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- EMDB-47171: Human LAS1L-NOL9 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-47171
TitleHuman LAS1L-NOL9 complex
Map data
Sample
  • Complex: Human LAS1L-NOL9 complex
    • Protein or peptide: Polynucleotide 5'-hydroxyl-kinase NOL9
    • Protein or peptide: Ribosomal biogenesis protein LAS1L
    • Protein or peptide: Ribosomal biogenesis protein LAS1L
KeywordsComplex / RNA BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsHuang J / Tong L
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47171.png

Downloads & links

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Map

FileDownload / File: emd_47171.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.27
Minimum - Maximum-3.262097 - 4.4541607
Average (Standard dev.)0.0002693829 (±0.06486875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47171_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47171_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Human LAS1L-NOL9 complex

EntireName: Human LAS1L-NOL9 complex
Components
  • Complex: Human LAS1L-NOL9 complex
    • Protein or peptide: Polynucleotide 5'-hydroxyl-kinase NOL9
    • Protein or peptide: Ribosomal biogenesis protein LAS1L
    • Protein or peptide: Ribosomal biogenesis protein LAS1L

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Supramolecule #1: Human LAS1L-NOL9 complex

SupramoleculeName: Human LAS1L-NOL9 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Polynucleotide 5'-hydroxyl-kinase NOL9

MacromoleculeName: Polynucleotide 5'-hydroxyl-kinase NOL9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: polynucleotide 5'-hydroxyl-kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.021492 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNSASSCHRP LLIPPVRPVG PGRALLLLPV EQGFTFSGIC RVTCLYGQVQ VFGFTISQGQ PAQDIFSVYT HSCLSIHALH YSQPEKSKK ELKREARNLL KSHLNLDDRR WSMQNFSPQC SIVLLEHLKT ATVNFITSYP GSSYIFVQES PTPQIKPEYL A LRSVGIRR ...String:
SNSASSCHRP LLIPPVRPVG PGRALLLLPV EQGFTFSGIC RVTCLYGQVQ VFGFTISQGQ PAQDIFSVYT HSCLSIHALH YSQPEKSKK ELKREARNLL KSHLNLDDRR WSMQNFSPQC SIVLLEHLKT ATVNFITSYP GSSYIFVQES PTPQIKPEYL A LRSVGIRR EKKRKGLQLT ESTLSALEEL VNVSCEEVDG CPVILVCGSQ DVGKSTFNRY LINHLLNSLP CVDYLECDLG QT EFTPPGC ISLLNITEPV LGPPFTHLRT PQKMVYYGKP SCKNNYENYI DIVKYVFSAY KRESPLIVNT MGWVSDQGLL LLI DLIRLL SPSHVVQFRS DHSKYMPDLT PQYVDDMDGL YTKSKTKMRN RRFRLAAFAD ALEFADEEKE SPVEFTGHKL IGVY TDFAF RITPRNRESH NKILRDLSIL SYLSQLQPPM PKPLSPLHSL TPYQVPFNAV ALRITHSDVA PTHILYAVNA SWVGL CKIQ DDVRGYTNGP ILLAQTPICD CLGFGICRGI DMEKRLYHIL TPVPPEELRT VNCLLVGAIA IPHCVLKCQR GIEGTV PYV TTDYNFKLPG ASEKIGAREP EEAHKEKPYR RPKFCRKMK

UniProtKB: Polynucleotide 5'-hydroxyl-kinase NOL9

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Macromolecule #2: Ribosomal biogenesis protein LAS1L

MacromoleculeName: Ribosomal biogenesis protein LAS1L / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.170799 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNMSWESGAG PGLGSQGMDL VWSAWYGKCV KGKGSLPLSA HGIVVAWLSR AEWDQVTVYL FCDDHKLQRY ALNRITVWRS RSGNELPLA VASTADLIRC KLLDVTGGLG TDELRLLYGM ALVRFVNLIS ERKTKFAKVP LKCLAQEVNI PDWIVDLRHE L THKKMPHI ...String:
SNMSWESGAG PGLGSQGMDL VWSAWYGKCV KGKGSLPLSA HGIVVAWLSR AEWDQVTVYL FCDDHKLQRY ALNRITVWRS RSGNELPLA VASTADLIRC KLLDVTGGLG TDELRLLYGM ALVRFVNLIS ERKTKFAKVP LKCLAQEVNI PDWIVDLRHE L THKKMPHI NDCRRGCYFV LDWLQKTYWC RQLENSLRET WELE

UniProtKB: Ribosomal biogenesis protein LAS1L

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Macromolecule #3: Ribosomal biogenesis protein LAS1L

MacromoleculeName: Ribosomal biogenesis protein LAS1L / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.958731 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
SNGQESPTAE NARLLAQKRG ALQGSAWQVS SEDVRWDTFP LGRMPGQTED PAELMLENYD TMYLLDQPVL E

UniProtKB: Ribosomal biogenesis protein LAS1L

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 590896
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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