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- PDB-7uwf: Human Rix1 sub-complex scaffold -

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Basic information

Entry
Database: PDB / ID: 7uwf
TitleHuman Rix1 sub-complex scaffold
Components
  • Modulator of non-genomic activity of estrogen receptor
  • WD repeat-containing protein 18
KeywordsSTRUCTURAL PROTEIN / scaffold / complex / WD-repeat / solenoid
Function / homology
Function and homology information


rixosome complex / dynein axonemal particle / nuclear pre-replicative complex / Major pathway of rRNA processing in the nucleolus and cytosol / DNA-templated DNA replication / rRNA processing / nucleolus / nucleoplasm / 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 RIX1, N-terminal / WD repeat-containing protein WDR18/Ipi3/RID3 / rRNA processing/ribosome biogenesis / Armadillo-like helical / Armadillo-type fold / G-protein beta WD-40 repeat ...Uncharacterised domain NUC202 / WD repeat-containing protein 18, C-terminal domain / PELP1, middle domain / Alternative WD40 repeat motif / Pre-rRNA-processing protein RIX1, N-terminal / WD repeat-containing protein WDR18/Ipi3/RID3 / rRNA processing/ribosome biogenesis / Armadillo-like helical / 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. / WD domain, G-beta repeat / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsGordon, J. / Stanley, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES103247 United States
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM reveals the architecture of the PELP1-WDR18 molecular scaffold.
Authors: Jacob Gordon / Fleur L Chapus / Elizabeth G Viverette / Jason G Williams / Leesa J Deterding / Juno M Krahn / Mario J Borgnia / Joseph Rodriguez / Alan J Warren / Robin E Stanley /
Abstract: PELP1 (Proline-, Glutamic acid-, Leucine-rich protein 1) is a large scaffolding protein that functions in many cellular pathways including steroid receptor (SR) coactivation, heterochromatin ...PELP1 (Proline-, Glutamic acid-, Leucine-rich protein 1) is a large scaffolding protein that functions in many cellular pathways including steroid receptor (SR) coactivation, heterochromatin maintenance, and ribosome biogenesis. PELP1 is a proto-oncogene whose expression is upregulated in many human cancers, but how the PELP1 scaffold coordinates its diverse cellular functions is poorly understood. Here we show that PELP1 serves as the central scaffold for the human Rix1 complex whose members include WDR18, TEX10, and SENP3. We reconstitute the mammalian Rix1 complex and identified a stable sub-complex comprised of the conserved PELP1 Rix1 domain and WDR18. We determine a 2.7 Å cryo-EM structure of the subcomplex revealing an interconnected tetrameric assembly and the architecture of PELP1's signaling motifs, including eleven LxxLL motifs previously implicated in SR signaling and coactivation of Estrogen Receptor alpha (ERα) mediated transcription. However, the structure shows that none of these motifs is in a conformation that would support SR binding. Together this work establishes that PELP1 scaffolds the Rix1 complex, and association with WDR18 may direct PELP1's activity away from SR coactivation.
History
DepositionMay 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
C: Modulator of non-genomic activity of estrogen receptor
B: WD repeat-containing protein 18
D: Modulator of non-genomic activity of estrogen receptor


Theoretical massNumber of molelcules
Total (without water)236,8084
Polymers236,8084
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAILEA1 - 361
d_21ens_1ALAILEC1 - 361
d_11ens_2GLYLEUB1 - 519
d_21ens_2GLYLEUD1 - 519

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999978126822, -0.00594701158989, 0.00289463813487), (0.00594609682035, -0.999982269151, -0.000324525538713), (0.00289651676762, -0.000307306641699, 0.999995757868)253.591198758, 252.781503646, -0.386563742351
2given(-0.99997815173, -0.00594537864851, 0.00288938307469), (0.0059446158694, -0.999982293483, -0.000272510330384), (0.00289095209088, -0.000255328104026, 0.999995788593)253.592124396, 252.777150973, -0.390224368661

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Components

#1: Protein WD repeat-containing protein 18


Mass: 49183.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293FT / Gene: WDR18 / Cell line (production host): HEK293FT / Production host: Homo sapiens (human) / References: UniProt: Q9BV38
#2: Protein Modulator of non-genomic activity of estrogen receptor / Proline- / glutamic acid- and leucine-rich protein 1


Mass: 69220.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293FT / Gene: PELP1 / Cell line (production host): HEK293FT / Production host: Homo sapiens (human) / References: UniProt: C9JFV4

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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 Rix1 sub-complex scaffold / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 236.76 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293FT / Plasmid: pcDNA3.1
Buffer solutionpH: 7.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
1cryoSPARC3.2.0particle selection
2SerialEMimage acquisition
4cryoSPARC3.2.0CTF correction
7Cootmodel fitting
9cryoSPARC3.2.0initial Euler assignment
10cryoSPARC3.2.0final Euler assignment
12cryoSPARC3.2.03D reconstruction
13Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278192 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 21.72 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003513430
ELECTRON MICROSCOPYf_angle_d0.603818252
ELECTRON MICROSCOPYf_chiral_restr0.04272182
ELECTRON MICROSCOPYf_plane_restr0.00532310
ELECTRON MICROSCOPYf_dihedral_angle_d4.12061856
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000712098982819
ens_2d_2BELECTRON MICROSCOPYNCS constraints0.0511065317382

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