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- EMDB-50566: Cryo-EM structure of S. cerevisiae Rai1-Rat1-Rtt103(252-273) complex. -

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Basic information

Entry
Database: EMDB / ID: EMD-50566
TitleCryo-EM structure of S. cerevisiae Rai1-Rat1-Rtt103(252-273) complex.
Map data
Sample
  • Complex: Cryo-EM structure of S. cerevisiae Rai1-Rat1-Rtt103(252-273) complex.
    • Protein or peptide: Decapping nuclease RAI1
    • Protein or peptide: 5'-3' exoribonuclease 2
    • Protein or peptide: Regulator of Ty1 transposition protein 103
  • Ligand: MAGNESIUM ION
KeywordsRai1 nuclease / Rtt103 binding / structured / RNA binding / RNA BINDING PROTEIN
Function / homology
Function and homology information


RNA polymerase II termination complex / sno(s)RNA processing / positive regulation of termination of RNA polymerase II transcription / RNA NAD+-cap (NAD+-forming) hydrolase activity / termination of RNA polymerase II transcription, poly(A)-coupled / Las1 complex / termination of RNA polymerase II transcription, exosome-dependent / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / phosphodiesterase decapping endonuclease activity ...RNA polymerase II termination complex / sno(s)RNA processing / positive regulation of termination of RNA polymerase II transcription / RNA NAD+-cap (NAD+-forming) hydrolase activity / termination of RNA polymerase II transcription, poly(A)-coupled / Las1 complex / termination of RNA polymerase II transcription, exosome-dependent / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / RNA polymerase II C-terminal domain phosphoserine binding / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping / 5'-3' RNA exonuclease activity / nuclear mRNA surveillance / transposable element silencing / mRNA 3'-end processing / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA polymerase II transcribes snRNA genes / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / enzyme regulator activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA splicing, via spliceosome / mRNA processing / rRNA processing / site of double-strand break / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / rRNA binding / nucleotide binding / mRNA binding / chromatin / mitochondrion / DNA binding / RNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
: / 5'-3' exoribonuclease type 2 / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain / RAI1-like / RAI1-like family / RAI1 like PD-(D/E)XK nuclease ...: / 5'-3' exoribonuclease type 2 / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain / RAI1-like / RAI1-like family / RAI1 like PD-(D/E)XK nuclease / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS
Similarity search - Domain/homology
Decapping nuclease RAI1 / 5'-3' exoribonuclease 2 / Regulator of Ty1 transposition protein 103
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsDikunova A / Kubicek K / Noskova N / Stefl R
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Czech Science Foundation Czech Republic
CitationJournal: Structure / Year: 2025
Title: Assembly of the Xrn2/Rat1-Rai1-Rtt103 termination complexes in mesophilic and thermophilic organisms.
Authors: Alzbeta Dikunova / Nikola Noskova / Jan H Overbeck / Martin Polak / David Stelzig / David Zapletal / Karel Kubicek / Jiri Novacek / Remco Sprangers / Richard Stefl /
Abstract: The 5'-3' exoribonuclease Xrn2, known as Rat1 in yeasts, terminates mRNA transcription by RNA polymerase II (RNAPII). In the torpedo model of termination, the activity of Xrn2/Rat1 is enhanced by ...The 5'-3' exoribonuclease Xrn2, known as Rat1 in yeasts, terminates mRNA transcription by RNA polymerase II (RNAPII). In the torpedo model of termination, the activity of Xrn2/Rat1 is enhanced by Rai1, which is recruited to the termination site by Rtt103, an adaptor protein binding to the RNAPII C-terminal domain (CTD). The overall architecture of the Xrn2/Rat1-Rai1-Rtt103 complex remains unknown. We combined structural biology methods to characterize the torpedo complex from Saccharomyces cerevisiae and Chaetomium thermophilum. Comparison of the structures from these organisms revealed a conserved protein core fold of the subunits, but significant variability in their interaction interfaces. We found that in the mesophile, Rtt103 utilizes an unstructured region to augment a Rai1 β-sheet, while in the thermophile Rtt103 binds to a C-terminal helix of Rai1 via its CTD-interacting domain with an α-helical fold. These different torpedo complex assemblies reflect adaptations to the environment and impact complex recruitment to RNAPII.
History
DepositionJun 7, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50566.png

Downloads & links

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Map

FileDownload / File: emd_50566.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 384 pix.
= 375.3 Å		0.98 Å/pix.
x 384 pix.
= 375.3 Å		0.98 Å/pix.
x 384 pix.
= 375.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97734 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.49873358 - 0.9835829
Average (Standard dev.)-0.0009273362 (±0.015369621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 375.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50566_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #1

Fileemd_50566_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of S. cerevisiae Rai1-Rat1-Rtt103(252-273) complex.

EntireName: Cryo-EM structure of S. cerevisiae Rai1-Rat1-Rtt103(252-273) complex.
Components
  • Complex: Cryo-EM structure of S. cerevisiae Rai1-Rat1-Rtt103(252-273) complex.
    • Protein or peptide: Decapping nuclease RAI1
    • Protein or peptide: 5'-3' exoribonuclease 2
    • Protein or peptide: Regulator of Ty1 transposition protein 103
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM structure of S. cerevisiae Rai1-Rat1-Rtt103(252-273) complex.

