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- EMDB-4291: Human R2TP complex-subgroup2 -

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Basic information

Entry
Database: EMDB / ID: EMD-4291
TitleHuman R2TP complex-subgroup2
Map data
Sample
  • Complex: Human R2TP complex - subgroup 2
    • Protein or peptide: RUVBL1
    • Protein or peptide: RUVBL2
    • Protein or peptide: PIH1D1
Function / homology
Function and homology information


TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / pre-snoRNP complex / establishment of protein localization to chromatin / : / R2TP complex ...TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / pre-snoRNP complex / establishment of protein localization to chromatin / : / R2TP complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / positive regulation of telomerase RNA localization to Cajal body / regulation of double-strand break repair / Ino80 complex / box C/D snoRNP assembly / protein folding chaperone complex / NuA4 histone acetyltransferase complex / regulation of chromosome organization / regulation of DNA replication / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / positive regulation of double-strand break repair via homologous recombination / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / epithelial cell differentiation / Deposition of new CENPA-containing nucleosomes at the centromere / DNA helicase activity / telomere maintenance / TBP-class protein binding / positive regulation of TORC1 signaling / positive regulation of DNA repair / histone reader activity / cellular response to estradiol stimulus / phosphoprotein binding / Formation of the beta-catenin:TCF transactivating complex / ADP binding / DNA Damage Recognition in GG-NER / negative regulation of canonical Wnt signaling pathway / positive regulation of protein serine/threonine kinase activity / euchromatin / chromatin DNA binding / beta-catenin binding / nuclear matrix / transcription corepressor activity / cellular response to UV / rRNA processing / UCH proteinases / nucleosome / positive regulation of canonical Wnt signaling pathway / unfolded protein binding / protein folding / HATs acetylate histones / ATPase binding / histone binding / spermatogenesis / regulation of apoptotic process / DNA helicase / DNA recombination / transcription coactivator activity / regulation of cell cycle / protein stabilization / Ub-specific processing proteases / cadherin binding / chromatin remodeling / ribonucleoprotein complex / 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 / nucleolus / protein kinase binding / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
PIH1D1/2/3, CS-like domain / PIH1 CS-like domain / : / PIH1, N-terminal / : / PIH1 N-terminal domain / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / RuvB-like / RuvB-like, AAA-lid domain ...PIH1D1/2/3, CS-like domain / PIH1 CS-like domain / : / PIH1, N-terminal / : / PIH1 N-terminal domain / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / 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 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA polymerase II-associated protein 3 / PIH1 domain-containing protein 1 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.57 Å
AuthorsMunoz-Hernandez H / Pearl LH / Llorca O
CitationJournal: Nat Commun / Year: 2018
Title: RPAP3 provides a flexible scaffold for coupling HSP90 to the human R2TP co-chaperone complex.
Authors: Fabrizio Martino / Mohinder Pal / Hugo Muñoz-Hernández / Carlos F Rodríguez / Rafael Núñez-Ramírez / David Gil-Carton / Gianluca Degliesposti / J Mark Skehel / S Mark Roe / ...Authors: Fabrizio Martino / Mohinder Pal / Hugo Muñoz-Hernández / Carlos F Rodríguez / Rafael Núñez-Ramírez / David Gil-Carton / Gianluca Degliesposti / J Mark Skehel / S Mark Roe / Chrisostomos Prodromou / Laurence H Pearl / Oscar Llorca /
Abstract: The R2TP/Prefoldin-like co-chaperone, in concert with HSP90, facilitates assembly and cellular stability of RNA polymerase II, and complexes of PI3-kinase-like kinases such as mTOR. However, the ...The R2TP/Prefoldin-like co-chaperone, in concert with HSP90, facilitates assembly and cellular stability of RNA polymerase II, and complexes of PI3-kinase-like kinases such as mTOR. However, the mechanism by which this occurs is poorly understood. Here we use cryo-EM and biochemical studies on the human R2TP core (RUVBL1-RUVBL2-RPAP3-PIH1D1) which reveal the distinctive role of RPAP3, distinguishing metazoan R2TP from the smaller yeast equivalent. RPAP3 spans both faces of a single RUVBL ring, providing an extended scaffold that recruits clients and provides a flexible tether for HSP90. A 3.6 Å cryo-EM structure reveals direct interaction of a C-terminal domain of RPAP3 and the ATPase domain of RUVBL2, necessary for human R2TP assembly but absent from yeast. The mobile TPR domains of RPAP3 map to the opposite face of the ring, associating with PIH1D1, which mediates client protein recruitment. Thus, RPAP3 provides a flexible platform for bringing HSP90 into proximity with diverse client proteins.
History
DepositionFeb 5, 2018-
Header (metadata) releaseFeb 21, 2018-
Map releaseApr 4, 2018-
UpdateApr 25, 2018-
Current statusApr 25, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0096
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0096
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4291.png

