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- EMDB-50048: Cryo-EM structure of Ch. thermophilum Rai1-Rat1 dimer. -

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Basic information

Entry
Database: EMDB / ID: EMD-50048
TitleCryo-EM structure of Ch. thermophilum Rai1-Rat1 dimer.
Map data
Sample
  • Complex: Cryo-EM structure of Ch. thermophilum Rai1-Rat1 complex
    • Protein or peptide: Decapping nuclease
    • Protein or peptide: 5'-3' exoribonuclease
  • Ligand: MAGNESIUM ION
KeywordsRai1 nuclease / Rtt103 binding / structured / RNA binding / RNA BINDING PROTEIN
Function / homology
Function and homology information


mRNA 5'-diphosphatase activity / NAD-cap decapping / 5'-3' RNA exonuclease activity / nuclease activity / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / DNA-templated transcription termination / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding ...mRNA 5'-diphosphatase activity / NAD-cap decapping / 5'-3' RNA exonuclease activity / nuclease activity / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / DNA-templated transcription termination / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide 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
Similarity search - Domain/homology
5'-3' exoribonuclease / Decapping nuclease
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 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
DepositionApr 8, 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_50048.png

Downloads & links

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Map

FileDownload / File: emd_50048.map.gz / Format: CCP4 / Size: 166.4 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 352 pix.
= 293.568 Å		0.83 Å/pix.
x 352 pix.
= 293.568 Å		0.83 Å/pix.
x 352 pix.
= 293.568 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0577
Minimum - Maximum-0.28447726 - 0.5088338
Average (Standard dev.)-0.00005282751 (±0.009951936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 293.568 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50048_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50048_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Ch. thermophilum Rai1-Rat1 complex

EntireName: Cryo-EM structure of Ch. thermophilum Rai1-Rat1 complex
Components
  • Complex: Cryo-EM structure of Ch. thermophilum Rai1-Rat1 complex
    • Protein or peptide: Decapping nuclease
    • Protein or peptide: 5'-3' exoribonuclease
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM structure of Ch. thermophilum Rai1-Rat1 complex

SupramoleculeName: Cryo-EM structure of Ch. thermophilum Rai1-Rat1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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Macromolecule #1: Decapping nuclease

MacromoleculeName: Decapping nuclease / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 46.165219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPIEFTIQPP DHYAGVNEPV KRPREFTCFS YDRERRFHLG DRSLKWFYPA YIPSDLSRGY QNWQRHDDSI DEHLDGLLAA IADYEKQTG KPIDAHVTTW RGMMTKIMAT PYDQEEWEMN ATFYRGCIFI EENHAFARRK KMMESSRPAR SDGISPNLMQ Y WGYKFETL ...String:
MPIEFTIQPP DHYAGVNEPV KRPREFTCFS YDRERRFHLG DRSLKWFYPA YIPSDLSRGY QNWQRHDDSI DEHLDGLLAA IADYEKQTG KPIDAHVTTW RGMMTKIMAT PYDQEEWEMN ATFYRGCIFI EENHAFARRK KMMESSRPAR SDGISPNLMQ Y WGYKFETL STIPRPWGEV SRDEIESRDD EIVNNMEQYC SVVRTGFGNT IVCLGGEVDA IWDAKPETPG EPINWVELKT SR MITNTGI QTAFDQKLLK YWIQSFLLGV PRIIVGFRDQ DGILRSMEEY ETLNIPYEVR RRGLAKWDGN VCIRFAALFL QWL RLNITE EGVWRIRRPF RGSRIELTKI EQVGHGAIIT EEFMNWRIKL DLQKAKQQAL EEGKQDQGEE GQKAAAPAAA

UniProtKB: Decapping nuclease

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Macromolecule #2: 5'-3' exoribonuclease

MacromoleculeName: 5'-3' exoribonuclease / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 119.988188 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGIPAAFRWL SNKYPKIISP VVEERPIVMP DGTEIPVDAT RPNPNGEEFD NLYLDMNGIV HPCSHPEDKP APKDEEEMMI EIFKYTDRI VKMVRPRKIL MIAVDGVAPR AKMNQQRSRR FRAAQEAKEK EEEKKQLLKM LRKEKGSNMQ EEPLETVVKK A FDSNSITP ...String:
MGIPAAFRWL SNKYPKIISP VVEERPIVMP DGTEIPVDAT RPNPNGEEFD NLYLDMNGIV HPCSHPEDKP APKDEEEMMI EIFKYTDRI VKMVRPRKIL MIAVDGVAPR AKMNQQRSRR FRAAQEAKEK EEEKKQLLKM LRKEKGSNMQ EEPLETVVKK A FDSNSITP GTPFMDILAA SLRYWCAYKL NTDPAWAKLK VIISDATVPG EGEHKIMEFI RSQRSSPEHN PNTRHVIYGL DA DLIMLGL ATHEPHFRVL REDVFFQEAK ARLCKLCGQK GHDERSCKGE AKQKQGEFDE KDHAQPLKPF IWLHVSILRE YLA AELEVP NLPFRWDLER AIDDWVFLCF FVGNDFLPHL PALEIRENGI DTLTAIWKDN LPIMGGYLTK DGHVDLERAQ YILN GLAKQ EDAIFRRRRE VEERREANAK RRKLNQQGAH AKGAADSHAG KSGRKHVPEA AGPLPGMALF PITNPPPPAI THDMV MKGR SVDQANLANK SAASVLKSQI QSMMAQKAAT NANGAEKDVS ADGTTTAPAS ALGKRKAELI EEDAATNTDT DSVTDG TGS DNEGPVDTVR LWEEGYADRY YEQKFKVDPK DIEFRHKVGR AYAEGLAWVL QYYYQGCPSW EWFYPYHYAP FAADFVD LA KMEIKFEKGR ISRPFEQLMS VLPAASRHAI PEVYHDLMTD PNSPIIDFYP EEFEIDLNGK KMAWQGVALL PFIEMPRL L AAMKEREHLL SEEDRARNEP GFDVLLISDA HPGLYEDITS HFYSKKQGAP KFKLNPRRSD GLAGKVEKIE GYVPHGSLV YPLARNSMPD VDYDRSITVR YIMPSSAHQH KSMLLRGVKL PPPALSRSDI EIIRSKAKNA GRSYGGAPLR NNYNSNGSRR EQPINYAAN APSALPSRNY GSYPGNYGGA NNYGNGYGSG YYPPPGWQPP PPGYPGFGVG VPPPPPPARL AGTPGGYGQG Y GQGYGQGY NQSYGTGYGS GYSSSYQQSA PDRYRPAPAP PPPSTHGYHS GYQSQQSYQG QHHRAGPPLP PSSNNTRRDG RY DDRRGYD DRRDARRDNN PYRDERRYR

UniProtKB: 5'-3' exoribonuclease

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / 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

Concentration1.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMTristris(hydroxymethyl)-aminoethan
2.0 mMMgSO4magnesium sulfate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / 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: 5822035
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 622117
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: 422 / Avg.num./class: 400 / Software - Name: cryoSPARC (ver. 4.4.1)

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