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- PDB-9dum: Human PELP1-WDR18-TEX10 complex -

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Basic information

Entry
Database: PDB / ID: 9dum
TitleHuman PELP1-WDR18-TEX10 complex
Components
  • Proline-, glutamic acid- and leucine-rich protein 1
  • Testis-expressed protein 10
  • WD repeat-containing protein 18
KeywordsSTRUCTURAL PROTEIN / Complex
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 / mitochondrion / RNA binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
Uncharacterised domain NUC202 / WD repeat-containing protein 18, C-terminal domain / PELP1, middle domain / Alternative WD40 repeat motif / Pre-rRNA-processing protein Ipi1, N-terminal / Rix1 complex component involved in 60S ribosome maturation / Pre-rRNA-processing protein RIX1, N-terminal / WD repeat-containing protein WDR18/Ipi3/RID3 / rRNA processing/ribosome biogenesis / HEAT repeat profile. ...Uncharacterised domain NUC202 / WD repeat-containing protein 18, C-terminal domain / PELP1, middle domain / Alternative WD40 repeat motif / Pre-rRNA-processing protein Ipi1, N-terminal / Rix1 complex component involved in 60S ribosome maturation / Pre-rRNA-processing protein RIX1, N-terminal / WD repeat-containing protein WDR18/Ipi3/RID3 / rRNA processing/ribosome biogenesis / HEAT repeat profile. / HEAT, type 2 / Armadillo-like helical / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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 / Testis-expressed protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 18
B: WD repeat-containing protein 18
C: Proline-, glutamic acid- and leucine-rich protein 1
D: Proline-, glutamic acid- and leucine-rich protein 1
H: Testis-expressed protein 10
G: Testis-expressed protein 10


Theoretical massNumber of molelcules
Total (without water)443,8796
Polymers443,8796
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein WD repeat-containing protein 18


Mass: 47660.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR18 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BV38
#2: Protein Proline-, glutamic acid- and leucine-rich protein 1 / Modulator of non-genomic activity of estrogen receptor / Transcription factor HMX3


Mass: 68266.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PELP1, HMX3, MNAR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8IZL8
#3: Protein Testis-expressed protein 10


Mass: 106013.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEX10, L18, Nbla10363 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NXF1
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 PELP1-WDR18-TEX10 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8 / Details: 20mM Hepes pH8.0, 400mM NaCl, 5mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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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: 2000 nm / Nominal defocus min: 1000 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: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268599 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318931
ELECTRON MICROSCOPYf_angle_d0.49625693
ELECTRON MICROSCOPYf_dihedral_angle_d6.0912606
ELECTRON MICROSCOPYf_chiral_restr0.0393048
ELECTRON MICROSCOPYf_plane_restr0.0043222

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