of contact with WDR18, while the helix at the C terminus of WDR18 interacts with the helical domain of LAS1L. The structural observations are supported by our mutagenesis studies. Mutations in both WDR18-TEX10 contact regions can block the binding of TEX10, while truncation of the C-terminal helix of WDR18 can abolish the binding of LAS1L. The structures also reveal substantial conformational differences for TEX10 between the PELP1-WDR18-TEX10 complex alone and that in complex with pre-ribosome.


  • Organizational Affiliation
    • Department of Biological Sciences, Columbia University, New York, NY, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polynucleotide 5'-hydroxyl-kinase NOL9
A, B
602Homo sapiensMutation(s): 0 
Gene Names: NOL9
EC: 2.7.1.78
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SY16 (Homo sapiens)
Explore Q5SY16 
Go to UniProtKB:  Q5SY16
PHAROS:  Q5SY16
GTEx:  ENSG00000162408 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SY16
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal biogenesis protein LAS1L
C, D
202Homo sapiensMutation(s): 0 
Gene Names: LAS1LMSTP060
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4W2 (Homo sapiens)
Explore Q9Y4W2 
Go to UniProtKB:  Q9Y4W2
PHAROS:  Q9Y4W2
GTEx:  ENSG00000001497 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4W2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal biogenesis protein LAS1L
E, F
71Homo sapiensMutation(s): 0 
Gene Names: LAS1LMSTP060
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4W2 (Homo sapiens)
Explore Q9Y4W2 
Go to UniProtKB:  Q9Y4W2
PHAROS:  Q9Y4W2
GTEx:  ENSG00000001497 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4W2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118093

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-28
    Changes: Data collection