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- EMDB-8839: The Hsp90 Co-chaperon R2TP Forms a Hexameric Platform -

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Basic information

Entry
Database: EMDB / ID: 8839
TitleThe Hsp90 Co-chaperon R2TP Forms a Hexameric Platform
Map dataRvb1 and Rvb2 complexed with Tah1 and Pih1. Map with bfactor compensation applied.
SampleComplex of Rvb1 and Rvb2 together with Tah1 and Pih1:
SourceSaccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / 14 Å resolution
AuthorsTian S / Yu G / He H / Liu P / Marshall A / Demeler B / Stagg S / Li H
CitationJournal: Structure / Year: 2017
Title: Pih1p-Tah1p Puts a Lid on Hexameric AAA+ ATPases Rvb1/2p.
Authors: Shaoxiong Tian / Ge Yu / Huan He / Yu Zhao / Peilu Liu / Alan G Marshall / Borries Demeler / Scott M Stagg / Hong Li
Abstract: The Saccharomyces cerevisiae (Sc) R2TP complex affords an Hsp90-mediated and nucleotide-driven chaperone activity to proteins of small ribonucleoprotein particles (snoRNPs). The current lack of ...The Saccharomyces cerevisiae (Sc) R2TP complex affords an Hsp90-mediated and nucleotide-driven chaperone activity to proteins of small ribonucleoprotein particles (snoRNPs). The current lack of structural information on the ScR2TP complex, however, prevents a mechanistic understanding of this biological process. We characterized the structure of the ScR2TP complex made up of two AAA+ ATPases, Rvb1/2p, and two Hsp90 binding proteins, Tah1p and Pih1p, and its interaction with the snoRNP protein Nop58p by a combination of analytical ultracentrifugation, isothermal titration calorimetry, chemical crosslinking, hydrogen-deuterium exchange, and cryoelectron microscopy methods. We find that Pih1p-Tah1p interacts with Rvb1/2p cooperatively through the nucleotide-sensitive domain of Rvb1/2p. Nop58p further binds Pih1p-Tahp1 on top of the dome-shaped R2TP. Consequently, nucleotide binding releases Pih1p-Tah1p from Rvb1/2p, which offers a mechanism for nucleotide-driven binding and release of snoRNP intermediates.
DateDeposition: Jul 19, 2017 / Header (metadata) release: Oct 4, 2017 / Map release: Oct 4, 2017 / Last update: Feb 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.167
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.167
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8839.map.gz (map file in CCP4 format, 11944 KB)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
2.43 Å/pix.
= 349.92 Å
144 pix
2.43 Å/pix.
= 349.92 Å
144 pix
2.43 Å/pix.
= 349.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.43 Å
Density
Contour Level:0.167 (by author), 0.167 (movie #1):
Minimum - Maximum-0.10875608 - 0.27144766
Average (Standard dev.)0.00086830085 (0.022501906)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions144144144
Origin-72-72-72
Limit717171
Spacing144144144
CellA=B=C: 349.92 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.432.432.43
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z349.920349.920349.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-0.1090.2710.001

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Supplemental data

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Sample components

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Entire Complex of Rvb1 and Rvb2 together with Tah1 and Pih1

EntireName: Complex of Rvb1 and Rvb2 together with Tah1 and Pih1 / Number of components: 1
MassTheoretical: 358 kDa

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Component #1: protein, Complex of Rvb1 and Rvb2 together with Tah1 and Pih1

ProteinName: Complex of Rvb1 and Rvb2 together with Tah1 and Pih1 / Recombinant expression: No
MassTheoretical: 358 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 281.15 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: 58.68 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1000 - -3000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 83 - 93 K)
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 1396

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 4839
Details: Frames were aligned and dose compensated using DE_process_frames-2.5.1
3D reconstructionAlgorithm: FOURIER SPACE / Software: FREALIGN
CTF correction: Volume was additionally B-factor corrected after refinement
Resolution: 14 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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