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Yorodumi- PDB-7aho: RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aho | ||||||||||||
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Title | RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34 | ||||||||||||
Components |
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Keywords | TRANSLATION / RUVBL1-RUVBL2 / DHX34 / Nonsense-Mediated mRNA Decay / RNA degradation / Cryo-EM | ||||||||||||
Function / homology | Function and homology information promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / positive regulation of telomerase RNA localization to Cajal body / regulation of double-strand break repair ...promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / positive regulation of telomerase RNA localization to Cajal body / regulation of double-strand break repair / Ino80 complex / protein folding chaperone complex / box C/D snoRNP assembly / NuA4 histone acetyltransferase complex / regulation of chromosome organization / regulation of DNA replication / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / positive regulation of double-strand break repair via homologous recombination / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / telomere maintenance / DNA helicase activity / TBP-class protein binding / positive regulation of DNA repair / cellular response to estradiol stimulus / Formation of the beta-catenin:TCF transactivating complex / ADP binding / DNA Damage Recognition in GG-NER / negative regulation of canonical Wnt signaling pathway / euchromatin / chromatin DNA binding / beta-catenin binding / nuclear matrix / transcription corepressor activity / cellular response to UV / UCH proteinases / nucleosome / positive regulation of canonical Wnt signaling pathway / unfolded protein binding / protein folding / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / DNA helicase / DNA recombination / transcription coactivator activity / regulation of cell cycle / protein stabilization / Ub-specific processing proteases / cadherin binding / chromatin remodeling / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / DNA repair / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.18 Å | ||||||||||||
Authors | Lopez-Perrote, A. / Rodriguez, C.F. / Llorca, O. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: Elife / Year: 2020 Title: Regulation of RUVBL1-RUVBL2 AAA-ATPases by the nonsense-mediated mRNA decay factor DHX34, as evidenced by Cryo-EM. Authors: Andres López-Perrote / Nele Hug / Ana González-Corpas / Carlos F Rodríguez / Marina Serna / Carmen García-Martín / Jasminka Boskovic / Rafael Fernandez-Leiro / Javier F Caceres / Oscar Llorca / Abstract: Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades aberrant mRNAs and also regulates the expression of a wide range of physiological transcripts. RUVBL1 and RUVBL2 AAA-ATPases ...Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades aberrant mRNAs and also regulates the expression of a wide range of physiological transcripts. RUVBL1 and RUVBL2 AAA-ATPases form an hetero-hexameric ring that is part of several macromolecular complexes such as INO80, SWR1, and R2TP. Interestingly, RUVBL1-RUVBL2 ATPase activity is required for NMD activation by an unknown mechanism. Here, we show that DHX34, an RNA helicase regulating NMD initiation, directly interacts with RUVBL1-RUVBL2 in vitro and in cells. Cryo-EM reveals that DHX34 induces extensive changes in the N-termini of every RUVBL2 subunit in the complex, stabilizing a conformation that does not bind nucleotide and thereby down-regulates ATP hydrolysis of the complex. Using ATPase-deficient mutants, we find that DHX34 acts exclusively on the RUVBL2 subunits. We propose a model, where DHX34 acts to couple RUVBL1-RUVBL2 ATPase activity to the assembly of factors required to initiate the NMD response. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7aho.cif.gz | 315.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aho.ent.gz | 256.4 KB | Display | PDB format |
PDBx/mmJSON format | 7aho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aho_validation.pdf.gz | 926 KB | Display | wwPDB validaton report |
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Full document | 7aho_full_validation.pdf.gz | 942.6 KB | Display | |
Data in XML | 7aho_validation.xml.gz | 56.1 KB | Display | |
Data in CIF | 7aho_validation.cif.gz | 84.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/7aho ftp://data.pdbj.org/pub/pdb/validation_reports/ah/7aho | HTTPS FTP |
-Related structure data
Related structure data | 11789MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 52710.406 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL1, INO80H, NMP238, TIP49, TIP49A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y265, DNA helicase #2: Protein | Mass: 53047.488 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y230, DNA helicase #3: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34 Type: COMPLEX Details: Structure of the RUVBL1-RUVBL2 hetero-hexameric ring region after the interaction of RNA helicase DHX34 Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.44928 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3) |
Buffer solution | pH: 7.4 / Details: 50 mM Tris-HCl pH 7.4, 150 mM NaCl |
Buffer component | Units: mM / Name: TBS / Formula: Tris-NaCl |
Specimen | Conc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 47756 X / Nominal defocus max: 3 nm / Nominal defocus min: 1.5 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 48.1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3047 |
Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 353057 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101774 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2XSZ | ||||||||||||||||||||||||||||||||||||||||
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