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- EMDB-17949: Chaetomium thermophilum Las1-Grc3-complex -

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Basic information

Entry
Database: EMDB / ID: EMD-17949
TitleChaetomium thermophilum Las1-Grc3-complex
Map dataChaetomium thermophilum Las1-Grc3-complex - local resolution filtered
Sample
  • Complex: Chaetomium thermophilum Las1-Grc3-complex
    • Protein or peptide: Las1
    • Protein or peptide: Polynucleotide 5'-hydroxyl-kinase GRC3
Keywordsbiogenesis / pre-60S / 5S RNP / RIBOSOME
Function / homology
Function and homology information


polynucleotide 5'-hydroxyl-kinase activity / Las1 complex / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / maturation of LSU-rRNA / endonuclease activity / ATP binding / nucleus
Similarity search - Function
Las1 / Las1-like / Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain / Polyribonucleotide 5-hydroxyl-kinase Clp1/Grc3 / mRNA cleavage and polyadenylation factor CLP1 P-loop / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Polynucleotide 5'-hydroxyl-kinase GRC3 / Uncharacterized protein
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 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 17, 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_17949.png

Downloads & links

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Map

FileDownload / File: emd_17949.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChaetomium thermophilum Las1-Grc3-complex - local resolution filtered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 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: 0.7
Minimum - Maximum-2.0483022 - 4.1976185
Average (Standard dev.)0.0027471555 (±0.06764006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Chaetomium thermophilum Las1-Grc3-complex

Fileemd_17949_additional_1.map
AnnotationChaetomium thermophilum Las1-Grc3-complex
Projections & Slices
AxesZYX

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Additional map: Chaetomium thermophilum Las1-Grc3-complex - C1 symmetry - local...

Fileemd_17949_additional_2.map
AnnotationChaetomium thermophilum Las1-Grc3-complex - C1 symmetry - local resolution filtered
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Chaetomium thermophilum Las1-Grc3-complex - C1 symmetry

Fileemd_17949_additional_3.map
AnnotationChaetomium thermophilum Las1-Grc3-complex - C1 symmetry
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Additional map: Chaetomium thermophilum Las1-Grc3-complex - C1 symmetry - half map A

Fileemd_17949_additional_4.map
AnnotationChaetomium thermophilum Las1-Grc3-complex - C1 symmetry - half map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Chaetomium thermophilum Las1-Grc3-complex - C1 symmetry - half map B

Fileemd_17949_additional_5.map
AnnotationChaetomium thermophilum Las1-Grc3-complex - C1 symmetry - half map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Chaetomium thermophilum Las1-Grc3-complex - half map A

Fileemd_17949_half_map_1.map
AnnotationChaetomium thermophilum Las1-Grc3-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 Las1-Grc3-complex - half map B

Fileemd_17949_half_map_2.map
AnnotationChaetomium thermophilum Las1-Grc3-complex - half map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chaetomium thermophilum Las1-Grc3-complex

EntireName: Chaetomium thermophilum Las1-Grc3-complex
Components
  • Complex: Chaetomium thermophilum Las1-Grc3-complex
    • Protein or peptide: Las1
    • Protein or peptide: Polynucleotide 5'-hydroxyl-kinase GRC3

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Supramolecule #1: Chaetomium thermophilum Las1-Grc3-complex

SupramoleculeName: Chaetomium thermophilum Las1-Grc3-complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)

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Macromolecule #1: Las1

MacromoleculeName: Las1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 40.465246 KDa
SequenceString: MVQYIFTPWR NRAELLAVRA QFYPEHTSKT HLKKHHQSTF QDDEHIRSEK QKAVARVSMW MQRGGCPHMV ESTALLVAAI LSDEAQGSG AAGGYAVRAA YSAAFSRFVT GLLDSHQDKQ RKQSMYDVAK AVGLPAAFVE LRHQATHEQL PSLTRLRSAA R RALEWIWW ...String:
MVQYIFTPWR NRAELLAVRA QFYPEHTSKT HLKKHHQSTF QDDEHIRSEK QKAVARVSMW MQRGGCPHMV ESTALLVAAI LSDEAQGSG AAGGYAVRAA YSAAFSRFVT GLLDSHQDKQ RKQSMYDVAK AVGLPAAFVE LRHQATHEQL PSLTRLRSAA R RALEWIWW YYWKGLGPVD MVQRGVNGKG VAGVGDTSES EEKDVGEEGG DAAARCREGV VRLLESDVRV GGEAINGPGK EE LLAEFGE ALVLTTLDAA AGNTRDVGVL RRAIGLMREI VNGGDEDCMQ LENGKGNRDV EKLKEELKKG WEEIKRLAQE KED SGDDQT EDEDVDMEAE EEDKKEQQSG WVLYDEKEWV PKPIGIV

UniProtKB: Uncharacterized protein

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Macromolecule #2: Polynucleotide 5'-hydroxyl-kinase GRC3

MacromoleculeName: Polynucleotide 5'-hydroxyl-kinase GRC3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 81.434789 KDa
SequenceString: MTSTKKRKLE GSASESGNNT PILSAFAARQ QLWAQSLVVQ AQKQPQSVDN SKHVTERRSA TPISAAQVLR KSKRKSPEDS PITPATPAT PVETEEEKPS KPSSPRELLR HHSSFQPNNS NFQRKAGGRL VLSTPDVERF VILGNYGVKV HQGEVTIAGA T LTPIDDVQ ...String:
MTSTKKRKLE GSASESGNNT PILSAFAARQ QLWAQSLVVQ AQKQPQSVDN SKHVTERRSA TPISAAQVLR KSKRKSPEDS PITPATPAT PVETEEEKPS KPSSPRELLR HHSSFQPNNS NFQRKAGGRL VLSTPDVERF VILGNYGVKV HQGEVTIAGA T LTPIDDVQ WVHAPHCHAL PVLRTANDTV IELLPCPTAQ GLRELARLNP LFGRLWNETS DTFQIIYTSA DAPKRTSLRE LA SHPAWNK KISELLTSTR RKPSPILFIC GPKSSGKSTF GRLLTNRLMT DRAGHKSRSW KPVMVLDLDP GQPEFSPPGV VSL TKLRRP NLAPPFCHPG LSFGEKGLDG GNEGMTTVRM HAIASVTPAL DPAHFIACAR DLFAYYRRSA SQENIPLVVN TPGW IQGTG LDLLAELIAV LRPTEVLYMS EDGPEETVSA LREACASSST IPFTMLPSQP NSSGEGGGGG AASWTPATLR SMAMQ SYFH LSPFSRDQQG GPGCEWNPTP LTHLCPWRVR LAGRPDERGV LGIVCYDHQY APELVSDAIN GMVMGLVRIE KKEALR GLA VPGDTSLSFT SSTSQGGCDD ELDSDSNSSS APSFTSSSPS HLNSTPLLPL IPNPTGSPLS PQYTSLVGLV LIRGVSL TA SNPELHLLTP VPPSVLHSFR GDELVLVAGK FDAPTWAYVE GLYWKSNSKA AKRVDEERED EDREESGGVE EEEEQDEV P WVEMLHGSAG RDVGSRVWRV RRDLGRS

UniProtKB: Polynucleotide 5'-hydroxyl-kinase GRC3

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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: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104264
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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