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- EMDB-4287: Human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to... -

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Basic information

Entry
Database: EMDB / ID: EMD-4287
TitleHuman R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to 1 RBD domain from RPAP3
Map dataStructure of a human R2TP subcomplex, comprising a RUVBL1-RUVBL2 hexamer bound to one RBD domain of RPAP3
Sample
  • Complex: a human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to 1 RBD domain of RPAP3
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: RNA polymerase II-associated protein 3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsR2TP / HSP90 co-chaperone / PIH1D1 / RPAP3 / RUVBL1-RUVBL2 / CHAPERONE
Function / homology
Function and homology information


promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / Ino80 complex ...promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / Ino80 complex / regulation of double-strand break repair / box C/D snoRNP assembly / protein folding chaperone complex / regulation of chromosome organization / NuA4 histone acetyltransferase complex / 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 / regulation of DNA repair / RNA polymerase II core promoter sequence-specific DNA binding / DNA helicase activity / Deposition of new CENPA-containing nucleosomes at the centromere / TBP-class protein binding / telomere maintenance / positive regulation of DNA repair / cellular response to estradiol stimulus / Formation of the beta-catenin:TCF transactivating complex / negative regulation of canonical Wnt signaling pathway / euchromatin / DNA Damage Recognition in GG-NER / beta-catenin binding / ADP binding / chromatin DNA binding / nuclear matrix / transcription corepressor activity / cellular response to UV / UCH proteinases / positive regulation of canonical Wnt signaling pathway / nucleosome / unfolded protein binding / protein folding / HATs acetylate histones / ATPase binding / regulation of apoptotic process / DNA recombination / spermatogenesis / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / transcription coactivator activity / regulation of cell cycle / protein stabilization / Ub-specific processing proteases / nuclear speck / ciliary basal body / cilium / cadherin binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / ribonucleoprotein complex / cell division / DNA repair / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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 / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / 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 ...: / 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 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsMartino F / Munoz-Hernandez H / Rodriguez CF / Pearl LH / Llorca O
Funding support Spain, 3 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessSAF2014-52301-R Spain
Spanish Ministry of Economy and CompetitivenessSAF2017-82632-P Spain
Spanish Ministry of Economy and CompetitivenessSAF2014-59993-JIN Spain
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 28, 2018-
Map releaseApr 4, 2018-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6fo1
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4287.png

Downloads & links

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Map

FileDownload / File: emd_4287.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of a human R2TP subcomplex, comprising a RUVBL1-RUVBL2 hexamer bound to one RBD domain of RPAP3
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: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.11325202 - 0.24127227
Average (Standard dev.)0.0002597506 (±0.0047419416)
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-0.1130.2410.000

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Supplemental data

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Sample components

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Entire : a human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound ...

EntireName: a human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to 1 RBD domain of RPAP3
Components
  • Complex: a human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to 1 RBD domain of RPAP3
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: RNA polymerase II-associated protein 3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: a human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound ...

SupramoleculeName: a human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to 1 RBD domain of RPAP3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RuvB-like 1

MacromoleculeName: RuvB-like 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.296914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK ...String:
MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK QLKLDPSIFE SLQKERVEAG DVIYIEANSG AVKRQGRCDT YATEFDLEAE EYVPLPKGDV HKKKEIIQDV TL HDLDVAN ARPQGGQDIL SMMGQLMKPK KTEITDKLRG EINKVVNKYI DQGIAELVPG VLFVDEVHML DIECFTYLHR ALE SSIAPI VIFASNRGNC VIRGTEDITS PHGIPLDLLD RVMIIRTMLY TPQEMKQIIK IRAQTEGINI SEEALNHLGE IGTK TTLRY SVQLLTPANL LAKINGKDSI EKEHVEEISE LFYDAKSSAK ILADQQDKYM K

UniProtKB: RuvB-like 1

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Macromolecule #2: RuvB-like 2

MacromoleculeName: RuvB-like 2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.222465 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ...String:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ETIYDLGTKM IESLTKDKVQ AGDVITIDKA TGKISKLGRS FTRARDYDAM GSQTKFVQCP DGELQKRKEV VH TVSLHEI DVINSRTQGF LALFSGDTGE IKSEVREQIN AKVAEWREEG KAEIIPGVLF IDEVHMLDIE SFSFLNRALE SDM APVLIM ATNRGITRIR GTSYQSPHGI PIDLLDRLLI VSTTPYSEKD TKQILRIRCE EEDVEMSEDA YTVLTRIGLE TSLR YAIQL ITAASLVCRK RKGTEVQVDD IKRVYSLFLD ESRSTQYMKE YQDAFLFNEL KGETMDTS

