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- EMDB-20040: Precursor ribosomal RNA processing complex, State 2. -

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Basic information

Entry
Database: EMDB / ID: EMD-20040
TitlePrecursor ribosomal RNA processing complex, State 2.
Map data
Sample
  • Complex: Precursor Ribosomal RNA Processing Complex
    • Protein or peptide: Ribonuclease
    • Protein or peptide: CLP1_P domain-containing protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsComplex / Ribonuclease / Polynucleotide kinase / RNA BINDING PROTEIN
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 speciesChaetomium thermophilum (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPillon MC / Hsu AL
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 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.
History
DepositionMar 28, 2019-
Header (metadata) releaseApr 17, 2019-
Map releaseSep 11, 2019-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing 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
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  • 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-6of2
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20040.png

Downloads & links

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Map

FileDownload / File: emd_20040.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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-0.787425 - 28.107223999999999
Average (Standard dev.)0.004821982 (±0.7046653)
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-0.78728.1070.005

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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
Components
  • Complex: Precursor Ribosomal RNA Processing Complex
    • Protein or peptide: Ribonuclease
    • Protein or peptide: CLP1_P domain-containing protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Precursor Ribosomal RNA Processing Complex

SupramoleculeName: Precursor Ribosomal RNA Processing Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Precursor Ribosomal RNA Processing Complex coordinates removal of a transcribed spacer.
Source (natural)Organism: Chaetomium thermophilum (fungus)
Molecular weightTheoretical: 234 KDa

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Macromolecule #1: Ribonuclease

MacromoleculeName: Ribonuclease / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 43.842871 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGAMGSMV QYIFTPWRNR AELLAVRAQF YPEHTSKTHL KKHHQSTFQD DEHIRSEKQK AVARVSMWM QRGGCPHMVE STALLVAAIL SDEAQGSGAA GGYAVRAAYS AAFSRFVTGL LDSHQDKQRK QSMYDVAKAV G LPAAFVEL ...String:
MSYYHHHHHH DYDIPTTENL YFQGAMGSMV QYIFTPWRNR AELLAVRAQF YPEHTSKTHL KKHHQSTFQD DEHIRSEKQK AVARVSMWM QRGGCPHMVE STALLVAAIL SDEAQGSGAA GGYAVRAAYS AAFSRFVTGL LDSHQDKQRK QSMYDVAKAV G LPAAFVEL RHQATHEQLP SLTRLRSAAR RALEWIWWYY WKGLGPVDMV QRGVNGKGVA GVGDTSESEE KDVGEEGGDA AA RCREGVV RLLESDVRVG GEAINGPGKE ELLAEFGEAL VLTTLDAAAG NTRDVGVLRR AIGLMREIVN GGDEDCMQLE NGK GNRDVE KLKEELKKGW EEIKRLAQEK EDSGDDQTED EDVDMEAEEE DKKEQQSGWV LYDEKEWVPK PIGIV

UniProtKB: Uncharacterized protein

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Macromolecule #2: CLP1_P domain-containing protein

MacromoleculeName: CLP1_P domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 69.660539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHSSFQPNN SNFQRKAGGR LVLSTPDVER FVILGNYGVK VHQGEVTIAG ATLTPIDDVQ WVHAPHCHAL PVLRTANDTV IELLPCPTA QGLRELARLN PLFGRLWNET SDTFQIIYTS ADAPKRTSLR ELASHPAWNK KISELLTSTR RKPSPILFIC G PKSSGKST ...String:
MHHSSFQPNN SNFQRKAGGR LVLSTPDVER FVILGNYGVK VHQGEVTIAG ATLTPIDDVQ WVHAPHCHAL PVLRTANDTV IELLPCPTA QGLRELARLN PLFGRLWNET SDTFQIIYTS ADAPKRTSLR ELASHPAWNK KISELLTSTR RKPSPILFIC G PKSSGKST FGRLLTNRLM TDRAGHKSRS WKPVMVLDLD PGQPEFSPPG VVSLTKLRRP NLAPPFCHPG LSFGEKGLDG GN EGMTTVR MHAIASVTPA LDPAHFIACA RDLFAYYRRS ASQENIPLVV NTPGWIQGTG LDLLAELIAV LRPTEVLYMS EDG PEETVS ALREACASSS TIPFTMLPSQ PNSSGEGGGG GAASWTPATL RSMAMQSYFH LSPFSRDQQG GPGCEWNPTP LTHL CPWRV RLAGRPDERG VLGIVCYDHQ YAPELVSDAI NGMVMGLVRI EKKEALRGLA VPGDTSLSFT SSTSQGGCDD ELDSD SNSS SAPSFTSSSP SHLNSTPLLP LIPNPTGSPL SPQYTSLVGL VLIRGVSLTA SNPELHLLTP VPPSVLHSFR GDELVL VAG KFDAPTWAYV EGLYWKSNSK AAKRVDEERE DEDREESGGV EEEEEQDEVP WVEMLHGSAG RDVGSRVWRV RRDLGRS

UniProtKB: Polynucleotide 5'-hydroxyl-kinase GRC3

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70561
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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