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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: EMD-8839
TitleThe Hsp90 Co-chaperon R2TP Forms a Hexameric Platform
Map dataRvb1 and Rvb2 complexed with Tah1 and Pih1. Map with bfactor compensation applied.
Sample
  • Complex: Complex of Rvb1 and Rvb2 together with Tah1 and Pih1
    • Other: Rvb1p
    • Other: Rvb2p
    • Other: Pih1p
    • Other: Tah1p
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsTian S / Yu G / He H / Liu P / Marshall A / Demeler B / Stagg S / Li H
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM66958 United States
National Science Foundation (NSF, United States)DMR-11-57490 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM099604 United States
XSEDE allocationMCB-070039 United States
National Science Foundation (NSF, United States)ACI-1339649 United States
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.
History
DepositionJul 19, 2017-
Header (metadata) releaseOct 4, 2017-
Map releaseOct 4, 2017-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8839.png

Downloads & links

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Map

FileDownload / File: emd_8839.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRvb1 and Rvb2 complexed with Tah1 and Pih1. Map with bfactor compensation applied.
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.167 / Movie #1: 0.167
Minimum - Maximum-0.10875608 - 0.27144766
Average (Standard dev.)0.00086830085 (±0.022501906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 349.92 Å
α=β=γ: 90.0 °

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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Half map: Rvb1 and Rvb2 complexed with Tah1 and Pih1. Halfmap1

Fileemd_8839_half_map_1.map
AnnotationRvb1 and Rvb2 complexed with Tah1 and Pih1. Halfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Rvb1 and Rvb2 complexed with Tah1 and Pih1. Halfmap2

Fileemd_8839_half_map_2.map
AnnotationRvb1 and Rvb2 complexed with Tah1 and Pih1. Halfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Components
  • Complex: Complex of Rvb1 and Rvb2 together with Tah1 and Pih1
    • Other: Rvb1p
    • Other: Rvb2p
    • Other: Pih1p
    • Other: Tah1p

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Supramolecule #1: Complex of Rvb1 and Rvb2 together with Tah1 and Pih1

SupramoleculeName: Complex of Rvb1 and Rvb2 together with Tah1 and Pih1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 358 KDa

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Macromolecule #1: Rvb1p

MacromoleculeName: Rvb1p / type: other / ID: 1 / Classification: other
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MVAISEVKEN PGVNSSNSGA VTRTAAHTHI KGLGLDESGV AKRVEGGFVG QIEAREACGV IVDLIKAKKM SGRAILLAG GPSTGKTALA LAISQELGPK VPFCPLVGSE LYSVEVKKTE TLMENFRRAI GLRIKETKEV Y EGEVTELT PEDAENPLGG YGKTISHVIV ...String:
MVAISEVKEN PGVNSSNSGA VTRTAAHTHI KGLGLDESGV AKRVEGGFVG QIEAREACGV IVDLIKAKKM SGRAILLAG GPSTGKTALA LAISQELGPK VPFCPLVGSE LYSVEVKKTE TLMENFRRAI GLRIKETKEV Y EGEVTELT PEDAENPLGG YGKTISHVIV GLKSAKGTKT LRLDPTIYES IQREKVSIGD VIYIEANTGA VK RVGRSDA YATEFDLETE EYVPLPKGEV HKKKEIVQDV TLHDLDVANA RPQGGQDVIS MMGQLLKPKK TEI TEKLRQ EVNKVVAKYI DQGVAELIPG VLFIDEVNML DIEIFTYLNK ALESNIAPVV VLASNRGMTT VRGT EDVIS PHGVPPDLID RLLIVRTLPY DKDEIRTIIE RRATVERLQV ESSALDLLAT MGTETSLRYA LQLLA PCGI LAQTSNRKEI VVNDVNEAKL LFLDAKRSTK ILETSANYL
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: Rvb2p

