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- EMDB-80744: Cryo-EM structure of human LAS1L-NOL9 complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-80744
TitleCryo-EM structure of human LAS1L-NOL9 complex
Map datalocal resolution filtered map
Sample
  • Complex: LAS1 complex
    • Protein or peptide: Ribosomal biogenesis protein LAS1L
    • Protein or peptide: Polynucleotide 5'-hydroxyl-kinase NOL9
KeywordsLAS1L / NOL9 / ribosome / 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 / hydrolase activity / nucleolus / RNA binding / nucleoplasm / ATP binding / membrane / nucleus
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: 3.4 Å
AuthorsZhu J / Li Y / Cheng J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of human LAS1L-NOL9 complex
Authors: Zhu J / Li Y / Cheng J
History
DepositionMay 6, 2026-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80744.png

Downloads & links

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Map

FileDownload / File: emd_80744.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-4.1934576 - 4.766712
Average (Standard dev.)0.002837959 (±0.07589174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: local resolution filtered map using DeepEMhancer

Fileemd_80744_additional_1.map
Annotationlocal resolution filtered map using DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80744_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_80744_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LAS1 complex

EntireName: LAS1 complex
Components
  • Complex: LAS1 complex
    • Protein or peptide: Ribosomal biogenesis protein LAS1L
    • Protein or peptide: Polynucleotide 5'-hydroxyl-kinase NOL9

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Supramolecule #1: LAS1 complex

SupramoleculeName: LAS1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ribosomal biogenesis protein LAS1L

MacromoleculeName: Ribosomal biogenesis protein LAS1L / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.153734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSWESGAGPG LGSQGMDLVW SAWYGKCVKG KGSLPLSAHG IVVAWLSRAE WDQVTVYLFC DDHKLQRYAL NRITVWRSRS GNELPLAVA STADLIRCKL LDVTGGLGTD ELRLLYGMAL VRFVNLISER KTKFAKVPLK CLAQEVNIPD WIVDLRHELT H KKMPHIND ...String:
MSWESGAGPG LGSQGMDLVW SAWYGKCVKG KGSLPLSAHG IVVAWLSRAE WDQVTVYLFC DDHKLQRYAL NRITVWRSRS GNELPLAVA STADLIRCKL LDVTGGLGTD ELRLLYGMAL VRFVNLISER KTKFAKVPLK CLAQEVNIPD WIVDLRHELT H KKMPHIND CRRGCYFVLD WLQKTYWCRQ LENSLRETWE LEEFREGIEE EDQEEDKNIV VDDITEQKPE PQDDGKSTES DV KADGDSK GSEEVDSHCK KALSHKELYE RARELLVSYE EEQFTVLEKF RYLPKAIKAW NNPSPRVECV LAELKGVTCE NRE AVLDAF LDDGFLVPTF EQLAALQIEY EDGQTEVQRG EGTDPKSHKN VDLNDVLVPK PFSQFWQPLL RGLHSQNFTQ ALLE RMLSE LPALGISGIR PTYILRWTVE LIVANTKTGR NARRFSAGQW EARRGWRLFN CSASLDWPRM VESCLGSPCW ASPQL LRII FKAMGQGLPD EEQEKLLRIC SIYTQSGENS LVQEGSEASP IGKSPYTLDS LYWSVKPASS SFGSEAKAQQ QEEQGS VND VKEEEKEEKE VLPDQVEEEE ENDDQEEEEE DEDDEDDEEE DRMEVGPFST GQESPTAENA RLLAQKRGAL QGSAWQV SS EDVRWDTFPL GRMPGQTEDP AELMLENYDT MYLLDQPVLE QRLEPSTCKT DTLGLSCGVG SGNCSNSSSS NFEGLLWS Q GQLHGLKTGL QLF

UniProtKB: Ribosomal biogenesis protein LAS1L

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Macromolecule #2: Polynucleotide 5'-hydroxyl-kinase NOL9

MacromoleculeName: Polynucleotide 5'-hydroxyl-kinase NOL9 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: polynucleotide 5'-hydroxyl-kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 79.432734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADSGLLLKR GSCRSTWLRV RKARPQLILS RRPRRRLGSL RWCGRRRLRW RLLQAQASGV DWREGARQVS RAAAARRPNT ATPSPIPSP TPASEPESEP ELESASSCHR PLLIPPVRPV GPGRALLLLP VEQGFTFSGI CRVTCLYGQV QVFGFTISQG Q PAQDIFSV ...String:
MADSGLLLKR GSCRSTWLRV RKARPQLILS RRPRRRLGSL RWCGRRRLRW RLLQAQASGV DWREGARQVS RAAAARRPNT ATPSPIPSP TPASEPESEP ELESASSCHR PLLIPPVRPV GPGRALLLLP VEQGFTFSGI CRVTCLYGQV QVFGFTISQG Q PAQDIFSV YTHSCLSIHA LHYSQPEKSK KELKREARNL LKSHLNLDDR RWSMQNFSPQ CSIVLLEHLK TATVNFITSY PG SSYIFVQ ESPTPQIKPE YLALRSVGIR REKKRKGLQL TESTLSALEE LVNVSCEEVD GCPVILVCGS QDVGKSTFNR YLI NHLLNS LPCVDYLECD LGQTEFTPPG CISLLNITEP VLGPPFTHLR TPQKMVYYGK PSCKNNYENY IDIVKYVFSA YKRE SPLIV NTMGWVSDQG LLLLIDLIRL LSPSHVVQFR SDHSKYMPDL TPQYVDDMDG LYTKSKTKMR NRRFRLAAFA DALEF ADEE KESPVEFTGH KLIGVYTDFA FRITPRNRES HNKILRDLSI LSYLSQLQPP MPKPLSPLHS LTPYQVPFNA VALRIT HSD VAPTHILYAV NASWVGLCKI QDDVRGYTNG PILLAQTPIC DCLGFGICRG IDMEKRLYHI LTPVPPEELR TVNCLLV GA IAIPHCVLKC QRGIEGTVPY VTTDYNFKLP GASEKIGARE PEEAHKEKPY RRPKFCRKMK

UniProtKB: Polynucleotide 5'-hydroxyl-kinase NOL9

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 84043
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC

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