Downloads & links

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Map

FileDownload / File: emd_4291.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 304 pix.
= 322.24 Å		1.06 Å/pix.
x 304 pix.
= 322.24 Å		1.06 Å/pix.
x 304 pix.
= 322.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0096 / Movie #1: 0.0096
Minimum - Maximum-0.015653865 - 0.04465075
Average (Standard dev.)0.00023196575 (±0.0019080193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 322.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z304304304
origin x/y/z0.0000.0000.000
length x/y/z322.240322.240322.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-0.0160.0450.000

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Supplemental data

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Sample components

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Entire : Human R2TP complex - subgroup 2

EntireName: Human R2TP complex - subgroup 2
Components
  • Complex: Human R2TP complex - subgroup 2
    • Protein or peptide: RUVBL1
    • Protein or peptide: RUVBL2
    • Protein or peptide: PIH1D1

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Supramolecule #1: Human R2TP complex - subgroup 2

SupramoleculeName: Human R2TP complex - subgroup 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: RUVBL1

MacromoleculeName: RUVBL1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTAL ALAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT P CETENPMG GYGKTISHVI IGLKTAKGTK ...String:
MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTAL ALAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT P CETENPMG GYGKTISHVI IGLKTAKGTK QLKLDPSIFE SLQKERVEAG DVIYIEANSG AVKRQGRCDT YA TEFDLEA EEYVPLPKGD VHKKKEIIQD VTLHDLDVAN ARPQGGQDIL SMMGQLMKPK KTEITDKLRG EIN KVVNKY IDQGIAELVP GVLFVDEVHM LDIECFTYLH RALESSIAPI VIFASNRGNC VIRGTEDITS PHGI PLDLL DRVMIIRTML YTPQEMKQII KIRAQTEGIN ISEEALNHLG EIGTKTTLRY SVQLLTPANL LAKIN GKDS IEKEHVEEIS ELFYDAKSSA KILADQQDKY MK

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Macromolecule #2: RUVBL2

MacromoleculeName: RUVBL2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQP GTGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE G EVVEIQID RPATGTGSKV GKLTLKTTEM ...String:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQP GTGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE G EVVEIQID RPATGTGSKV GKLTLKTTEM ETIYDLGTKM IESLTKDKVQ AGDVITIDKA TGKISKLGRS FT RARDYDA MGSQTKFVQC PDGELQKRKE VVHTVSLHEI DVINSRTQGF LALFSGDTGE IKSEVREQIN AKV AEWREE GKAEIIPGVL FIDEVHMLDI ESFSFLNRAL ESDMAPVLIM ATNRGITRIR GTSYQSPHGI PIDL LDRLL IVSTTPYSEK DTKQILRIRC EEEDVEMSED AYTVLTRIGL ETSLRYAIQL ITAASLVCRK RKGTE VQVD DIKRVYSLFL DESRSTQYMK EYQDAFLFNE LKGETMDTS

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Macromolecule #3: PIH1D1

MacromoleculeName: PIH1D1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANPKLLGMG LSEAEAIGAD SARFEELLLQ ASKELQQAQT TRPESTQIQP QPGFCIKTNS SEGKVFINIC HSPSIPPPA DVTEEELLQM LEEDQAGFRI PMSLGEPHAE LDAKGQGCTA YDVAVNSDFY RRMQNSDFLR E LVITIARE GLEDKYNLQL NPEWRMMKNR ...String:
MANPKLLGMG LSEAEAIGAD SARFEELLLQ ASKELQQAQT TRPESTQIQP QPGFCIKTNS SEGKVFINIC HSPSIPPPA DVTEEELLQM LEEDQAGFRI PMSLGEPHAE LDAKGQGCTA YDVAVNSDFY RRMQNSDFLR E LVITIARE GLEDKYNLQL NPEWRMMKNR PFMGSISQQN IRSEQRPRIQ ELGDLYTPAP GRAESGPEKP HL NLWLEAP DLLLAEVDLP KLDGALGLSL EIGENRLVMG GPQQLYHLDA YIPLQINSHE SKAAFHRKRK QLM VAMPLL PVPS

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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: 7.8
Component:
ConcentrationNameFormula
25.0 mMHEPES
130.0 mMsodium chlorideNaCl
10.0 mM2-Mercaptoethanol
0.5 mMADP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 182351
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)

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Atomic model buiding 1

RefinementProtocol: OTHER

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