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Yorodumi- PDB-8a5o: Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module... -
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-Basic information
Entry | Database: PDB / ID: 8a5o | ||||||||||||||||||
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Title | Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80 | ||||||||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / chromatin remodeler / INO80 / Actin-related protein | ||||||||||||||||||
Function / homology | Function and homology information RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / ascospore wall assembly / vacuole inheritance / mitotic recombination / actin cortical patch / regulation of TOR signaling / Swr1 complex ...RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / ascospore wall assembly / vacuole inheritance / mitotic recombination / actin cortical patch / regulation of TOR signaling / Swr1 complex / telomere maintenance via recombination / kinetochore assembly / Ino80 complex / regulation of metabolic process / SWI/SNF complex / ATP-dependent chromatin remodeler activity / DNA duplex unwinding / establishment of cell polarity / NuA4 histone acetyltransferase complex / actin filament bundle / chromosome, centromeric region / protein secretion / subtelomeric heterochromatin formation / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / endocytosis / double-strand break repair / chromatin organization / histone binding / transcription by RNA polymerase II / chromosome, telomeric region / cytoskeleton / chromatin remodeling / DNA repair / mRNA binding / DNA-templated transcription / DNA damage response / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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 | 8a5o.cif.gz | 347.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a5o.ent.gz | 265.8 KB | Display | PDB format |
PDBx/mmJSON format | 8a5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a5o_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8a5o_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8a5o_validation.xml.gz | 49.6 KB | Display | |
Data in CIF | 8a5o_validation.cif.gz | 74.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/8a5o ftp://data.pdbj.org/pub/pdb/validation_reports/a5/8a5o | HTTPS FTP |
-Related structure data
Related structure data | 15179MC 8a5aC 8a5dC 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: 72170.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: INO80, YGL150C, G1880 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P53115, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#2: Protein | Mass: 100322.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: ARP8, YOR141C, YOR3348C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12386 |
#3: Protein | Mass: 41735.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: ACT1, ABY1, END7, YFL039C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60010 |
#4: Protein | Mass: 54894.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: ARP4, ACT3, YJL081C, J1012 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P80428 |
#5: Protein | Mass: 13111.197 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: IES4, YOR189W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q08561 |
-Non-polymers , 2 types, 6 molecules
#6: Chemical | #7: Chemical | |
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-Details
Has ligand of interest | N |
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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: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
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: 47.37 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250000 / Symmetry type: POINT |