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- EMDB-47148: CRYO-EM STRUCTURE OF SACCHAROMYCES CEREVISIAE RAT1-RAI1-RTT103 COMPLEX -

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Entry
Database: EMDB / ID: EMD-47148
TitleCRYO-EM STRUCTURE OF SACCHAROMYCES CEREVISIAE RAT1-RAI1-RTT103 COMPLEX
Map data
Sample
  • Complex: Rat1-Rai1-Rtt103 complex
    • Protein or peptide: 5'-3' exoribonuclease 2
    • Protein or peptide: Decapping nuclease RAI1
    • Protein or peptide: Regulator of Ty1 transposition protein 103
  • Ligand: MAGNESIUM ION
KeywordsNuclease / Complex / Transcription termination / TRANSCRIPTION
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 / NAD-cap decapping / nuclear polyadenylation-dependent rRNA catabolic process / 5'-3' RNA exonuclease activity / nuclear mRNA surveillance / transposable element silencing / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 3'-end processing / 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 / nuclear-transcribed mRNA catabolic process / negative regulation of transcription elongation by RNA polymerase II / 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: 2.85 Å
AuthorsChu HF / Tong L
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129539 United States
Simons FoundationSF349247 United States
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis for the interaction between Saccharomyces cerevisiae Rtt103 and the Rat1-Rai1 complex.
Authors: Hsu-Feng Chu / Liang Tong /
Abstract: The Rat1 5'-3' exoribonuclease together with its partner Rai1 have important roles in Saccharomyces cerevisiae RNA polymerase II transcription termination. Rtt103 copurifies with Rat1-Rai1 in S. ...The Rat1 5'-3' exoribonuclease together with its partner Rai1 have important roles in Saccharomyces cerevisiae RNA polymerase II transcription termination. Rtt103 copurifies with Rat1-Rai1 in S. cerevisiae, but its mechanism of interaction with them is not known. We report here the cryo-EM structure of the S. cerevisiae Rat1-Rai1-Rtt103 ternary complex at 2.9 Å resolution. We found that a short segment of Rtt103 is in close contact with Rai1, while the rest of Rtt103, including its RNA polymerase II C-terminal domain interaction domain, shows no interactions with Rai1 or Rat1. This is in contrast to the observations on the Komagataella phaffii Rat1-Rai1-Rtt103 complex, where only the RNA polymerase II C-terminal domain interaction domain of Rtt103 has contacts with Rai1. Our structure reveals that S. cerevisiae Rtt103 Pro261 and Tyr263 have important contacts with Rai1, and we show that the P261G/Y263A mutation of Rtt103 blocks the interaction with Rat1-Rai1. Our structure suggests that, in yeast, this segment of Rtt103, which we have named the Rai1 interaction segment, likely helps the recruitment of Rat1-Rai1 to RNA polymerase II for termination.
History
DepositionSep 28, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47148.png

Downloads & links

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Map

FileDownload / File: emd_47148.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.456 Å		0.83 Å/pix.
x 256 pix.
= 211.456 Å		0.83 Å/pix.
x 256 pix.
= 211.456 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.9504241 - 1.3805941
Average (Standard dev.)0.00030265626 (±0.03397275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.456 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47148_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47148_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Rat1-Rai1-Rtt103 complex

EntireName: Rat1-Rai1-Rtt103 complex
Components
  • Complex: Rat1-Rai1-Rtt103 complex
    • Protein or peptide: 5'-3' exoribonuclease 2
    • Protein or peptide: Decapping nuclease RAI1
    • Protein or peptide: Regulator of Ty1 transposition protein 103
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Rat1-Rai1-Rtt103 complex

SupramoleculeName: Rat1-Rai1-Rtt103 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 114.204031 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 NYRNNKYSGN RNSLEHHHHH H

UniProtKB: 5'-3' exoribonuclease 2

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Macromolecule #2: Decapping nuclease RAI1

MacromoleculeName: Decapping nuclease RAI1 / type: protein_or_peptide / ID: 2 / 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: Trichoplusia ni (cabbage looper)
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 #3: Regulator of Ty1 transposition protein 103

MacromoleculeName: Regulator of Ty1 transposition protein 103 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 48.725473 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSSHHHHHH SSGLVPRGSH MPFSSEQFTT KLNTLEDSQE SISSASKWLL LQYRDAPKVA EMWKEYMLRP SVNTRRKLLG LYLMNHVVQ QAKGQKIIQF QDSFGKVAAE VLGRINQEFP RDLKKKLSRV VNILKERNIF SKQVVNDIER SLKTESSPVE A LVLPQKLK ...String:
MGSSHHHHHH SSGLVPRGSH MPFSSEQFTT KLNTLEDSQE SISSASKWLL LQYRDAPKVA EMWKEYMLRP SVNTRRKLLG LYLMNHVVQ QAKGQKIIQF QDSFGKVAAE VLGRINQEFP RDLKKKLSRV VNILKERNIF SKQVVNDIER SLKTESSPVE A LVLPQKLK DFAKDYEKLV KMHHNVCAMK MRFDKSSDEL DPSSSVYEEN FKTISKIGNM AKDIINESIL KRESGIHKLQ ST LDDEKRH LDEEQNMLSE IEFVLSAKDP SRLNKNVDED NIIPTYEVGD GDDDDDDGDN DDDDDDDDDD KNYDDRSNDS NYG VTNIST TDKKNEVVEK TDSEHKNSTH NPSDNQFGMK RTHDMIGHDD ANDIPEKKVH LDSKTSEDGT FNSEDGHYEL DIEG HVGAQ TDEGVENSGG VSSSIQDLLS KLAN

UniProtKB: Regulator of Ty1 transposition protein 103

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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

Concentration0.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
200.0 mMNaClsodium choloride
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 14 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.27 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 614995
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 552608
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9dso:
CRYO-EM STRUCTURE OF SACCHAROMYCES CEREVISIAE RAT1-RAI1-RTT103 COMPLEX

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