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- EMDB-17879: Chaetomium thermophilum Rix1-complex -

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Basic information

Entry
Database: EMDB / ID: EMD-17879
TitleChaetomium thermophilum Rix1-complex
Map dataChaetomium thermophilum Rix1-complex - local resolution filtered
Sample
  • Complex: Chaetomium thermophilum Rix1-complex
    • Protein or peptide: Pre-rRNA-processing protein IPI3
    • Protein or peptide: Pre-rRNA-processing protein RIX1
Keywordsbiogenesis / pre-60S / 5S RNP / RIBOSOME
Function / homology
Function and homology information


rixosome complex / rRNA processing / nucleus
Similarity search - Function
Pre-rRNA-processing protein RIX1, N-terminal / WD repeat-containing protein WDR18/Ipi3/RID3 / rRNA processing/ribosome biogenesis / Armadillo-type fold / Trp-Asp (WD) repeats 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
Pre-rRNA-processing protein IPI3 / Pre-rRNA-processing protein RIX1
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsThoms M / Cheng J / Denk T / Berninghausen O / Beckmann R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: EMBO Rep / Year: 2023
Title: Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Authors: Matthias Thoms / Benjamin Lau / Jingdong Cheng / Lisa Fromm / Timo Denk / Nikola Kellner / Dirk Flemming / Paulina Fischer / Laurent Falquet / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from ...The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from Chaetomium thermophilum, which consists of two sub-modules, the sphere-like Rix1-Ipi3-Ipi1 and the butterfly-like Las1-Grc3 complex, connected by a flexible linker. The Rix1 complex of the rixosome utilizes Sda1 as landing platform on nucleoplasmic pre-60S particles to wedge between the 5S rRNA tip and L1-stalk, thereby facilitating the 180° rotation of the immature 5S RNP towards its mature conformation. Upon rixosome positioning, the other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase can reach a strategic position at the pre-60S foot to cleave and 5' phosphorylate the nearby ITS2 pre-rRNA. Finally, inward movement of the L1 stalk permits the flexible Nop53 N-terminus with its AIM motif to become positioned at the base of the L1-stalk to facilitate Mtr4 helicase-exosome participation for completing ITS2 removal. Thus, the rixosome structure elucidates the coordination of two central ribosome biogenesis events, but its role in gene silencing may adapt similar strategies.
History
DepositionJul 15, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17879.png

Downloads & links

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Map

FileDownload / File: emd_17879.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChaetomium thermophilum Rix1-complex - local resolution filtered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 280 pix.
= 292.6 Å		1.05 Å/pix.
x 280 pix.
= 292.6 Å		1.05 Å/pix.
x 280 pix.
= 292.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-2.1849456 - 3.5356953
Average (Standard dev.)0.0046066 (±0.08521241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 292.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Chaetomium thermophilum Rix1-complex

Fileemd_17879_additional_1.map
AnnotationChaetomium thermophilum Rix1-complex
Projections & Slices
AxesZYX

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Additional map: Chaetomium thermophilum Rix1-complex - C1 symmetry - local...

Fileemd_17879_additional_2.map
AnnotationChaetomium thermophilum Rix1-complex - C1 symmetry - local resolution filtered
Projections & Slices
AxesZYX

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Additional map: Chaetomium thermophilum Rix1-complex - C1 symmetry

Fileemd_17879_additional_3.map
AnnotationChaetomium thermophilum Rix1-complex - C1 symmetry
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: Chaetomium thermophilum Rix1-complex - C1 symmetry - half map A

Fileemd_17879_additional_4.map
AnnotationChaetomium thermophilum Rix1-complex - C1 symmetry - half map A
Projections & Slices
AxesZYX

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Additional map: Chaetomium thermophilum Rix1-complex - C1 symmetry - half map B

Fileemd_17879_additional_5.map
AnnotationChaetomium thermophilum Rix1-complex - C1 symmetry - half map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Chaetomium thermophilum Rix1-complex - half map A

Fileemd_17879_half_map_1.map
AnnotationChaetomium thermophilum Rix1-complex - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Chaetomium thermophilum Rix1-complex - half map B

Fileemd_17879_half_map_2.map
AnnotationChaetomium thermophilum Rix1-complex - half map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Chaetomium thermophilum Rix1-complex

EntireName: Chaetomium thermophilum Rix1-complex
Components
  • Complex: Chaetomium thermophilum Rix1-complex
    • Protein or peptide: Pre-rRNA-processing protein IPI3
    • Protein or peptide: Pre-rRNA-processing protein RIX1

