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- EMDB-3678: Structure of the yeast R2TP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-3678
TitleStructure of the yeast R2TP complex
Map dataStructure of the yeast R2TP complex
Sample
  • Complex: Yeast R2TP complex
    • Protein or peptide: Rvb1p
    • Protein or peptide: Rvb2p
    • Protein or peptide: Pih1p
    • Protein or peptide: Tah1p
Function / homology
Function and homology information


R2TP complex / Swr1 complex / Ino80 complex / 5'-3' DNA helicase activity / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / DNA helicase activity / rRNA processing / DNA helicase ...R2TP complex / Swr1 complex / Ino80 complex / 5'-3' DNA helicase activity / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / DNA helicase activity / rRNA processing / DNA helicase / protein stabilization / chromatin remodeling / DNA repair / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding / nucleus
Similarity search - Function
Pih1, Ascomycota, CS domain / Fungal Pih1 CS domain / PIH1, N-terminal / PIH1 N-terminal domain / 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 ...Pih1, Ascomycota, CS domain / Fungal Pih1 CS domain / PIH1, N-terminal / PIH1 N-terminal domain / 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
Pih1p / RuvB-like protein 1 / RuvB-like protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.37 Å
AuthorsRivera-Calzada A / Pal M / Munoz-Hernandez H / Luque-Ortega JR / Gil-Carton D / Degliesposti G / Skehel JM / Prodromou C / Pearl LH / Llorca O
CitationJournal: Structure / Year: 2017
Title: The Structure of the R2TP Complex Defines a Platform for Recruiting Diverse Client Proteins to the HSP90 Molecular Chaperone System.
Authors: Angel Rivera-Calzada / Mohinder Pal / Hugo Muñoz-Hernández / Juan R Luque-Ortega / David Gil-Carton / Gianluca Degliesposti / J Mark Skehel / Chrisostomos Prodromou / Laurence H Pearl / Oscar Llorca /
Abstract: The R2TP complex, comprising the Rvb1p-Rvb2p AAA-ATPases, Tah1p, and Pih1p in yeast, is a specialized Hsp90 co-chaperone required for the assembly and maturation of multi-subunit complexes. These ...The R2TP complex, comprising the Rvb1p-Rvb2p AAA-ATPases, Tah1p, and Pih1p in yeast, is a specialized Hsp90 co-chaperone required for the assembly and maturation of multi-subunit complexes. These include the small nucleolar ribonucleoproteins, RNA polymerase II, and complexes containing phosphatidylinositol-3-kinase-like kinases. The structure and stoichiometry of yeast R2TP and how it couples to Hsp90 are currently unknown. Here, we determine the 3D organization of yeast R2TP using sedimentation velocity analysis and cryo-electron microscopy. The 359-kDa complex comprises one Rvb1p/Rvb2p hetero-hexamer with domains II (DIIs) forming an open basket that accommodates a single copy of Tah1p-Pih1p. Tah1p-Pih1p binding to multiple DII domains regulates Rvb1p/Rvb2p ATPase activity. Using domain dissection and cross-linking mass spectrometry, we identified a unique region of Pih1p that is essential for interaction with Rvb1p/Rvb2p. These data provide a structural basis for understanding how R2TP couples an Hsp90 dimer to a diverse set of client proteins and complexes.
History
DepositionApr 20, 2017-
Header (metadata) releaseJun 7, 2017-
Map releaseJun 7, 2017-
UpdateJan 31, 2018-
Current statusJan 31, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • 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_3678.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the yeast R2TP complex
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.018430166 - 0.060380638
Average (Standard dev.)0.0008508967 (±0.004211602)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 268.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z268.000268.000268.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0180.0600.001

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Supplemental data

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Sample components

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Entire : Yeast R2TP complex

EntireName: Yeast R2TP complex
Components
  • Complex: Yeast R2TP complex
    • Protein or peptide: Rvb1p
    • Protein or peptide: Rvb2p
    • Protein or peptide: Pih1p
    • Protein or peptide: Tah1p

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Supramolecule #1: Yeast R2TP complex

SupramoleculeName: Yeast R2TP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightExperimental: 359 KDa

