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- EMDB-19078: Saccharomyces cerevisiae Prp43 helicase in complex with Pxr1 -

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Basic information

Entry
Database: EMDB / ID: EMD-19078
TitleSaccharomyces cerevisiae Prp43 helicase in complex with Pxr1
Map data
Sample
  • Complex: Saccharomyces cerevisiae Prp43-Pxr1 complex
    • Protein or peptide: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
    • Protein or peptide: Glutathione S-transferase class-mu 26 kDa isozyme,Protein PXR1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordspreribosome / helicase / ribosome assembly / inhibitor / RNA BINDING PROTEIN
Function / homology
Function and homology information


spliceosomal complex disassembly / telomerase inhibitor activity / post-mRNA release spliceosomal complex / box C/D sno(s)RNA 3'-end processing / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of telomere maintenance via telomerase / glutathione transferase / glutathione transferase activity / 90S preribosome / glutathione metabolic process ...spliceosomal complex disassembly / telomerase inhibitor activity / post-mRNA release spliceosomal complex / box C/D sno(s)RNA 3'-end processing / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of telomere maintenance via telomerase / glutathione transferase / glutathione transferase activity / 90S preribosome / glutathione metabolic process / enzyme activator activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / helicase activity / small-subunit processome / spliceosomal complex / rRNA processing / nucleic acid binding / RNA helicase activity / RNA helicase / mRNA binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding
Similarity search - Function
: / DHX15, DEXH-box helicase domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold ...: / DHX15, DEXH-box helicase domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / Glutathione S-transferase, C-terminal domain / : / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Thioredoxin-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Glutathione S-transferase class-mu 26 kDa isozyme / Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 / Protein PXR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsRabl J / Portugal Calisto D / Panse VG
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationNCCR RNA & Disease Switzerland
CitationJournal: Nat Commun / Year: 2024
Title: An inhibitory segment within G-patch activators tunes Prp43-ATPase activity during ribosome assembly.
Authors: Daniela Portugal-Calisto / Alexander Gregor Geiger / Julius Rabl / Oscar Vadas / Michaela Oborská-Oplová / Jarosław Mazur / Federica Richina / Purnima Klingauf-Nerurkar / Erich Michel / ...Authors: Daniela Portugal-Calisto / Alexander Gregor Geiger / Julius Rabl / Oscar Vadas / Michaela Oborská-Oplová / Jarosław Mazur / Federica Richina / Purnima Klingauf-Nerurkar / Erich Michel / Alexander Leitner / Daniel Boehringer / Vikram Govind Panse /
Abstract: Mechanisms by which G-patch activators tune the processive multi-tasking ATP-dependent RNA helicase Prp43 (DHX15 in humans) to productively remodel diverse RNA:protein complexes remain elusive. Here, ...Mechanisms by which G-patch activators tune the processive multi-tasking ATP-dependent RNA helicase Prp43 (DHX15 in humans) to productively remodel diverse RNA:protein complexes remain elusive. Here, a comparative study between a herein and previously characterized activators, Tma23 and Pxr1, respectively, defines segments that organize Prp43 function during ribosome assembly. In addition to the activating G-patch, we discover an inhibitory segment within Tma23 and Pxr1, I-patch, that restrains Prp43 ATPase activity. Cryo-electron microscopy and hydrogen-deuterium exchange mass spectrometry show how I-patch binds to the catalytic RecA-like domains to allosterically inhibit Prp43 ATPase activity. Tma23 and Pxr1 contain dimerization segments that organize Prp43 into higher-order complexes. We posit that Prp43 function at discrete locations on pre-ribosomal RNA is coordinated through toggling interactions with G-patch and I-patch segments. This could guarantee measured and timely Prp43 activation, enabling precise control over multiple RNA remodelling events occurring concurrently during ribosome formation.
History
DepositionDec 8, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19078.png

Downloads & links

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Map

FileDownload / File: emd_19078.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 264 pix.
= 221.76 Å		0.84 Å/pix.
x 264 pix.
= 221.76 Å		0.84 Å/pix.
x 264 pix.
= 221.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.8438013 - 1.3480159
Average (Standard dev.)-0.00021760516 (±0.030044533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 221.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19078_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_19078_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Saccharomyces cerevisiae Prp43-Pxr1 complex

