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- EMDB-20042: Precursor ribosomal RNA processing complex, apo-state. -

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Basic information

Entry
Database: EMDB / ID: EMD-20042
TitlePrecursor ribosomal RNA processing complex, apo-state.
Map data
SamplePrecursor Ribosomal RNA Processing Complex:
Ribonuclease / CLP1_P domain-containing protein
Function / homologyLas1 / Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain / Las1-like / mRNA cleavage and polyadenylation factor CLP1 P-loop / Las1 complex / rRNA processing / endonuclease activity / CLP1_P domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesChaetomium thermophilum (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPillon MC / Hsu AL / Krahn JM / Williams JG / Goslen KH / Sobhany M / Borgnia MJ / Stanley RE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health SciencesZIA ES103247 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Cryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex.
Authors: Monica C Pillon / Allen L Hsu / Juno M Krahn / Jason G Williams / Kevin H Goslen / Mack Sobhany / Mario J Borgnia / Robin E Stanley /
Abstract: Ribosome assembly is a complex process reliant on the coordination of trans-acting enzymes to produce functional ribosomal subunits and secure the translational capacity of cells. The ...Ribosome assembly is a complex process reliant on the coordination of trans-acting enzymes to produce functional ribosomal subunits and secure the translational capacity of cells. The endoribonuclease (RNase) Las1 and the polynucleotide kinase (PNK) Grc3 assemble into a multienzyme complex, herein designated RNase PNK, to orchestrate processing of precursor ribosomal RNA (rRNA). RNase PNK belongs to the functionally diverse HEPN nuclease superfamily, whose members rely on distinct cues for nuclease activation. To establish how RNase PNK coordinates its dual enzymatic activities, we solved a series of cryo-EM structures of Chaetomium thermophilum RNase PNK in multiple conformational states. The structures reveal that RNase PNK adopts a butterfly-like architecture, harboring a composite HEPN nuclease active site flanked by discrete RNA kinase sites. We identify two molecular switches that coordinate nuclease and kinase function. Together, our structures and corresponding functional studies establish a new mechanism of HEPN nuclease activation essential for ribosome production.
Validation ReportPDB-ID: 6of4

SummaryFull reportAbout validation report
History
DepositionMar 28, 2019-
Header (metadata) releaseApr 17, 2019-
Map releaseSep 11, 2019-
UpdateSep 18, 2019-
Current statusSep 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6of4
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20042.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 224 pix.
= 241.92 Å
1.08 Å/pix.
x 224 pix.
= 241.92 Å
1.08 Å/pix.
x 224 pix.
= 241.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-0.5715813 - 28.728421999999998
Average (Standard dev.)0.017774632 (±0.67335343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 241.92001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z241.920241.920241.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.57228.7280.018

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Supplemental data

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Sample components

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Entire Precursor Ribosomal RNA Processing Complex

EntireName: Precursor Ribosomal RNA Processing Complex
Details: Precursor Ribosomal RNA Processing Complex coordinates removal of a transcribed spacer.
Number of components: 3

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Component #1: protein, Precursor Ribosomal RNA Processing Complex

ProteinName: Precursor Ribosomal RNA Processing Complex
Details: Precursor Ribosomal RNA Processing Complex coordinates removal of a transcribed spacer.
Recombinant expression: No
MassTheoretical: 234 kDa
SourceSpecies: Chaetomium thermophilum (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Ribonuclease

ProteinName: Ribonuclease / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 43.842871 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, CLP1_P domain-containing protein

ProteinName: CLP1_P domain-containing protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 69.660539 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 102753
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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