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Macromolecule #1: Rvb1p

MacromoleculeName: Rvb1p / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MMVAISEVKE NPGVNSSNSG AVTRTAAHTH IKGLGLDESG VAKRVEGGFV GQIEAREACG V IVDLIKAK KMSGRAILLA GGPSTGKTAL ALAISQELGP KVPFCPLVGS ELYSVEVKKT ET LMENFRR AIGLRIKETK EVYEGEVTEL ...String:
MGSSHHHHHH SSGLVPRGSH MMVAISEVKE NPGVNSSNSG AVTRTAAHTH IKGLGLDESG VAKRVEGGFV GQIEAREACG V IVDLIKAK KMSGRAILLA GGPSTGKTAL ALAISQELGP KVPFCPLVGS ELYSVEVKKT ET LMENFRR AIGLRIKETK EVYEGEVTEL TPEDAENPLG GYGKTISHVI VGLKSAKGTK TLR LDPTIY ESIQREKVSI GDVIYIEANT GAVKRVGRSD AYATEFDLET EEYVPLPKGE VHKK KEIVQ DVTLHDLDVA NARPQGGQDV ISMMGQLLKP KKTEITEKLR QEVNKVVAKY IDQGV AELI PGVLFIDEVN MLDIEIFTYL NKALESNIAP VVVLASNRGM TTVRGTEDVI SPHGVP PDL IDRLLIVRTL PYDKDEIRTI IERRATVERL QVESSALDLL ATMGTETSLR YALQLLA PC GILAQTSNRK EIVVNDVNEA KLLFLDAKRS TKILETSANY L

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Macromolecule #2: Rvb2p

MacromoleculeName: Rvb2p / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEQKLISEED LLRSEEQKLI SEEDLLRSEE QKLISEEDLL RSE SRGSHH HHHHLEVLFQ GPAS MSIQT SDPNETSDLK SLSLIAAHSH ITGLGLDENL QPRPTSEGMV GQLQARRAAG VILKM VQNG TIAGRAVLVA GPPSTGKTAL AMGVSQSLGK DVPFTAIAGS ...String:
MEQKLISEED LLRSEEQKLI SEEDLLRSEE QKLISEEDLL RSE SRGSHH HHHHLEVLFQ GPAS MSIQT SDPNETSDLK SLSLIAAHSH ITGLGLDENL QPRPTSEGMV GQLQARRAAG VILKM VQNG TIAGRAVLVA GPPSTGKTAL AMGVSQSLGK DVPFTAIAGS EIFSLELSKT EALTQA FRK SIGIKIKEET ELIEGEVVEI QIDRSITGGH KQGKLTIKTT DMETIYELGN KMIDGLT KE KVLAGDVISI DKASGKITKL GRSFARSRDY DAMGADTRFV QCPEGELQKR KTVVHTVS L HEIDVINSRT QGFLALFTGD TGEIRSEVRD QINTKVAEWK EEGKAEIVPG VLFIDEVHM LDIECFSFIN RALEDEFAPI VMMATNRGVS KTRGTNYKSP HGLPLDLLDR SIIITTKSYN EQEIKTILS IRAQEEEVEL SSDALDLLTK TGVETSLRYS SNLISVAQQI AMKRKNNTVE V EDVKRAYL LFLDSARSVK YVQENESQYI DDQGNVQISI AKSADPDAMD TTE

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Macromolecule #3: Pih1p

MacromoleculeName: Pih1p / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSHHHHHHMA DFLLRPIKQR HRNEDKYVSV DAADGSVSKI EPIADFVIKT KLLSANGPEK LQDGRKVFIN VCHSPLVPKP EVDFNARIVF PLIIQNEWEI PIITSCYRMD HDKKGQECYV WDCCINSDCS RWICDDIQLR EILVEWCLES CEIRDSVVLC RDRIAFPKMK ...String:
MSHHHHHHMA DFLLRPIKQR HRNEDKYVSV DAADGSVSKI EPIADFVIKT KLLSANGPEK LQDGRKVFIN VCHSPLVPKP EVDFNARIVF PLIIQNEWEI PIITSCYRMD HDKKGQECYV WDCCINSDCS RWICDDIQLR EILVEWCLES CEIRDSVVLC RDRIAFPKMK KKGAELPALE VLNDELHQDY KAKMHKIIEE EAGDPMSILR GRNDDGDDNN DPDDGTLPPL FPIENKISGA KIEEIDKNEI AHRNLKQAPA PAPAPHEQQE DVPEYEVKMK RFKGAAYKLR ILIENKAPNS KPDRFSPSYN FAENILYING KLSIPLPRDI VVNAADIKIF HIRKERTLYI YI

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Macromolecule #4: Tah1p

MacromoleculeName: Tah1p / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH WSHPQFEKGG GSGGGSGGSS AWSHPQFEKL EVLFQGPHMM SQFEKQKEQG NSLFKQGLY REAVHCYDQL ITAQPQNPVG YSNKAMALIK LGEYTQAIQM CQQGLRYTST AEHVAIRSKL QYRLELAQGA VGSVQIPVVE VDELPEGYDR S

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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

Concentration0.45 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
140.0 mMNaClSodium chlorideSodium Chloride
5.0 mMMgCl2Magnesium Chloride
0.5 mMC10H16N2O8EDTAEthylenediaminetetraacetic acid
0.5 mMC9H16ClO6PTCEP
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 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 / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 39000
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 / Digitization - Frames/image: 2-19 / Average exposure time: 12.0 sec. / Average electron dose: 48.0 e/Å2
Details: Data was collected at two different tilts: 0 and 35 degrees.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 346693
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final 3D classificationSoftware - Name: RELION (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 38962

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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