MacromoleculeName: Rvb2p / type: other / ID: 2 / Classification: other
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MSIQTSDPNE TSDLKSLSLI AAHSHITGLG LDENLQPRPT SEGMVGQLQA RRAAGVILKM VQNGTIAGRA VLVAGPPST GKTALAMGVS QSLGKDVPFT AIAGSEIFSL ELSKTEALTQ AFRKSIGIKI KEETELIEGE V VEIQIDRS ITGGHKQGKL TIKTTDMETI ...String:
MSIQTSDPNE TSDLKSLSLI AAHSHITGLG LDENLQPRPT SEGMVGQLQA RRAAGVILKM VQNGTIAGRA VLVAGPPST GKTALAMGVS QSLGKDVPFT AIAGSEIFSL ELSKTEALTQ AFRKSIGIKI KEETELIEGE V VEIQIDRS ITGGHKQGKL TIKTTDMETI YELGNKMIDG LTKEKVLAGD VISIDKASGK ITKLGRSFAR SR DYDAMGA DTRFVQCPEG ELQKRKTVVH TVSLHEIDVI NSRTQGFLAL FTGDTGEIRS EVRDQINTKV AEW KEEGKA EIVPGVLFID EVHMLDIECF SFINRALEDE FAPIVMMATN RGVSKTRGTN YKSPHGLPLD LLDR SIIIT TKSYNEQEIK TILSIRAQEE EVELSSDALD LLTKTGVETS LRYSSNLISV AQQIAMKRKN NTVEV EDVK RAYLLFLDSA RSVKYVQENE SQYIDDQGNV QISIAKSADP DAMDTTE
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #3: Pih1p

MacromoleculeName: Pih1p / type: other / ID: 3 / Classification: other
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MADFLLRPIK QRHRNEDKYV SVDAADGSVS KIEPIADFVI KTKLLSANGP EKLQDGRKVF INVCHSPLVP KPEVDFNAR IVFPLIIQNE WEIPIITSCY RMDHDKKGQE CYVWDCCINS DCSRWICDDI QLREILVEWC L ESCEIRDS VVLCRDRIAF PKMKKKGAEL ...String:
MADFLLRPIK QRHRNEDKYV SVDAADGSVS KIEPIADFVI KTKLLSANGP EKLQDGRKVF INVCHSPLVP KPEVDFNAR IVFPLIIQNE WEIPIITSCY RMDHDKKGQE CYVWDCCINS DCSRWICDDI QLREILVEWC L ESCEIRDS VVLCRDRIAF PKMKKKGAEL PALEVLNDEL HQDYKAKMHK IIEEEAGDPM SILRGRNDDG DD NNDPDDG TLPPLFPIEN KISGAKIEEI DKNEIAHRNL KQAPAPAPAP HEQQEDVPEY EVKMKRFKGA AYK LRILIE NKAPNSKPDR FSPSYNFAEN ILYINGKLSI PLPRDIVVNA ADIKIFHIRK ERTLYIYI
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #4: Tah1p

MacromoleculeName: Tah1p / type: other / ID: 4 / Classification: other
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
MSQFEKQKEQ GNSLFKQGLY REAVHCYDQL ITAQPQNPVG YSNKAMALIK LGEYTQAIQM CQQGLRYTST AEHVAIRSK LQYRLELAQG AVGSVQIPVV EVDELPEGYD RS
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 83.0 K / Max: 93.0 K
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Number real images: 1396 / Average electron dose: 58.68 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: -3.0 µm / Calibrated defocus min: -1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsFrames were aligned and dose compensated using DE_process_frames-2.5.1
Particle selectionNumber selected: 54712 / Details: 54712 particles picked
CTF correctionSoftware: (Name: ACE (ver. 1), CTFFIND (ver. 3))
Details: Volume was additionally B-factor corrected after refinement
Startup modelType of model: OTHER
Details: Initial model was used from a previous negative stain reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 4839
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN
Final 3D classificationSoftware - Name: FREALIGN
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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