+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3678 | |||||||||
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Title | Structure of the yeast R2TP complex | |||||||||
Map data | Structure of the yeast R2TP complex | |||||||||
Sample |
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Function / homology | Function and homology information R2TP complex / Swr1 complex / Ino80 complex / 5'-3' DNA helicase activity / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / DNA helicase activity / rRNA processing / DNA helicase ...R2TP complex / Swr1 complex / Ino80 complex / 5'-3' DNA helicase activity / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / DNA helicase activity / rRNA processing / DNA helicase / protein stabilization / chromatin remodeling / DNA repair / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.37 Å | |||||||||
Authors | Rivera-Calzada A / Pal M / Munoz-Hernandez H / Luque-Ortega JR / Gil-Carton D / Degliesposti G / Skehel JM / Prodromou C / Pearl LH / Llorca O | |||||||||
Citation | Journal: Structure / Year: 2017 Title: The Structure of the R2TP Complex Defines a Platform for Recruiting Diverse Client Proteins to the HSP90 Molecular Chaperone System. Authors: Angel Rivera-Calzada / Mohinder Pal / Hugo Muñoz-Hernández / Juan R Luque-Ortega / David Gil-Carton / Gianluca Degliesposti / J Mark Skehel / Chrisostomos Prodromou / Laurence H Pearl / Oscar Llorca / Abstract: The R2TP complex, comprising the Rvb1p-Rvb2p AAA-ATPases, Tah1p, and Pih1p in yeast, is a specialized Hsp90 co-chaperone required for the assembly and maturation of multi-subunit complexes. These ...The R2TP complex, comprising the Rvb1p-Rvb2p AAA-ATPases, Tah1p, and Pih1p in yeast, is a specialized Hsp90 co-chaperone required for the assembly and maturation of multi-subunit complexes. These include the small nucleolar ribonucleoproteins, RNA polymerase II, and complexes containing phosphatidylinositol-3-kinase-like kinases. The structure and stoichiometry of yeast R2TP and how it couples to Hsp90 are currently unknown. Here, we determine the 3D organization of yeast R2TP using sedimentation velocity analysis and cryo-electron microscopy. The 359-kDa complex comprises one Rvb1p/Rvb2p hetero-hexamer with domains II (DIIs) forming an open basket that accommodates a single copy of Tah1p-Pih1p. Tah1p-Pih1p binding to multiple DII domains regulates Rvb1p/Rvb2p ATPase activity. Using domain dissection and cross-linking mass spectrometry, we identified a unique region of Pih1p that is essential for interaction with Rvb1p/Rvb2p. These data provide a structural basis for understanding how R2TP couples an Hsp90 dimer to a diverse set of client proteins and complexes. | |||||||||
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_3678.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-3678-v30.xml emd-3678.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
Images | emd_3678.png | 305.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3678 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3678 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3678.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the yeast R2TP complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 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 : Yeast R2TP complex
Entire | Name: Yeast R2TP complex |
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Components |
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-Supramolecule #1: Yeast R2TP complex
Supramolecule | Name: Yeast R2TP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Experimental: 359 KDa |
