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- EMDB-11789: RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34 -

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Basic information

Entry
Database: EMDB / ID: EMD-11789
TitleRUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34
Map dataCryo-EM structure of RUVBL1-RUVBL2 ATPase core
Sample
  • Complex: RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
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 / Swr1 complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body ...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 / Swr1 complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body / Ino80 complex / box C/D snoRNP assembly / protein folding chaperone complex / NuA4 histone acetyltransferase complex / regulation of chromosome organization / positive regulation of double-strand break repair via homologous recombination / regulation of DNA replication / MLL1 complex / TFIID-class transcription factor complex binding / regulation of embryonic development / Telomere Extension By Telomerase / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / positive regulation of DNA repair / DNA helicase activity / TBP-class protein binding / telomere maintenance / cellular response to estradiol stimulus / ADP binding / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / negative regulation of canonical Wnt signaling pathway / euchromatin / chromatin DNA binding / beta-catenin binding / nuclear matrix / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / UCH proteinases / cellular response to UV / nucleosome / unfolded protein binding / protein folding / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / DNA helicase / DNA recombination / transcription coactivator activity / protein stabilization / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / cadherin binding / cell cycle / 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 / ATP hydrolysis activity / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsLopez-Perrote A / Rodriguez CF / Llorca O
Funding support Spain, 3 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesSAF2017-82632-P Spain
Other governmentP2018/NMT4443 Spain
Other governmentY2018/BIO4747 Spain
CitationJournal: 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
DepositionSep 25, 2020-
Header (metadata) releaseNov 25, 2020-
Map releaseNov 25, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7aho
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11789.png

Downloads & links

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Map

FileDownload / File: emd_11789.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of RUVBL1-RUVBL2 ATPase core
Voxel sizeX=Y=Z: 1.047 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.07816297 - 0.1286409
Average (Standard dev.)0.00018695688 (±0.0032119767)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 293.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0471.0471.047
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z293.160293.160293.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0780.1290.000

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Supplemental data

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Sample components

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Entire : RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34

EntireName: RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34
Components
  • Complex: RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34

SupramoleculeName: RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Structure of the RUVBL1-RUVBL2 hetero-hexameric ring region after the interaction of RNA helicase DHX34
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 (DE3)
Molecular weightTheoretical: 0.44928 kDa/nm

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Macromolecule #1: RuvB-like 1

MacromoleculeName: RuvB-like 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.710406 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHHHSS GENLYFQGSH MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLA GPPGTGKTAL ALAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT P CETENPMG ...String:
HHHHHHHHSS GENLYFQGSH MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLA GPPGTGKTAL ALAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT P CETENPMG GYGKTISHVI IGLKTAKGTK QLKLDPSIFE SLQKERVEAG DVIYIEANSG AVKRQGRCDT YATEFDLEAE EY VPLPKGD VHKKKEIIQD VTLHDLDVAN ARPQGGQDIL SMMGQLMKPK KTEITDKLRG EINKVVNKYI DQGIAELVPG VLF VDEVHM LDIECFTYLH RALESSIAPI VIFASNRGNC VIRGTEDITS PHGIPLDLLD RVMIIRTMLY TPQEMKQIIK IRAQ TEGIN ISEEALNHLG EIGTKTTLRY SVQLLTPANL LAKINGKDSI EKEHVEEISE LFYDAKSSAK ILADQQDKYM K

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Macromolecule #2: RuvB-like 2

MacromoleculeName: RuvB-like 2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.047488 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADLNWISAG HAIADVGTMA TVTATTKVPE IRDVTRIERI GAHSHIRGLG LDDALEPRQA SQGMVGQLAA RRAAGVVLEM IREGKIAGR AVLIAGQPGT GKTAIAMGMA QALGPDTPFT AIAGSEIFSL EMSKTEALTQ AFRRSIGVRI KEETEIIEGE V VEIQIDRP ...String:
MADLNWISAG HAIADVGTMA TVTATTKVPE IRDVTRIERI GAHSHIRGLG LDDALEPRQA SQGMVGQLAA RRAAGVVLEM IREGKIAGR AVLIAGQPGT GKTAIAMGMA QALGPDTPFT AIAGSEIFSL EMSKTEALTQ AFRRSIGVRI KEETEIIEGE V VEIQIDRP ATGTGSKVGK LTLKTTEMET IYDLGTKMIE SLTKDKVQAG DVITIDKATG KISKLGRSFT RARDYDAMGS QT KFVQCPD GELQKRKEVV HTVSLHEIDV INSRTQGFLA LFSGDTGEIK SEVREQINAK VAEWREEGKA EIIPGVLFID EVH MLDIES FSFLNRALES DMAPVLIMAT NRGITRIRGT SYQSPHGIPI DLLDRLLIVS TTPYSEKDTK QILRIRCEEE DVEM SEDAY TVLTRIGLET SLRYAIQLIT AASLVCRKRK GTEVQVDDIK RVYSLFLDES RSTQYMKEYQ DAFLFNELKG ETMDT S

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

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

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

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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

Concentration0.35 mg/mL
BufferpH: 7.4 / Component - Formula: Tris-NaCl / Component - Name: TBS / Details: 50 mM Tris-HCl pH 7.4, 150 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47756 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.0015 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3047 / Average electron dose: 48.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 353057
CTF correctionSoftware - Name: RELION
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 101774
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2xsz

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7aho:
RUVBL1-RUVBL2 heterohexameric ring after binding of RNA helicase DHX34

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