UniProtKB: RuvB-like 2

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Macromolecule #3: RNA polymerase II-associated protein 3

MacromoleculeName: RNA polymerase II-associated protein 3 / type: protein_or_peptide / ID: 3
Details: MTSANKAIELQLQVKQNAEELQDFMRDLENWEKDIKQKDMELRRQNGVPEENLPPIRNGN FRKKKKGKAKESSKKTREENTKNRIKSYDYEAWAKLDVDRILDELDKDDSTHESLSQESE SEEDGIHVDSQKALVLKEKGNKYFKQGKYDEAIDCYTKGMDADPYNPVLPTNRASAYFRL ...Details: MTSANKAIELQLQVKQNAEELQDFMRDLENWEKDIKQKDMELRRQNGVPEENLPPIRNGN FRKKKKGKAKESSKKTREENTKNRIKSYDYEAWAKLDVDRILDELDKDDSTHESLSQESE SEEDGIHVDSQKALVLKEKGNKYFKQGKYDEAIDCYTKGMDADPYNPVLPTNRASAYFRL KKFAVAESDCNLAVALNRSYTKAYSRRGAARFALQKLEEAKKDYERVLELEPNNFEATNE LRKISQALASKENSYPKEADIVIKSTEGERKQIEAQQNKQQAISEKDRGNGFFKEGKYER AIECYTRGIAADGANALLPANRAMAYLKIQKYEEAEKDCTQAILLDGSYSKAFARRGTAR TFLGKLNEAKQDFETVLLLEPGNKQAVTELSKIKKELIEKGHWDDVFLDSTQRQNVVKPI DNPPHPGSTKPLKKVIIEETGNLIQTIDVPDSTTAAAPENNPINLANVIAATGTTSKKNS SQDDLFPTSDTPRAKVLKIEEVSDTSSLQPQASLKQDVCQSYSEKMPIEIEQKPAQFATT VLPPIPANSFQLESDFRQLKSSPDMLYQYLKQIEPSLYPKLFQKNLDPDVFNQIVKILHD FYIEKEKPLLIFEILQRLSELKRFDMAVMFMSETEKKIARALFNHIDKSGLKDSSVEELK KRYGG
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.830547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTSANKAIEL QLQVKQNAEE LQDFMRDLEN WEKDIKQKDM ELRRQNGVPE ENLPPIRNGN FRKKKKGKAK ESSKKTREEN TKNRIKSYD YEAWAKLDVD RILDELDKDD STHESLSQES ESEEDGIHVD SQKALVLKEK GNKYFKQGKY DEAIDCYTKG M DADPYNPV ...String:
MTSANKAIEL QLQVKQNAEE LQDFMRDLEN WEKDIKQKDM ELRRQNGVPE ENLPPIRNGN FRKKKKGKAK ESSKKTREEN TKNRIKSYD YEAWAKLDVD RILDELDKDD STHESLSQES ESEEDGIHVD SQKALVLKEK GNKYFKQGKY DEAIDCYTKG M DADPYNPV LPTNRASAYF RLKKFAVAES DCNLAVALNR SYTKAYSRRG AARFALQKLE EAKKDYERVL ELEPNNFEAT NE LRKISQA LASKENSYPK EADIVIKSTE GERKQIEAQQ NKQQAISEKD RGNGFFKEGK YERAIECYTR GIAADGANAL LPA NRAMAY LKIQKYEEAE KDCTQAILLD GSYSKAFARR GTARTFLGKL NEAKQDFETV LLLEPGNKQA VTELSKIKKE LIEK GHWDD VFLDSTQRQN VVKPIDNPPH PGSTKPLKKV IIEETGNLIQ TIDVPDSTTA AAPENNPINL ANVIAATGTT SKKNS SQDD LFPTSDTPRA KVLKIEEVSD TSSLQPQASL KQDVCQSYSE KMPIEIEQKP AQFATTVLPP IPANSFQLES DFRQLK SSP DMLYQYLKQI EPSLYPKLFQ KNLDPDVFNQ IVKILHDFYI EKEKPLLIFE ILQRLSELKR FDMAVMFMSE TEKKIAR AL FNHIDKSGLK DSSVEELKKR YGG

UniProtKB: RNA polymerase II-associated protein 3

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 101742
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6fo1:
Human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to 1 RBD domain from RPAP3.

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