SupramoleculeName: Cryo-EM structure of S. cerevisiae Rai1-Rat1-Rtt103(252-273) complex.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: 5'-3' exoribonuclease 2

MacromoleculeName: 5'-3' exoribonuclease 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 116.08493 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGVPSFFRWL SRKYPKIISP VLEEQPQIVD GVILPLDYSA SNPNGELDNL YLDMNGIVHP CSHPENKPPP ETEDEMLLAV FEYTNRVLN MARPRKVLVM AVDGVAPRAK MNQQRARRFR SARDAQIENE AREEIMRQRE EVGEIIDDAV RNKKTWDSNA I TPGTPFMD ...String:
MGVPSFFRWL SRKYPKIISP VLEEQPQIVD GVILPLDYSA SNPNGELDNL YLDMNGIVHP CSHPENKPPP ETEDEMLLAV FEYTNRVLN MARPRKVLVM AVDGVAPRAK MNQQRARRFR SARDAQIENE AREEIMRQRE EVGEIIDDAV RNKKTWDSNA I TPGTPFMD KLAAALRYWT AFKLATDPGW KNLQVIISDA TVPGEGEHKI MNFIRSQRAD PEYNPNTTHC IYGLDADLIF LG LATHEPH FKILREDVFA QDNRKRNNLK DTINMTEEEK QFLQKQNSEQ PFLWLHINVL REYLSAELWV PGLPFTFDLE RAI DDWVFM CFFCGNDFLP HLPCLDVREN SIDILLDIWK VVLPKLKTYM TCDGVLNLPS VETLLQHLGS REGDIFKTRH IQEA RKKEA FERRKAQKNM SKGQDRHPTV ATEQLQMYDT QGNLAKGSWN LTTSDMVRLK KELMLANEGN EEAIAKVKQQ SDKNN ELMK DISKEEIDDA VSKANKTNFN LAEVMKQKII NKKHRLEKDN EEEEIAKDSK KVKTEKAESE CDLDAEIKDE IVADVN DRE NSETTEVSRD SPVHSTVNVS EGPKNGVFDT DEFVKLFEPG YHERYYTAKF HVTPQDIEQL RKDMVKCYIE GVAWVLM YY YQGCASWNWF YPYHYAPLAT DFHGFSHLEI KFEEGTPFLP YEQLMSVLPA ASGHALPKIF RSLMSEPDSE IIDFYPEE F PIDMNGKKMS WQGIALLPFI DQDRLLTAVR AQYPLLSDAE RARNIRGEPV LLISNKNANY ERFSKKLYSK ENNNNNVVV KFQHFKSGLS GIVSKDVEGF ELNGKIVCPI QGGSLPNLST TLILKMSYRL IPLPSRNKSI ILNGFIPSEP VLTAYDLDSI MYKYNNQNY SRRWNFGNDL KQNIVPVGPK GITQYKPRTG GYRAFFYFAE LSRNNVQPAH NYGRNSYNSQ PGFNNSRYDG G NNNYRQNS NYRNNNYSGN RNSGQYSGNS YSRNNKQSRY DNSRANRR

UniProtKB: 5'-3' exoribonuclease 2

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Macromolecule #2: Regulator of Ty1 transposition protein 103

MacromoleculeName: Regulator of Ty1 transposition protein 103 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 2.454404 KDa
SequenceString:
KNVDEDNIIP TYEVGDGDDD DD

UniProtKB: Regulator of Ty1 transposition protein 103

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Macromolecule #3: Decapping nuclease RAI1

MacromoleculeName: Decapping nuclease RAI1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 44.571445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGVSANLFVK QRGSTTALKQ PKEIGFYSRT KDEEYLISDD TNLNYYYLPD AELDRKLDLS SGFQKFKDYY KDFEDRCSLR GLLETIESS ERHKGKKINA DIITFRGIAR KLISCAFDSP SFNTVDLRIV SFNGQLFIKE VPEAVNAAKA SSATEAGRNI N QDLNVFTG ...String:
MGVSANLFVK QRGSTTALKQ PKEIGFYSRT KDEEYLISDD TNLNYYYLPD AELDRKLDLS SGFQKFKDYY KDFEDRCSLR GLLETIESS ERHKGKKINA DIITFRGIAR KLISCAFDSP SFNTVDLRIV SFNGQLFIKE VPEAVNAAKA SSATEAGRNI N QDLNVFTG YKFETLATLS NPLQYTPREV IEKRTKRIVS HGDEYISVVR TGVGNCKLIL GAEVDCIFDF KENGRDNLKH YA ELKCTQQ VANISDTHKF ERKLFRTWLQ CFLVGIPRII YGFKDDHYVL KTVEEFSTEE VPVLLKNNNP QVGSACLEAI KWY GLLTEW LLKMIPRDED PHSQIRAFKL VFENNHLRLS EIEESDEEYS GLIDGEHILS NGFKEWRKSL K

UniProtKB: Decapping nuclease RAI1

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / 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

Concentration1.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
120.0 mMNaClsodium chloride
25.0 mMTristris(hydroxymethyl)-aminoethan
2.0 mMMgSO4magnesium sulfate
0.1 %Glycerolglycerol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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 / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4091013
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 284130
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 100 / Avg.num./class: 400 / Software - Name: cryoSPARC (ver. 4.4.1)

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Atomic model buiding 1

Initial model
ChainDetails
chain_id: A, source_name: Other, initial_model_type: in silico modelScRai1-Rat1 PDB ID:8Q6V, ModelAngelo
chain_id: B, source_name: Other, initial_model_type: in silico modelScRai1-Rat1 PDB ID:8Q6V, ModelAngelo
chain_id: D, residue_range: 252-273, source_name: Other, initial_model_type: in silico modelRtt103, AlphaFold
DetailsAs initial model was used previously estimated ScRai1-Rat1 dimer. The position of investigated peptide was predicted by AlphaFold and manually built into the corresponding cryo-EM using Coot. For final geometry estimation was used ISOLDE.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9fms:
Cryo-EM structure of S. cerevisiae Rai1-Rat1-Rtt103(252-273) complex.

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