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Yorodumi- EMDB-3083: Architecture and nucleotide-driven conformational states of the R... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3083 | |||||||||
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Title | Architecture and nucleotide-driven conformational states of the Rvb1/Rvb2 dodecamer | |||||||||
Map data | apo-state Rvb1/2 focused reconstruction | |||||||||
Sample |
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Keywords | Rvb1 / Rvb2 | |||||||||
Function / homology | Function and homology information R2TP complex / Swr1 complex / Ino80 complex / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / DNA helicase activity / rRNA processing / 5'-3' DNA helicase activity / DNA helicase ...R2TP complex / Swr1 complex / Ino80 complex / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / DNA helicase activity / rRNA processing / 5'-3' DNA helicase activity / DNA helicase / chromatin remodeling / protein stabilization / DNA repair / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.4 Å | |||||||||
Authors | Ewens CA / Su M / Zhao L / Houry WA / Southworth DR | |||||||||
Citation | Journal: Structure / Year: 2016 Title: Architecture and Nucleotide-Dependent Conformational Changes of the Rvb1-Rvb2 AAA+ Complex Revealed by Cryoelectron Microscopy. Authors: Caroline A Ewens / Min Su / Liang Zhao / Nardin Nano / Walid A Houry / Daniel R Southworth / Abstract: Rvb1 and Rvb2 are essential AAA+ proteins that interact together during the assembly and activity of diverse macromolecules including chromatin remodelers INO80 and SWR-C, and ribonucleoprotein ...Rvb1 and Rvb2 are essential AAA+ proteins that interact together during the assembly and activity of diverse macromolecules including chromatin remodelers INO80 and SWR-C, and ribonucleoprotein complexes including telomerase and snoRNPs. ATP hydrolysis by Rvb1/2 is required for function; however, the mechanism that drives substrate remodeling is unknown. Here we determined the architecture of the yeast Rvb1/2 dodecamer using cryoelectron microscopy and identify that the substrate-binding insertion domain undergoes conformational changes in response to nucleotide state. 2D and 3D classification defines the dodecamer flexibility, revealing distinct arrangements and the hexamer-hexamer interaction interface. Reconstructions of the apo, ATP, and ADP states identify that Rvb1/2 undergoes substantial conformational changes that include a twist in the insertion-domain position and a corresponding rotation of the AAA+ ring. These results reveal how the ATP hydrolysis cycle of the AAA+ domains directs insertion-domain movements that could provide mechanical force during remodeling or helicase activities. | |||||||||
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_3083.map.gz | 5.9 MB | EMDB map data format | |
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Header (meta data) | emd-3083-v30.xml emd-3083.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_3083.png | 93.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3083 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3083 | HTTPS FTP |
-Validation report
Summary document | emd_3083_validation.pdf.gz | 225 KB | Display | EMDB validaton report |
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Full document | emd_3083_full_validation.pdf.gz | 224.2 KB | Display | |
Data in XML | emd_3083_validation.xml.gz | 4.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3083 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3083 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3083.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | apo-state Rvb1/2 focused reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2 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 : apo-state Rvb1/2 focused reconstruction
Entire | Name: apo-state Rvb1/2 focused reconstruction |
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Components |
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-Supramolecule #1000: apo-state Rvb1/2 focused reconstruction
Supramolecule | Name: apo-state Rvb1/2 focused reconstruction / type: sample / ID: 1000 / Oligomeric state: heterododecamer / Number unique components: 2 |
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Molecular weight | Experimental: 600 KDa / Theoretical: 600 KDa Method: size exclusion chromatography with multiangle light scattering |
-Macromolecule #1: Rvb1
Macromolecule | Name: Rvb1 / type: protein_or_peptide / ID: 1 / Name.synonym: Pontin / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Molecular weight | Experimental: 50 KDa / Theoretical: 50 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta 2 / Recombinant plasmid: pColaDuet |
Sequence | UniProtKB: RuvB-like protein 1 |
-Macromolecule #2: Rvb2
Macromolecule | Name: Rvb2 / type: protein_or_peptide / ID: 2 / Name.synonym: Reptin / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Molecular weight | Experimental: 50 KDa / Theoretical: 50 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta 2 / Recombinant plasmid: pColaDuet |
Sequence | UniProtKB: RuvB-like protein 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 / Details: 25mM HEPES, 150mM KCl, 6mM betaME |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV / Method: 1s blot |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Nov 9, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 3800 / Average electron dose: 5 e/Å2 Details: Every image is the average of 30 frames recorded by the direct electron detector |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: per micrograph |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: OTHER / Software - Name: relion, boxer, eman2, cftfind, spider / Number images used: 66597 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: chimera, situs |
Details | The domains were separately fitted by manual docking |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation |