+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4289 | |||||||||
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Title | Human R2TP complex-C3symmetry | |||||||||
Map data | R2TP-C3symmetry. | |||||||||
Sample |
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Function / homology | Function and homology information TORC1 complex assembly / promoter-enhancer loop anchoring activity / snoRNA localization / positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / pre-snoRNP complex / Swr1 complex ...TORC1 complex assembly / promoter-enhancer loop anchoring activity / snoRNA localization / positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / pre-snoRNP complex / Swr1 complex / dynein axonemal particle / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body / Ino80 complex / box C/D snoRNP assembly / protein folding chaperone complex / NuA4 histone acetyltransferase complex / regulation of chromosome organization / positive regulation of double-strand break repair via homologous recombination / regulation of DNA replication / MLL1 complex / TFIID-class transcription factor complex binding / regulation of embryonic development / Telomere Extension By Telomerase / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / positive regulation of DNA repair / positive regulation of TORC1 signaling / epithelial cell differentiation / DNA helicase activity / TBP-class protein binding / telomere maintenance / histone reader activity / cellular response to estradiol stimulus / ADP binding / phosphoprotein binding / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / negative regulation of canonical Wnt signaling pathway / euchromatin / positive regulation of protein serine/threonine kinase activity / chromatin DNA binding / beta-catenin binding / rRNA processing / nuclear matrix / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / UCH proteinases / cellular response to UV / nucleosome / unfolded protein binding / protein folding / HATs acetylate histones / ATPase binding / histone binding / spermatogenesis / regulation of apoptotic process / DNA helicase / DNA recombination / transcription coactivator activity / protein stabilization / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / cadherin binding / cell cycle / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / DNA repair / centrosome / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Martino F / Munoz-Hernandez H / Rodriguez CF / Pearl LH / Llorca O | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4289.map.gz | 117.1 MB | EMDB map data format | |
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Header (meta data) | emd-4289-v30.xml emd-4289.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_4289.png | 60 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4289 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4289 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4289.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | R2TP-C3symmetry. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human R2TP complex processed applying C3 symmetry
Entire | Name: Human R2TP complex processed applying C3 symmetry |
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Components |
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-Supramolecule #1: Human R2TP complex processed applying C3 symmetry
Supramolecule | Name: Human R2TP complex processed applying C3 symmetry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: RUVBL1
Macromolecule | Name: RUVBL1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: RUVBL2
Macromolecule | Name: RUVBL2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: RPAP3
Macromolecule | Name: RPAP3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: PIH1D1
Macromolecule | Name: PIH1D1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 52.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf (ver. 1.06) |
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Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 96406 |
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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