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- EMDB-4553: Truncated human R2TP complex, structure 4 (ADP-empty) -

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Basic information

Entry
Database: EMDB / ID: EMD-4553
TitleTruncated human R2TP complex, structure 4 (ADP-empty)
Map data
SampleRUVBL1-RUVBL2 in an open conformation (ADP-empty):
RuvB-like 1 / RuvB-like 2 / ligand
Function / homology
Function and homology information


HATs acetylate histones / UCH proteinases / DNA Damage Recognition in GG-NER / Deposition of new CENPA-containing nucleosomes at the centromere / Ub-specific processing proteases / Telomere Extension By Telomerase / Formation of the beta-catenin:TCF transactivating complex / negative regulation of estrogen receptor binding / transcriptional activation by promoter-enhancer looping / positive regulation of telomerase RNA localization to Cajal body ...HATs acetylate histones / UCH proteinases / DNA Damage Recognition in GG-NER / Deposition of new CENPA-containing nucleosomes at the centromere / Ub-specific processing proteases / Telomere Extension By Telomerase / Formation of the beta-catenin:TCF transactivating complex / negative regulation of estrogen receptor binding / transcriptional activation by promoter-enhancer looping / positive regulation of telomerase RNA localization to Cajal body / histone H2A acetylation / establishment of protein localization to chromatin / R2TP complex / Swr1 complex / ATP-dependent 5'-3' DNA helicase activity / Ino80 complex / NuA4 histone acetyltransferase complex / box C/D snoRNP assembly / regulation of growth / DNA helicase activity / ATP-dependent DNA helicase activity / MLL1 complex / CENP-A containing nucleosome assembly / TFIID-class transcription factor complex binding / beta-catenin-TCF complex assembly / nuclear euchromatin / histone H4 acetylation / positive regulation of histone acetylation / histone acetylation / RNA polymerase II core promoter sequence-specific DNA binding / DNA helicase / ADP binding / TBP-class protein binding / RNA polymerase II distal enhancer sequence-specific DNA binding / cellular response to estradiol stimulus / chromatin DNA binding / microtubule organizing center / cellular response to UV / negative regulation of canonical Wnt signaling pathway / nuclear matrix / transcription corepressor activity / intracellular / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / ribonucleoprotein complex / protein folding / spermatogenesis / unfolded protein binding / ATPase binding / transcription coactivator activity / chromatin remodeling / ATPase activity / DNA recombination / cadherin binding / cell cycle / centrosome / protein deubiquitination / cell division / regulation of transcription by RNA polymerase II / DNA repair / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular exosome / membrane / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
RuvB-like helicase 2 / AAA+ ATPase domain / TIP49, P-loop domain / RuvB-like / P-loop containing nucleoside triphosphate hydrolase / RuvB-like helicase 1 / RuvB-like, AAA-lid domain / TIP49 P-loop domain / TIP49 AAA-lid domain
RuvB-like 2 / RuvB-like 1
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.63 Å
AuthorsMunoz-Hernandez H / Rodriguez CF / Llorca O
CitationJournal: Sci Adv / Year: 2019
Title: Structural mechanism for regulation of the AAA-ATPases RUVBL1-RUVBL2 in the R2TP co-chaperone revealed by cryo-EM.
Authors: Hugo Muñoz-Hernández / Mohinder Pal / Carlos F Rodríguez / Rafael Fernandez-Leiro / Chrisostomos Prodromou / Laurence H Pearl / Oscar Llorca /
Abstract: The human R2TP complex (RUVBL1-RUVBL2-RPAP3-PIH1D1) is an HSP90 co-chaperone required for the maturation of several essential multiprotein complexes, including RNA polymerase II, small nucleolar ...The human R2TP complex (RUVBL1-RUVBL2-RPAP3-PIH1D1) is an HSP90 co-chaperone required for the maturation of several essential multiprotein complexes, including RNA polymerase II, small nucleolar ribonucleoproteins, and PIKK complexes such as mTORC1 and ATR-ATRIP. RUVBL1-RUVBL2 AAA-ATPases are also primary components of other essential complexes such as INO80 and Tip60 remodelers. Despite recent efforts, the molecular mechanisms regulating RUVBL1-RUVBL2 in these complexes remain elusive. Here, we report cryo-EM structures of R2TP and show how access to the nucleotide-binding site of RUVBL2 is coupled to binding of the client recruitment component of R2TP (PIH1D1) to its DII domain. This interaction induces conformational rearrangements that lead to the destabilization of an N-terminal segment of RUVBL2 that acts as a gatekeeper to nucleotide exchange. This mechanism couples protein-induced motions of the DII domains with accessibility of the nucleotide-binding site in RUVBL1-RUVBL2, and it is likely a general mechanism shared with other RUVBL1-RUVBL2-containing complexes.
Validation ReportPDB-ID: 6qi9

SummaryFull reportAbout validation report
DateDeposition: Jan 18, 2019 / Header (metadata) release: Feb 13, 2019 / Map release: May 15, 2019 / Update: May 15, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6qi9
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4553.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 260 pix.
= 278.2 Å
1.07 Å/pix.
x 260 pix.
= 278.2 Å
1.07 Å/pix.
x 260 pix.
= 278.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.032253817 - 0.059564065
Average (Standard dev.)0.00015664156 (±0.0017792217)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 278.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z278.200278.200278.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0320.0600.000

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Supplemental data

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Sample components

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Entire RUVBL1-RUVBL2 in an open conformation (ADP-empty)

EntireName: RUVBL1-RUVBL2 in an open conformation (ADP-empty) / Number of components: 4

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Component #1: protein, RUVBL1-RUVBL2 in an open conformation (ADP-empty)

ProteinName: RUVBL1-RUVBL2 in an open conformation (ADP-empty) / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #2: protein, RuvB-like 1

ProteinName: RuvB-like 1 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 50.296914 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, RuvB-like 2

ProteinName: RuvB-like 2 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 51.222465 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #4: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.18 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 33466
3D reconstructionSoftware: RELION / Resolution: 4.63 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 6FO1
Output model

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