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- EMDB-19815: RUVBL1/2 in complex with ATP and CB-6644 inhibitor -

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Basic information

Entry
Database: EMDB / ID: EMD-19815
TitleRUVBL1/2 in complex with ATP and CB-6644 inhibitor
Map dataCryoEM map (Refine3D) for RUVBL1/2-ATP-CB6644 complex
Sample
  • Complex: Hetero-hexameric RUVBL1-RUVBL2 complex bound to ATP and the CB-6644 inhibitor
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2]benzodiazepin-2-yl]amino]-2,2-dimethyl-4-oxidanylidene-butyl]benzamide
  • Ligand: MAGNESIUM ION
KeywordsRUVBL1 / RUVBL2 / CB-6644 / Inhibitor / Chaperone
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 / protein folding chaperone complex / box C/D snoRNP assembly / NuA4 histone acetyltransferase complex / regulation of chromosome organization / positive regulation of double-strand break repair via homologous recombination / regulation of DNA replication / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / 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 / TBP-class protein binding / DNA helicase activity / telomere maintenance / cellular response to estradiol stimulus / ADP binding / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / euchromatin / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / beta-catenin binding / nuclear matrix / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / UCH proteinases / cellular response to UV / unfolded protein binding / nucleosome / protein folding / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / DNA recombination / DNA helicase / transcription coactivator activity / protein stabilization / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / cadherin binding / ribonucleoprotein complex / cell cycle / 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 / ATP hydrolysis 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: 2.4 Å
AuthorsLopez-Perrote A / Llorca O / Garcia-Martin C
Funding support Spain, 1 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2020-114429RB-I00 Spain
CitationJournal: Cell Rep Phys Sci / Year: 2024
Title: Mechanism of allosteric inhibition of RUVBL1-RUVBL2 by the small-molecule CB-6644
Authors: Garcia-Martin C / Lopez-Perrote A / Boskovic J / Llorca O
History
DepositionMar 7, 2024-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19815.png

Downloads & links

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Map

FileDownload / File: emd_19815.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map (Refine3D) for RUVBL1/2-ATP-CB6644 complex
Voxel sizeX=Y=Z: 0.8238 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.026953187 - 0.12370724
Average (Standard dev.)-0.00001670857 (±0.0033901613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 247.14001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map (Postprocess) for RUVBL1/2-ATP-CB6644 complex

Fileemd_19815_additional_1.map
AnnotationSharpened map (Postprocess) for RUVBL1/2-ATP-CB6644 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 (unfiltered) for RUVBL1/2-ATP-CB6644 complex

Fileemd_19815_half_map_1.map
AnnotationHalf map 2 (unfiltered) for RUVBL1/2-ATP-CB6644 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 (unfiltered) for RUVBL1/2-ATP-CB6644 complex

Fileemd_19815_half_map_2.map
AnnotationHalf map 1 (unfiltered) for RUVBL1/2-ATP-CB6644 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hetero-hexameric RUVBL1-RUVBL2 complex bound to ATP and the CB-66...

EntireName: Hetero-hexameric RUVBL1-RUVBL2 complex bound to ATP and the CB-6644 inhibitor
Components
  • Complex: Hetero-hexameric RUVBL1-RUVBL2 complex bound to ATP and the CB-6644 inhibitor
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2]benzodiazepin-2-yl]amino]-2,2-dimethyl-4-oxidanylidene-butyl]benzamide
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Hetero-hexameric RUVBL1-RUVBL2 complex bound to ATP and the CB-66...

SupramoleculeName: Hetero-hexameric RUVBL1-RUVBL2 complex bound to ATP and the CB-6644 inhibitor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 310.47 kDa/nm

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Macromolecule #1: RuvB-like 1

MacromoleculeName: RuvB-like 1 / type: protein_or_peptide / ID: 1
Details: Sequence contains three extra aminoacids (GSH) at the N-terminus due to protease cleavage that do not affect the structure and activity of the protein
Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.579188 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMKIEEVK STTKTQRIAS HSHVKGLGLD ESGLAKQAAS GLVGQENARE ACGVIVELIK SKKMAGRAVL LAGPPGTGKT ALALAIAQE LGSKVPFCPM VGSEVYSTEI KKTEVLMENF RRAIGLRIKE TKEVYEGEVT ELTPCETENP MGGYGKTISH V IIGLKTAK ...String:
GSHMKIEEVK STTKTQRIAS HSHVKGLGLD ESGLAKQAAS GLVGQENARE ACGVIVELIK SKKMAGRAVL LAGPPGTGKT ALALAIAQE LGSKVPFCPM VGSEVYSTEI KKTEVLMENF RRAIGLRIKE TKEVYEGEVT ELTPCETENP MGGYGKTISH V IIGLKTAK GTKQLKLDPS IFESLQKERV EAGDVIYIEA NSGAVKRQGR CDTYATEFDL EAEEYVPLPK GDVHKKKEII QD VTLHDLD VANARPQGGQ DILSMMGQLM KPKKTEITDK LRGEINKVVN KYIDQGIAEL VPGVLFVDEV HMLDIECFTY LHR ALESSI APIVIFASNR GNCVIRGTED ITSPHGIPLD LLDRVMIIRT MLYTPQEMKQ IIKIRAQTEG INISEEALNH LGEI GTKTT LRYSVQLLTP ANLLAKINGK DSIEKEHVEE ISELFYDAKS SAKILADQQD KYMK

UniProtKB: RuvB-like 1

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Macromolecule #2: RuvB-like 2

MacromoleculeName: RuvB-like 2 / type: protein_or_peptide / ID: 2
Details: A strectch of 18 extra residues is present at the N-terminus due to cloning design that do not affect the structure and activity of the protein,A strectch of 18 extra residues is present at ...Details: A strectch of 18 extra residues is present at the N-terminus due to cloning design that do not affect the structure and activity of the protein,A strectch of 18 extra residues is present at the N-terminus due to cloning design that do not affect the structure and activity of the protein
Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.100969 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 SSLT KDKVQAGDVI TIDKATGKIS KLGRSFTRAR DYDAMGSQTK FVQCPDGELQ KRKEVVHTVS LHEIDVINSR TQGFLA LFS GDTGEIKSEV REQINAKVAE WREEGKAEII PGVLFIDEVH MLDIESFSFL NRALESDMAP VLIMATNRGI TRIRGTS YQ SPHGIPIDLL DRLLIVSTTP YSEKDTKQIL RIRCEEEDVE MSEDAYTVLT RIGLETSLRY AIQLITAASL VCRKRKGT E VQVDDIKRVY SLFLDESRST QYMKEYQDAF LFNELKGETM DTS

UniProtKB: RuvB-like 2, RuvB-like 2

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #4: 5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-ox...

MacromoleculeName: 5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2]benzodiazepin-2-yl]amino]-2,2-dimethyl-4-oxidanylidene-butyl]benzamide
type: ligand / ID: 4 / Number of copies: 3 / Formula: A1H5V
Molecular weightTheoretical: 573.055 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / 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

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTristris(hydroxymethyl)aminomethane
150.0 mMNaClSodium chloridesodium chloride
20.0 mMMgCl2magnesium chloride
20.0 mMATPAdenosine triphosphateadenosine triphosphate
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 10.0 kPa
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 277 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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: RELION ModelAngelo
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 393823
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-9ema:
RUVBL1/2 in complex with ATP and CB-6644 inhibitor

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