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- EMDB-9356: Cryo-EM structure of singly-bound SNF2h-nucleosome complex with S... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9356 | ||||||||||||||||||
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Title | Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at the flanking DNA proximal side | ||||||||||||||||||
![]() | cryosparc v2 non-uniform refinement; sharpened and resampled to fit into common orientation | ||||||||||||||||||
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![]() | ISWI / Chromatin / Nucleosome / DNA / SNF2h / histones / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||||||||||||||
Function / homology | ![]() histone octamer slider activity / RSF complex / ACF complex / WICH complex / negative regulation of mitotic chromosome condensation / CHRAC / NoRC complex / : / B-WICH complex / NURF complex ...histone octamer slider activity / RSF complex / ACF complex / WICH complex / negative regulation of mitotic chromosome condensation / CHRAC / NoRC complex / : / B-WICH complex / NURF complex / rDNA heterochromatin formation / chromatin silencing complex / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase III / negative regulation of transcription by RNA polymerase I / positive regulation of transcription by RNA polymerase I / regulation of DNA replication / ATP-dependent activity, acting on DNA / pericentric heterochromatin / heterochromatin formation / nucleosome binding / condensed chromosome / Deposition of new CENPA-containing nucleosomes at the centromere / helicase activity / positive regulation of DNA replication / cellular response to leukemia inhibitory factor / DNA-templated transcription initiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / fibrillar center / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / site of double-strand break / histone binding / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA damage response / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||||||||
![]() | Armache J-P / Gamarra N / Johnson SL / Leonard JD / Wu S / Narlikar GN | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome. Authors: Jean Paul Armache / Nathan Gamarra / Stephanie L Johnson / John D Leonard / Shenping Wu / Geeta J Narlikar / Yifan Cheng / ![]() Abstract: The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome ...The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeF that capture two potential reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, appear disordered. The disordered acidic patch is expected to inhibit the second SNF2h protomer, while disorder near the dyad is expected to promote DNA translocation. The other structure doesn't show octamer deformation, but surprisingly shows a 2 bp translocation. FRET studies indicate that ADP-BeF predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation. | ||||||||||||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 74.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.3 KB 22.3 KB | Display Display | ![]() |
Images | ![]() | 244.4 KB | ||
Filedesc metadata | ![]() | 7.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 641.9 KB | Display | ![]() |
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Full document | ![]() | 641.5 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 7.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ne3MC ![]() 9351C ![]() 9352C ![]() 9353C ![]() 9354C ![]() 9355C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | cryosparc v2 non-uniform refinement; sharpened and resampled to fit into common orientation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2156 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Cryo-EM structure of singly-bound SNF2h-nucleosome complex with S...
+Supramolecule #1: Cryo-EM structure of singly-bound SNF2h-nucleosome complex with S...
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B
+Macromolecule #5: Histone H2B
+Macromolecule #8: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
+Macromolecule #6: DNA (156-MER)
+Macromolecule #7: DNA (156-MER)
+Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK I Details: 2.5 ul of nucleosome-443 SNF2h complexes were applied to a glow discharged Quantifoil holey carbon grid (1.2 um hole size, 400 mesh), blotted in a Vitrobot Mark I (FEI Company) using 6 ...Details: 2.5 ul of nucleosome-443 SNF2h complexes were applied to a glow discharged Quantifoil holey carbon grid (1.2 um hole size, 400 mesh), blotted in a Vitrobot Mark I (FEI Company) using 6 seconds blotting at 100% humidity, and then plunge-frozen in liquid ethane cooled by liquid nitrogen.. |
Details | This sample was monodisperse |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 41.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-6ne3: |