-Macromolecule #1: Rvb1p
Macromolecule | Name: Rvb1p / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MMVAISEVKE NPGVNSSNSG AVTRTAAHTH IKGLGLDESG VAKRVEGGFV GQIEAREACG V IVDLIKAK KMSGRAILLA GGPSTGKTAL ALAISQELGP KVPFCPLVGS ELYSVEVKKT ET LMENFRR AIGLRIKETK EVYEGEVTEL ...String: MGSSHHHHHH SSGLVPRGSH MMVAISEVKE NPGVNSSNSG AVTRTAAHTH IKGLGLDESG VAKRVEGGFV GQIEAREACG V IVDLIKAK KMSGRAILLA GGPSTGKTAL ALAISQELGP KVPFCPLVGS ELYSVEVKKT ET LMENFRR AIGLRIKETK EVYEGEVTEL TPEDAENPLG GYGKTISHVI VGLKSAKGTK TLR LDPTIY ESIQREKVSI GDVIYIEANT GAVKRVGRSD AYATEFDLET EEYVPLPKGE VHKK KEIVQ DVTLHDLDVA NARPQGGQDV ISMMGQLLKP KKTEITEKLR QEVNKVVAKY IDQGV AELI PGVLFIDEVN MLDIEIFTYL NKALESNIAP VVVLASNRGM TTVRGTEDVI SPHGVP PDL IDRLLIVRTL PYDKDEIRTI IERRATVERL QVESSALDLL ATMGTETSLR YALQLLA PC GILAQTSNRK EIVVNDVNEA KLLFLDAKRS TKILETSANY L |
-Macromolecule #2: Rvb2p
Macromolecule | Name: Rvb2p / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MEQKLISEED LLRSEEQKLI SEEDLLRSEE QKLISEEDLL RSE SRGSHH HHHHLEVLFQ GPAS MSIQT SDPNETSDLK SLSLIAAHSH ITGLGLDENL QPRPTSEGMV GQLQARRAAG VILKM VQNG TIAGRAVLVA GPPSTGKTAL AMGVSQSLGK DVPFTAIAGS ...String: MEQKLISEED LLRSEEQKLI SEEDLLRSEE QKLISEEDLL RSE SRGSHH HHHHLEVLFQ GPAS MSIQT SDPNETSDLK SLSLIAAHSH ITGLGLDENL QPRPTSEGMV GQLQARRAAG VILKM VQNG TIAGRAVLVA GPPSTGKTAL AMGVSQSLGK DVPFTAIAGS EIFSLELSKT EALTQA FRK SIGIKIKEET ELIEGEVVEI QIDRSITGGH KQGKLTIKTT DMETIYELGN KMIDGLT KE KVLAGDVISI DKASGKITKL GRSFARSRDY DAMGADTRFV QCPEGELQKR KTVVHTVS L HEIDVINSRT QGFLALFTGD TGEIRSEVRD QINTKVAEWK EEGKAEIVPG VLFIDEVHM LDIECFSFIN RALEDEFAPI VMMATNRGVS KTRGTNYKSP HGLPLDLLDR SIIITTKSYN EQEIKTILS IRAQEEEVEL SSDALDLLTK TGVETSLRYS SNLISVAQQI AMKRKNNTVE V EDVKRAYL LFLDSARSVK YVQENESQYI DDQGNVQISI AKSADPDAMD TTE |
-Macromolecule #3: Pih1p
Macromolecule | Name: Pih1p / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSHHHHHHMA DFLLRPIKQR HRNEDKYVSV DAADGSVSKI EPIADFVIKT KLLSANGPEK LQDGRKVFIN VCHSPLVPKP EVDFNARIVF PLIIQNEWEI PIITSCYRMD HDKKGQECYV WDCCINSDCS RWICDDIQLR EILVEWCLES CEIRDSVVLC RDRIAFPKMK ...String: MSHHHHHHMA DFLLRPIKQR HRNEDKYVSV DAADGSVSKI EPIADFVIKT KLLSANGPEK LQDGRKVFIN VCHSPLVPKP EVDFNARIVF PLIIQNEWEI PIITSCYRMD HDKKGQECYV WDCCINSDCS RWICDDIQLR EILVEWCLES CEIRDSVVLC RDRIAFPKMK KKGAELPALE VLNDELHQDY KAKMHKIIEE EAGDPMSILR GRNDDGDDNN DPDDGTLPPL FPIENKISGA KIEEIDKNEI AHRNLKQAPA PAPAPHEQQE DVPEYEVKMK RFKGAAYKLR ILIENKAPNS KPDRFSPSYN FAENILYING KLSIPLPRDI VVNAADIKIF HIRKERTLYI YI |
-Macromolecule #4: Tah1p
Macromolecule | Name: Tah1p / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH WSHPQFEKGG GSGGGSGGSS AWSHPQFEKL EVLFQGPHMM SQFEKQKEQG NSLFKQGLY REAVHCYDQL ITAQPQNPVG YSNKAMALIK LGEYTQAIQM CQQGLRYTST AEHVAIRSKL QYRLELAQGA VGSVQIPVVE VDELPEGYDR S |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.45 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / 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 / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 39000 |
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 / Digitization - Frames/image: 2-19 / Average exposure time: 12.0 sec. / Average electron dose: 48.0 e/Å2 Details: Data was collected at two different tilts: 0 and 35 degrees. |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 346693 |
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CTF correction | Software - Name: Gctf (ver. 1.06) |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3) |
Final 3D classification | Software - Name: RELION (ver. 1.3) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 38962 |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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