EntireName: Saccharomyces cerevisiae Prp43-Pxr1 complex
Components
  • Complex: Saccharomyces cerevisiae Prp43-Pxr1 complex
    • Protein or peptide: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
    • Protein or peptide: Glutathione S-transferase class-mu 26 kDa isozyme,Protein PXR1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Saccharomyces cerevisiae Prp43-Pxr1 complex

SupramoleculeName: Saccharomyces cerevisiae Prp43-Pxr1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Recombinantly expressed helicase Prp43 in complex with Pxr1 regulatory protein
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43

MacromoleculeName: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 91.728195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHSA ALEVLFQGPG YQDPNSVQAL ARPTSVDMGS KRRFSSEHPD PVETSIPEQA AEIAEELSKQ HPLPSEEPLV HHDAGEFKG LQRHHTSAEE AQKLEDGKIN PFTGREFTPK YVDILKIRRE LPVHAQRDEF LKLYQNNQIM VFVGETGSGK T TQIPQFVL ...String:
MAHHHHHHSA ALEVLFQGPG YQDPNSVQAL ARPTSVDMGS KRRFSSEHPD PVETSIPEQA AEIAEELSKQ HPLPSEEPLV HHDAGEFKG LQRHHTSAEE AQKLEDGKIN PFTGREFTPK YVDILKIRRE LPVHAQRDEF LKLYQNNQIM VFVGETGSGK T TQIPQFVL FDEMPHLENT QVACTQPRRV AAMSVAQRVA EEMDVKLGEE VGYSIRFENK TSNKTILKYM TDGMLLREAM ED HDLSRYS CIILDEAHER TLATDILMGL LKQVVKRRPD LKIIIMSATL DAEKFQRYFN DAPLLAVPGR TYPVELYYTP EFQ RDYLDS AIRTVLQIHA TEEAGDILLF LTGEDEIEDA VRKISLEGDQ LVREEGCGPL SVYPLYGSLP PHQQQRIFEP APES HNGRP GRKVVISTNI AETSLTIDGI VYVVDPGFSK QKVYNPRIRV ESLLVSPISK ASAQQRAGRA GRTRPGKCFR LYTEE AFQK ELIEQSYPEI LRSNLSSTVL ELKKLGIDDL VHFDFMDPPA PETMMRALEE LNYLACLDDE GNLTPLGRLA SQFPLD PML AVMLIGSFEF QCSQEILTIV AMLSVPNVFI RPTKDKKRAD DAKNIFAHPD GDHITLLNVY HAFKSDEAYE YGIHKWC RD HYLNYRSLSA ADNIRSQLER LMNRYNLELN TTDYESPKYF DNIRKALASG FFMQVAKKRS GAKGYITVKD NQDVLIHP S TVLGHDAEWV IYNEFVLTSK NYIRTVTSVR PEWLIEIAPA YYDLSNFQKG DVKLSLERIK EKVDRLNELK QGKNKKKSK HSKK

UniProtKB: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43

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Macromolecule #2: Glutathione S-transferase class-mu 26 kDa isozyme,Protein PXR1

MacromoleculeName: Glutathione S-transferase class-mu 26 kDa isozyme,Protein PXR1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 42.26566 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM ...String:
MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM CLDAFPKLVC FKKRIEAIPQ IDKYLKSSKY IAWPLQGWQA TFGGGDHPPK SDLEVLFQGP LGSMGLAATR TK QRFGLDP RNTAWSNDTS RFGHQFLEKF GWKPGMGLGL SPMNSNTSHI KVSIKDDNVG LGAKLKRKDK KDEFDNGECA GLD VFQRIL GRLNGKESKI SEELDTQRKQ KIIDGKWGIH FVKGEVLAST WD

UniProtKB: Glutathione S-transferase class-mu 26 kDa isozyme, Protein PXR1

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 258878
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8rdy:
Saccharomyces cerevisiae Prp43 helicase in complex with Pxr1

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