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- EMDB-26831: Human Rix1 sub-complex scaffold -

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Basic information

Entry
Database: EMDB / ID: EMD-26831
TitleHuman Rix1 sub-complex scaffold
Map dataPrimary map used for modeling. Has been locally filtered using cryoSPARC.
Sample
  • Complex: Human Rix1 sub-complex scaffold
    • Protein or peptide: WD repeat-containing protein 18
    • Protein or peptide: Modulator of non-genomic activity of estrogen receptor
Keywordsscaffold / complex / WD-repeat / solenoid / STRUCTURAL PROTEIN
Function / homology
Function and homology information


: / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsGordon J / Stanley RE
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26831.png

Downloads & links

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Map

FileDownload / File: emd_26831.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map used for modeling. Has been locally filtered using cryoSPARC.
Voxel sizeX=Y=Z: 1.056 Å
Density
Contour LevelBy AUTHOR: 1.04
Minimum - Maximum-7.811353 - 12.987435
Average (Standard dev.)0.010742185 (±0.27391955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_26831_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_26831_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Rix1 sub-complex scaffold

EntireName: Human Rix1 sub-complex scaffold
Components
  • Complex: Human Rix1 sub-complex scaffold
    • Protein or peptide: WD repeat-containing protein 18
    • Protein or peptide: Modulator of non-genomic activity of estrogen receptor

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Supramolecule #1: Human Rix1 sub-complex scaffold

SupramoleculeName: Human Rix1 sub-complex scaffold / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 236.76 kDa/nm

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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: 49.183957 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAPMEVAVC TDSAAPMWSC IVWELHSGAN LLTYRGGQAG PRGLALLNGE YLLAAQLGKN YISAWELQRK DQLQQKIMCP GPVTCLTAS PNGLYVLAGV AESIHLWEVS TGNLLVILSR HYQDVSCLQF TGDSSHFISG GKDCLVLVWS LCSVLQADPS R IPAPRHVW ...String:
MAAPMEVAVC TDSAAPMWSC IVWELHSGAN LLTYRGGQAG PRGLALLNGE YLLAAQLGKN YISAWELQRK DQLQQKIMCP GPVTCLTAS PNGLYVLAGV AESIHLWEVS TGNLLVILSR HYQDVSCLQF TGDSSHFISG GKDCLVLVWS LCSVLQADPS R IPAPRHVW SHHALPITDL HCGFGGPLAR VATSSLDQTV KLWEVSSGEL LLSVLFDVSI MAVTMDLAEH HMFCGGSEGS IF QVDLFTW PGQRERSFHP EQDAGKVFKG HRNQVTCLSV STDGSVLLSG SHDETVRLWD VQSKQCIRTV ALKGPVTNAA ILL APVSML SSDFRPSLPL PHFNKHLLGA EHGDEPRHGG LTLRLGLHQQ GSEPSYLDRT EQLQAVLCST MEKSVLGGQD QLRV RVTEL EDEVRNLRKI NRDLFDFSTR FITRPAKLES RGPYPYDVPD YA

UniProtKB: WD repeat-containing protein 18

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Macromolecule #2: Modulator of non-genomic activity of estrogen receptor

MacromoleculeName: Modulator of non-genomic activity of estrogen receptor
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.220078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKGT MAAAVLSGPS AGSAAGVPGG TGGLSAVSSG PRLRLLLLES VSGLLQPRTG SAVAPVHPPN RSAPHLPGLM CLLRLHGSV GGAQNLSALG ALVSLSNARL SSIKTRFEGL CLLSLLVGES PTELFQQHCV SWLRSIQQVL QTQDPPATME L AVAVLRDL ...String:
DYKDDDDKGT MAAAVLSGPS AGSAAGVPGG TGGLSAVSSG PRLRLLLLES VSGLLQPRTG SAVAPVHPPN RSAPHLPGLM CLLRLHGSV GGAQNLSALG ALVSLSNARL SSIKTRFEGL CLLSLLVGES PTELFQQHCV SWLRSIQQVL QTQDPPATME L AVAVLRDL LRYAAQLPAL FRDISMNHLP GLLTSLLGLR PECEQSALEG MKACMTYFPR ACGSLKGKLA SFFLSRVDAL SP QLQQLAC ECYSRLPSLG AGFSQGLKHT ESWEQELHSL LASLHTLLGA LYEGAETAPV QNEGPGVEML LSSEDGDAHV LLQ LRQRFS GLARCLGLML SSEFGAPVSV PVQEILDFIC RTLSVSSKNI SLHGDGPLRL LLLPSIHLEA LDLLSALILA CGSR LLRFG ILIGRLLPQV LNSWSIGRDS LSPGQERPYS TVRTKVYAIL ELWVQVCGAS AGMLQGGASG EALLTHLLSD ISPPA DALK LRSPRGSPDG SLQTGKPSAP KKLKLDVGEA MAPPSHRKGD SNANSDVCAA ALRGLSRTIL MCGPLIKEET HRRLHD LVL PLVMGVQQGE VLGSSPYTSS RCRRELYCLL LALLLAPSPR CPPPLACALQ AFSLGQREDS LEVSSFCSEA LVTCAAL TH PRVPPLQPMG

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: 7.7
GridModel: C-flat-1.2/1.3 / Material: GOLD / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 278192

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7uwf:
Human Rix1 sub-complex scaffold

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