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Yorodumi- EMDB-4287: Human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to... -
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-Basic information
Entry | Database: EMDB / ID: EMD-4287 | ||||||||||||
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Title | Human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to 1 RBD domain from RPAP3. | ||||||||||||
Map data | Structure of a human R2TP subcomplex, comprising a RUVBL1-RUVBL2 hexamer bound to one RBD domain of RPAP3 | ||||||||||||
Sample |
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Function / homology | Function and homology information promoter-enhancer loop anchoring activity / 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 / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body ...promoter-enhancer loop anchoring activity / 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 / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body / Ino80 complex / protein folding chaperone complex / box C/D snoRNP assembly / 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 / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / DNA helicase activity / positive regulation of DNA repair / TBP-class protein binding / telomere maintenance / cellular response to estradiol stimulus / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / euchromatin / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / ADP binding / beta-catenin binding / nuclear matrix / transcription corepressor activity / UCH proteinases / cellular response to UV / nucleosome / unfolded protein binding / positive regulation of canonical Wnt signaling pathway / protein folding / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / DNA recombination / DNA helicase / transcription coactivator activity / protein stabilization / Ub-specific processing proteases / regulation of cell cycle / chromatin remodeling / ribonucleoprotein complex / cadherin binding / cell cycle / 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 / positive regulation of DNA-templated transcription / protein homodimerization activity / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.57 Å | ||||||||||||
Authors | Martino F / Munoz-Hernandez H / Rodriguez CF / Pearl LH / Llorca O | ||||||||||||
Funding support | Spain, 3 items
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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_4287.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-4287-v30.xml emd-4287.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4287_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_4287.png | 58.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4287 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4287 | HTTPS FTP |
-Validation report
Summary document | emd_4287_validation.pdf.gz | 246 KB | Display | EMDB validaton report |
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Full document | emd_4287_full_validation.pdf.gz | 245.1 KB | Display | |
Data in XML | emd_4287_validation.xml.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4287 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4287 | HTTPS FTP |
-Related structure data
Related structure data | 6fo1MC 4289C 4290C 4291C M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_4287.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of a human R2TP subcomplex, comprising a RUVBL1-RUVBL2 hexamer bound to one RBD domain of RPAP3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : a human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound ...
Entire | Name: a human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to 1 RBD domain of RPAP3 |
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Components |
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-Supramolecule #1: a human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound ...
Supramolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: RuvB-like 1
Macromolecule | Name: RuvB-like 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50.296914 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: RuvB-like 2
Macromolecule | Name: RuvB-like 2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 51.222465 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #3: RNA polymerase II-associated protein 3
Macromolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 75.830547 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-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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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-6fo1: |