[English] 日本語
Yorodumi
- PDB-8rdy: Saccharomyces cerevisiae Prp43 helicase in complex with Pxr1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rdy
TitleSaccharomyces cerevisiae Prp43 helicase in complex with Pxr1
Components
  • Glutathione S-transferase class-mu 26 kDa isozyme,Protein PXR1
  • Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
KeywordsRNA BINDING PROTEIN / preribosome / helicase / ribosome assembly / inhibitor
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
ADENOSINE-5'-DIPHOSPHATE / 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)
Schistosoma japonicum (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsRabl, J. / Portugal Calisto, D. / Panse, V.G.
Funding support Switzerland, 1items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
B: Glutathione S-transferase class-mu 26 kDa isozyme,Protein PXR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4454
Polymers133,9942
Non-polymers4522
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2660 Å2
ΔGint-30 kcal/mol
Surface area31510 Å2
MethodPISA

-
Components

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


Mass: 91728.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP43 / Production host: Escherichia coli (E. coli) / References: UniProt: P53131
#2: Protein Glutathione S-transferase class-mu 26 kDa isozyme,Protein PXR1 / G-patch nucleolar protein / PinX1-related protein 1


Mass: 42265.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PXR1, GNO1, YGR280C / Production host: Escherichia coli (E. coli) / References: UniProt: P08515, UniProt: P53335
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Saccharomyces cerevisiae Prp43-Pxr1 complex / Type: COMPLEX
Details: Recombinantly expressed helicase Prp43 in complex with Pxr1 regulatory protein
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

-
Processing

EM software
IDNameCategory
1Topazparticle selection
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 258878 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035620
ELECTRON MICROSCOPYf_angle_d0.5017615
ELECTRON MICROSCOPYf_dihedral_angle_d4.735766
ELECTRON MICROSCOPYf_chiral_restr0.039844
ELECTRON MICROSCOPYf_plane_restr0.003989

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more