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- EMDB-4289: Human R2TP complex-C3symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-4289
TitleHuman R2TP complex-C3symmetry
Map dataR2TP-C3symmetry.
Sample
  • Complex: Human R2TP complex processed applying C3 symmetry
    • Protein or peptide: RUVBL1
    • Protein or peptide: RUVBL2
    • Protein or peptide: RPAP3
    • 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: 3.8 Å
AuthorsMartino F / Munoz-Hernandez H / Rodriguez CF / 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) releaseMar 14, 2018-
Map releaseApr 4, 2018-
UpdateApr 4, 2018-
Current statusApr 4, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4289.png

Downloads & links

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Map

FileDownload / File: emd_4289.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationR2TP-C3symmetry.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 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: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.060696788 - 0.119324505
Average (Standard dev.)0.00016353861 (±0.003949601)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z339.200339.200339.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0610.1190.000

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Supplemental data

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Sample components

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Entire : Human R2TP complex processed applying C3 symmetry

EntireName: Human R2TP complex processed applying C3 symmetry
Components
  • Complex: Human R2TP complex processed applying C3 symmetry
    • Protein or peptide: RUVBL1
    • Protein or peptide: RUVBL2
    • Protein or peptide: RPAP3
    • Protein or peptide: PIH1D1

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Supramolecule #1: Human R2TP complex processed applying C3 symmetry

SupramoleculeName: Human R2TP complex processed applying C3 symmetry / 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 PPGTGKTALA LAIAQELGSK VPFCPMVGSE VYSTEIKKTE VLMENFRRAI GLRIKETKEV YEGEVTELTP CETENPMGGY GKTISHVIIG LKTAKGTKQL ...String:
MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGSK VPFCPMVGSE VYSTEIKKTE VLMENFRRAI GLRIKETKEV YEGEVTELTP CETENPMGGY GKTISHVIIG LKTAKGTKQL KLDPSIFESL QKERVEAGDV IYIEANSGAV KRQGRCDTYA TEFDLEAEEY VPLPKGDVHK KKEIIQDVTL HDLDVANARP QGGQDILSMM GQLMKPKKTE ITDKLRGEIN KVVNKYIDQG IAELVPGVLF VDEVHMLDIE CFTYLHRALE SSIAPIVIFA SNRGNCVIRG TEDITSPHGI PLDLLDRVMI IRTMLYTPQE MKQIIKIRAQ TEGINISEEA LNHLGEIGTK TTLRYSVQLL TPANLLAKIN GKDSIEKEHV EEISELFYDA KSSAKILADQ QDKYMK

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Macromolecule #2: RUVBL2

MacromoleculeName: RUVBL2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMGM AQALGPDTPF TAIAGSEIFS LEMSKTEALT QAFRRSIGVR IKEETEIIEG EVVEIQIDRP ATGTGSKVGK LTLKTTEMET ...String:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMGM AQALGPDTPF TAIAGSEIFS LEMSKTEALT QAFRRSIGVR IKEETEIIEG EVVEIQIDRP ATGTGSKVGK LTLKTTEMET IYDLGTKMIE SLTKDKVQAG DVITIDKATG KISKLGRSFT RARDYDAMGS QTKFVQCPDG ELQKRKEVVH TVSLHEIDVI NSRTQGFLAL FSGDTGEIKS EVREQINAKV AEWREEGKAE IIPGVLFIDE VHMLDIESFS FLNRALESDM APVLIMATNR GITRIRGTSY QSPHGIPIDL LDRLLIVSTT PYSEKDTKQI LRIRCEEEDV EMSEDAYTVL TRIGLETSLR YAIQLITAAS LVCRKRKGTE VQVDDIKRV YSLFLDESRS TQYMKEYQDA FLFNELKGET MDTS

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Macromolecule #3: RPAP3

MacromoleculeName: RPAP3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MTSANKAIEL QLQVKQNAEE LQDFMRDLEN WEKDIKQKDM ELRRQNGVPE ENLPPIRNGN FRKKKKGKAK ESSKKTREEN TKNRIKSYDY EAWAKLDVDR ILDELDKDDS THESLSQESE SEEDGIHVDS QKALVLKEKG NKYFKQGKYD EAIDCYTKGM DADPYNPVLP ...String:
MTSANKAIEL QLQVKQNAEE LQDFMRDLEN WEKDIKQKDM ELRRQNGVPE ENLPPIRNGN FRKKKKGKAK ESSKKTREEN TKNRIKSYDY EAWAKLDVDR ILDELDKDDS THESLSQESE SEEDGIHVDS QKALVLKEKG NKYFKQGKYD EAIDCYTKGM DADPYNPVLP TNRASAYFRL KKFAVAESDC NLAVALNRSY TKAYSRRGAA RFALQKLEEA KKDYERVLEL EPNNFEATNE LRKISQALAS KENSYPKEAD IVIKSTEGER KQIEAQQNKQ QAISEKDRGN GFFKEGKYER AIECYTRGIA ADGANALLPA NRAMAYLKIQ KYEEAEKDCT QAILLDGSYS KAFARRGTAR TFLGKLNEAK QDFETVLLLE PGNKQAVTEL SKIKKKPLKK VIIEETGNLI QTIDVPDSTT AAAPENNPIN LANVIAATGT TSKKNSSQDD LFPTSDTPRA KVLKIEEVSD TSSLQPQASL KQDVCQSYSE KMPIEIEQKP AQFATTVLPP IPANSFQLES DFRQLKSSPD MLYQYLKQIE PSLYPKLFQK NLDPDVFNQI VKILHDFYIE KEKPLLIFEI LQRLSELKRF DMAVMFMSET EKKIARALFN HIDKSGLKDS SVEELKKRYG G

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Macromolecule #4: PIH1D1

MacromoleculeName: PIH1D1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MANPKLLGMG LSEAEAIGAD SARFEELLLQ ASKELQQAQT TRPESTQIQP QPGFCIKTNS SEGKVFINIC HSPSIPPPAD VTEEELLQML EEDQAGFRIP MSLGEPHAEL DAKGQGCTAY DVAVNSDFYR RMQNSDFLRE LVITIAREGL EDKYNLQLNP EWRMMKNRPF ...String:
MANPKLLGMG LSEAEAIGAD SARFEELLLQ ASKELQQAQT TRPESTQIQP QPGFCIKTNS SEGKVFINIC HSPSIPPPAD VTEEELLQML EEDQAGFRIP MSLGEPHAEL DAKGQGCTAY DVAVNSDFYR RMQNSDFLRE LVITIAREGL EDKYNLQLNP EWRMMKNRPF MGSISQQNIR SEQRPRIQEL GDLYTPAPGR AESGPEKPHL NLWLEAPDLL LAEVDLPKLD GALGLSLEIG ENRLVMGGPQ QLYHLDAYIP LQINSHESKA AFHRKRKQLM VAMPLLPVPS

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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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 96406
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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