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Yorodumi- PDB-8a5d: Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a5d | ||||||||||||||||||
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Title | Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of Chaetomium thermophilum INO80 | ||||||||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / chromatin remodeler / INO80 / Actin-related protein | ||||||||||||||||||
Function / homology | Function and homology information Ino80 complex / SWI/SNF complex / NuA4 histone acetyltransferase complex / double-strand break repair / nervous system development / cytoskeleton / hydrolase activity / chromatin remodeling / DNA repair / chromatin binding ...Ino80 complex / SWI/SNF complex / NuA4 histone acetyltransferase complex / double-strand break repair / nervous system development / cytoskeleton / hydrolase activity / chromatin remodeling / DNA repair / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP binding Similarity search - Function | ||||||||||||||||||
Biological species | Thermochaetoides thermophila (fungus) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||
Authors | Kunert, F. / Metzner, F.J. / Eustermann, S. / Jung, J. / Woike, S. / Schall, K. / Kostrewa, D. / Hopfner, K.P. | ||||||||||||||||||
Funding support | European Union, Germany, 5items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structural mechanism of extranucleosomal DNA readout by the INO80 complex. Authors: Franziska Kunert / Felix J Metzner / James Jung / Markus Höpfler / Stephan Woike / Kevin Schall / Dirk Kostrewa / Manuela Moldt / Jia-Xuan Chen / Susanne Bantele / Boris Pfander / Sebastian ...Authors: Franziska Kunert / Felix J Metzner / James Jung / Markus Höpfler / Stephan Woike / Kevin Schall / Dirk Kostrewa / Manuela Moldt / Jia-Xuan Chen / Susanne Bantele / Boris Pfander / Sebastian Eustermann / Karl-Peter Hopfner / Abstract: The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which ...The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a5d.cif.gz | 331.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a5d.ent.gz | 255.6 KB | Display | PDB format |
PDBx/mmJSON format | 8a5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a5d_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8a5d_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8a5d_validation.xml.gz | 48.2 KB | Display | |
Data in CIF | 8a5d_validation.cif.gz | 73.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/8a5d ftp://data.pdbj.org/pub/pdb/validation_reports/a5/8a5d | HTTPS FTP |
-Related structure data
Related structure data | 15165MC 8a5aC 8a5oC 8a5pC 8a5qC 8atfC 8av6C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 5 molecules GUVWX
#1: Protein | Mass: 37445.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Production host: Trichoplusia ni (cabbage looper) |
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#2: Protein | Mass: 84139.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0023770 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0S519 |
#3: Protein | Mass: 41735.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0062070 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0SE15 |
#4: Protein | Mass: 51761.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0055020 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0SBW4 |
#5: Protein | Mass: 29015.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0051540 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0SDE9 |
-Non-polymers , 2 types, 6 molecules
#6: Chemical | #7: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Source (natural) | Organism: Thermochaetoides thermophila (fungus) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 343000 / Symmetry type: POINT |