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- EMDB-47172: Human PELP1-WDR18 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-47172
TitleHuman PELP1-WDR18 complex
Map dataHuman PELP1-WDR18 complex
Sample
  • Complex: Human PELP1-WDR18 complex
    • Protein or peptide: WD repeat-containing protein 18
    • Protein or peptide: Proline-, glutamic acid- and leucine-rich protein 1
KeywordsComplex / STRUCTURAL PROTEIN
Function / homology
Function and homology information


rixosome complex / PTK6 Expression / dynein axonemal particle / SUMO binding / nuclear pre-replicative complex / MLL1 complex / cellular response to estrogen stimulus / Major pathway of rRNA processing in the nucleolus and cytosol / euchromatin / DNA-templated DNA replication ...rixosome complex / PTK6 Expression / dynein axonemal particle / SUMO binding / nuclear pre-replicative complex / MLL1 complex / cellular response to estrogen stimulus / Major pathway of rRNA processing in the nucleolus and cytosol / euchromatin / DNA-templated DNA replication / rRNA processing / chromatin binding / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
WD repeat-containing protein 18, C-terminal domain / WDR18 C-terminal helix / Uncharacterised domain NUC202 / PELP1, middle domain / WD repeat-containing protein WDR18/Ipi3/RID3 / Pre-rRNA-processing protein RIX1, N-terminal / rRNA processing/ribosome biogenesis / Armadillo-like helical / WD domain, G-beta repeat / Armadillo-type fold ...WD repeat-containing protein 18, C-terminal domain / WDR18 C-terminal helix / Uncharacterised domain NUC202 / PELP1, middle domain / WD repeat-containing protein WDR18/Ipi3/RID3 / Pre-rRNA-processing protein RIX1, N-terminal / rRNA processing/ribosome biogenesis / Armadillo-like helical / WD domain, G-beta repeat / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Proline-, glutamic acid- and leucine-rich protein 1 / WD repeat-containing protein 18
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 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_47172.png

Downloads & links

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Map

FileDownload / File: emd_47172.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman PELP1-WDR18 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-2.0978842 - 2.9027421
Average (Standard dev.)0.0003844099 (±0.05809952)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47172_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_47172_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Human PELP1-WDR18 complex

EntireName: Human PELP1-WDR18 complex
Components
  • Complex: Human PELP1-WDR18 complex
    • Protein or peptide: WD repeat-containing protein 18
    • Protein or peptide: Proline-, glutamic acid- and leucine-rich protein 1

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Supramolecule #1: Human PELP1-WDR18 complex

SupramoleculeName: Human PELP1-WDR18 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: WD repeat-containing protein 18

MacromoleculeName: WD repeat-containing protein 18 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.660301 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNMAAPMEVA VCTDSAAPMW SCIVWELHSG ANLLTYRGGQ AGPRGLALLN GEYLLAAQLG KNYISAWELQ RKDQLQQKIM CPGPVTCLT ASPNGLYVLA GVAESIHLWE VSTGNLLVIL SRHYQDVSCL QFTGDSSHFI SGGKDCLVLV WSLCSVLQAD P SRIPAPRH ...String:
SNMAAPMEVA VCTDSAAPMW SCIVWELHSG ANLLTYRGGQ AGPRGLALLN GEYLLAAQLG KNYISAWELQ RKDQLQQKIM CPGPVTCLT ASPNGLYVLA GVAESIHLWE VSTGNLLVIL SRHYQDVSCL QFTGDSSHFI SGGKDCLVLV WSLCSVLQAD P SRIPAPRH VWSHHALPIT DLHCGFGGPL ARVATSSLDQ TVKLWEVSSG ELLLSVLFDV SIMAVTMDLA EHHMFCGGSE GS IFQVDLF TWPGQRERSF HPEQDAGKVF KGHRNQVTCL SVSTDGSVLL SGSHDETVRL WDVQSKQCIR TVALKGPVTN AAI LLAPVS MLSSDFRPSL PLPHFNKHLL GAEHGDEPRH GGLTLRLGLH QQGSEPSYLD RTEQLQAVLC STMEKSVLGG QDQL RVRVT ELEDEVRNLR KINRDLFDFS TRFITRPAK

UniProtKB: WD repeat-containing protein 18

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Macromolecule #2: Proline-, glutamic acid- and leucine-rich protein 1

MacromoleculeName: Proline-, glutamic acid- and leucine-rich protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.266117 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNMAAAVLSG PSAGSAAGVP GGTGGLSAVS SGPRLRLLLL ESVSGLLQPR TGSAVAPVHP PNRSAPHLPG LMCLLRLHGS VGGAQNLSA LGALVSLSNA RLSSIKTRFE GLCLLSLLVG ESPTELFQQH CVSWLRSIQQ VLQTQDPPAT MELAVAVLRD L LRYAAQLP ...String:
SNMAAAVLSG PSAGSAAGVP GGTGGLSAVS SGPRLRLLLL ESVSGLLQPR TGSAVAPVHP PNRSAPHLPG LMCLLRLHGS VGGAQNLSA LGALVSLSNA RLSSIKTRFE GLCLLSLLVG ESPTELFQQH CVSWLRSIQQ VLQTQDPPAT MELAVAVLRD L LRYAAQLP ALFRDISMNH LPGLLTSLLG LRPECEQSAL EGMKACMTYF PRACGSLKGK LASFFLSRVD ALSPQLQQLA CE CYSRLPS LGAGFSQGLK HTESWEQELH SLLASLHTLL GALYEGAETA PVQNEGPGVE MLLSSEDGDA HVLLQLRQRF SGL ARCLGL MLSSEFGAPV SVPVQEILDF ICRTLSVSSK NISLHGDGPL RLLLLPSIHL EALDLLSALI LACGSRLLRF GILI GRLLP QVLNSWSIGR DSLSPGQERP YSTVRTKVYA ILELWVQVCG ASAGMLQGGA SGEALLTHLL SDISPPADAL KLRSP RGSP DGSLQTGKPS APKKLKLDVG EAMAPPSHRK GDSNANSDVC AAALRGLSRT ILMCGPLIKE ETHRRLHDLV LPLVMG VQQ GEVLGSSPYT SSRCRRELYC LLLALLLAPS PRCPPPLACA LQAFSLGQRE DSLEVSSFCS EALVTCAALT HPRVPPL QP MG

UniProtKB: Proline-, glutamic acid- and leucine-rich protein 1

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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 / Details: 20mM Hepes pH8.0, 250mM NaCl, 5mM DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 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: PDB ENTRY
PDB model - PDB ID:

7uwf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1076956
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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