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Supramolecule #1: Chaetomium thermophilum Rix1-complex

SupramoleculeName: Chaetomium thermophilum Rix1-complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)

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Macromolecule #1: Pre-rRNA-processing protein IPI3

MacromoleculeName: Pre-rRNA-processing protein IPI3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 47.627816 KDa
SequenceString: MLTEEFVSAI CGPPLSSNTA IAKDVGIYCH TLSPSYSVKS TFKKSSVPVN CLAVSDTHIF AGQHEKAYVH VYSRLRGNQE AFVALPERI RCLILIGDIL VVGTTEGRLM LWEICTGRLV STPARHVQAV SCVAATPSHV LTGSDDSDIH VWSLSQLLEL D SAAEHEPL ...String:
MLTEEFVSAI CGPPLSSNTA IAKDVGIYCH TLSPSYSVKS TFKKSSVPVN CLAVSDTHIF AGQHEKAYVH VYSRLRGNQE AFVALPERI RCLILIGDIL VVGTTEGRLM LWEICTGRLV STPARHVQAV SCVAATPSHV LTGSDDSDIH VWSLSQLLEL D SAAEHEPL RTLANHRAAI TALAVSPSDS ADTNFCVSAS KDKSCIIWNY QTGDALRTLI FPGYPLCMSL DPSSRAIFVS CE DSSLYVA EMFGEKPLLG PGSEDPSTVV QISTPFGATQ PDVGPASCLS VSYDGTMLLT GHPRGQIMRW DISENKSPVE LAN LNAAVT NLIFVSPFLT SKPTKTVNII KPSQAERAYT FTAQFEPMSF TKSRLDSLLN ATGFPADALE SAIVAFYQPV TQSA GDQEL QRQNEELWEI INEQRALQKE TLQRYVEAKS SR

UniProtKB: Pre-rRNA-processing protein IPI3

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Macromolecule #2: Pre-rRNA-processing protein RIX1

MacromoleculeName: Pre-rRNA-processing protein RIX1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 84.849219 KDa
SequenceString: MTAPPDLRVV CHRLASTPVD SLPRLCPLLI NHVLRCGGPL SEPQDAKGKD RTSETAMLVH KFRTHITSLL TGKSPAGRFT AVCLIKAVI DVGGWESLRS AEPWIRGLIG VLQKPDPLSS KELSIVTLTK LYILLQDYQT LIREMATPTL PGYATACLQL I KPPASGRP ...String:
MTAPPDLRVV CHRLASTPVD SLPRLCPLLI NHVLRCGGPL SEPQDAKGKD RTSETAMLVH KFRTHITSLL TGKSPAGRFT AVCLIKAVI DVGGWESLRS AEPWIRGLIG VLQKPDPLSS KELSIVTLTK LYILLQDYQT LIREMATPTL PGYATACLQL I KPPASGRP LKVPLNFVDT VAWSLSKLVV LYSTTMRPFS GQIKSALRPY IAPTSSDNVV VPQSLKENSR NLLILLTYTA PK NGSSDEW VKAIRATILD CHTTADQVFR AVRESWESTT GYHIQPVNAT GEPSGGGDSV DELPPWSGLQ AGAERLTGLL EYL TAYFNN PTRAPVNVPL GELLDLTTRL TLVIPPSLGA EDSIETNPAI GRDEKAELWS ALPDIHHAVL RLHCAIIRRL EANA IPLAT DIIDQMVRVS TASKQLPSVR ETAYILAKEI LLLAGSTLPK LTVDILIPLI QSSCHDILTA AGHAQPAQSQ SSVPV TASK QQKSSSPALT NADAFLPGQS SSSTPKTSTA SPVSQAASAL LPTFFTHLPQ KHLPPDIRGL LDRTAILSHN QSAMLA SCL HPYRDSRGRY YPSILPFLVR RFPRDESVEV LRSNLVKVGG SDASRGWDLS NGVTRDISYG REFAQEMISE EKGVVKE DE TFAKEIEPVK STAKPATSAN AWGVEMELDV EHVNVAPIPE TTNPFATVVG TTSQPSTLIQ PACPSSPLKR KSDAEEFD E GSRPKRVDTG KAVSHPQMAV ISSVPKPEED KSDESSDSEG SVQIDMTLED DEEDEEEEDE

UniProtKB: Pre-rRNA-processing protein RIX1

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 239033
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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