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- PDB-9dun: Human LAS1L-NOL9 complex -

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Basic information

Entry
Database: PDB / ID: 9dun
TitleHuman LAS1L-NOL9 complex
Components
  • (Ribosomal biogenesis protein LAS1L) x 2
  • Polynucleotide 5'-hydroxyl-kinase NOL9
KeywordsRNA BINDING PROTEIN / Complex
Function / homology
Function and homology information


ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / polynucleotide 5'-hydroxyl-kinase / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / polynucleotide 5'-hydroxyl-kinase activity / Las1 complex / intermediate filament cytoskeleton / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / MLL1 complex / Major pathway of rRNA processing in the nucleolus and cytosol ...ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / polynucleotide 5'-hydroxyl-kinase / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / polynucleotide 5'-hydroxyl-kinase activity / Las1 complex / intermediate filament cytoskeleton / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / MLL1 complex / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of LSU-rRNA / rRNA processing / endonuclease activity / Hydrolases; Acting on ester bonds / nucleolus / RNA binding / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
Polynucleotide 5'-hydroxyl-kinase NOL9, N-terminal domain / NOL9-like, C-terminal domain / Las1 / Las1-like / Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain / Polyribonucleotide 5-hydroxyl-kinase Clp1/Grc3 / mRNA cleavage and polyadenylation factor CLP1 P-loop / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Polynucleotide 5'-hydroxyl-kinase NOL9 / Ribosomal biogenesis protein LAS1L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsHuang, J. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
CitationJournal: Nat Commun / Year: 2025
Title: Molecular insights into the overall architecture of human rixosome.
Authors: Ji Huang / Liang Tong /
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, ...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.
History
DepositionOct 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
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Revision 1.1May 7, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polynucleotide 5'-hydroxyl-kinase NOL9
B: Polynucleotide 5'-hydroxyl-kinase NOL9
C: Ribosomal biogenesis protein LAS1L
D: Ribosomal biogenesis protein LAS1L
E: Ribosomal biogenesis protein LAS1L
F: Ribosomal biogenesis protein LAS1L


Theoretical massNumber of molelcules
Total (without water)198,3026
Polymers198,3026
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Polynucleotide 5'-hydroxyl-kinase NOL9 / Nucleolar protein 9


Mass: 68021.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOL9 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q5SY16, polynucleotide 5'-hydroxyl-kinase
#2: Protein Ribosomal biogenesis protein LAS1L / Endoribonuclease LAS1L / Protein LAS1 homolog


Mass: 23170.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAS1L, MSTP060 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9Y4W2, Hydrolases; Acting on ester bonds
#3: Protein Ribosomal biogenesis protein LAS1L / Endoribonuclease LAS1L / Protein LAS1 homolog


Mass: 7958.731 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAS1L, MSTP060 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9Y4W2, Hydrolases; Acting on ester bonds
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human LAS1L-NOL9 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 590896 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036826
ELECTRON MICROSCOPYf_angle_d0.5589285
ELECTRON MICROSCOPYf_dihedral_angle_d7.987943
ELECTRON MICROSCOPYf_chiral_restr0.0411080
ELECTRON MICROSCOPYf_plane_restr0.0051149

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