+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5638 | |||||||||
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Title | 3D Cryo-negative EM structure of nucleosome-bound SWR1 | |||||||||
Map data | Cryo-EM structure of SWR1 (S.c.) bound to recombinant nucleosomes | |||||||||
Sample |
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Keywords | chromatin remodeling / SWR1 / INO80 / nucleosome / Rvb1 / Rvb2 / AAA+ ATPase / histone / dimer exchange / H2A.Z | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 34.0 Å | |||||||||
Authors | Nguyen VQ / Ranjan A / Stengel F / Wei D / Aebersold R / Wu C / Leschziner AE | |||||||||
Citation | Journal: Cell / Year: 2013 Title: Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1. Authors: Vu Q Nguyen / Anand Ranjan / Florian Stengel / Debbie Wei / Ruedi Aebersold / Carl Wu / Andres E Leschziner / Abstract: The ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This ...The ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This localization of H2A.Z is conserved throughout eukaryotes. SWR1 is a 1 megadalton complex containing 14 different polypeptides, including the AAA+ ATPases Rvb1 and Rvb2. Using electron microscopy, we obtained the three-dimensional structure of SWR1 and mapped its major functional components. Our data show that SWR1 contains a single heterohexameric Rvb1/Rvb2 ring that, together with the catalytic subunit Swr1, brackets two independently assembled multisubunit modules. We also show that SWR1 undergoes a large conformational change upon engaging a limited region of the nucleosome core particle. Our work suggests an important structural role for the Rvbs and a distinct substrate-handling mode by SWR1, thereby providing a structural framework for understanding the complex dimer-exchange reaction. | |||||||||
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_5638.map.gz | 11.6 MB | EMDB map data format | |
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Header (meta data) | emd-5638-v30.xml emd-5638.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_5638.png | 65.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5638 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5638 | HTTPS FTP |
-Validation report
Summary document | emd_5638_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_5638_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_5638_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5638 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5638 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5638.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of SWR1 (S.c.) bound to recombinant nucleosomes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.45 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 : SWR1 (S.c.) bound to recombinant nucleosomes
Entire | Name: SWR1 (S.c.) bound to recombinant nucleosomes |
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Components |
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-Supramolecule #1000: SWR1 (S.c.) bound to recombinant nucleosomes
Supramolecule | Name: SWR1 (S.c.) bound to recombinant nucleosomes / type: sample / ID: 1000 / Number unique components: 15 |
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Molecular weight | Theoretical: 1.2 MDa |
-Macromolecule #1: SWR1
Macromolecule | Name: SWR1 / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W1588C-4C / synonym: Baker's yeast |
Molecular weight | Theoretical: 1.2 MDa |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Details: 25 mM HEPES-KOH, pH 7.6, 1 mM EDTA, 2 mM MgCl2, 0.01% NP-40, 1 mM DTT, 100 mM KCl |
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Staining | Type: NEGATIVE Details: Cryo-negative staining with 2% uranyl formate followed by freezing in liquid nitrogen |
Grid | Details: 200 mesh Quantifoil with glow-discharged thin carbon support |
Vitrification | Cryogen name: NITROGEN / Instrument: OTHER Method: Cryo-negative stain with 2% uranyl formate. Blotted and frozen in liquid nitrogen. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 100 K |
Details | Low-dose imaging |
Date | May 20, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 300 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 86700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | The dataset was classified using the maximum-likelihood based method in the RELION program. A selected 3D class was then refined against particles assigned to the class using RELION's "Autorefine" function. |
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CTF correction | Details: EMAN2 |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 12000 |