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Open data
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Basic information
Entry | Database: PDB / ID: 6fhs | ||||||||||||
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Title | CryoEM Structure of INO80core | ||||||||||||
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![]() | DNA BINDING PROTEIN | ||||||||||||
Function / homology | ![]() DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / attachment of spindle microtubules to kinetochore / R2TP complex / Swr1 complex / attachment of mitotic spindle microtubules to kinetochore / Ino80 complex / box C/D snoRNP assembly / NuA4 histone acetyltransferase complex ...DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / attachment of spindle microtubules to kinetochore / R2TP complex / Swr1 complex / attachment of mitotic spindle microtubules to kinetochore / Ino80 complex / box C/D snoRNP assembly / NuA4 histone acetyltransferase complex / DNA helicase activity / mitotic spindle / kinetochore / DNA helicase / chromatin remodeling / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.754 Å | ||||||||||||
![]() | Eustermann, S. / Schall, K. / Kostrewa, D. / Strauss, M. / Hopfner, K. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for ATP-dependent chromatin remodelling by the INO80 complex. Authors: Sebastian Eustermann / Kevin Schall / Dirk Kostrewa / Kristina Lakomek / Mike Strauss / Manuela Moldt / Karl-Peter Hopfner / ![]() Abstract: In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone ...In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP-dependent chromatin remodellers such as the 15-subunit INO80 complex . INO80 regulates gene expression, DNA repair and replication by sliding nucleosomes, the exchange of histone H2A.Z with H2A, and the positioning of + 1 and -1 nucleosomes at promoter DNA. The structures and mechanisms of these remodelling reactions are currently unknown. Here we report the cryo-electron microscopy structure of the evolutionarily conserved core of the INO80 complex from the fungus Chaetomium thermophilum bound to a nucleosome, at a global resolution of 4.3 Å and with major parts at 3.7 Å. The INO80 core cradles one entire gyre of the nucleosome through multivalent DNA and histone contacts. An Rvb1/Rvb2 AAA ATPase heterohexamer is an assembly scaffold for the complex and acts as a 'stator' for the motor and nucleosome-gripping subunits. The Swi2/Snf2 ATPase motor binds to nucleosomal DNA at superhelical location -6, unwraps approximately 15 base pairs, disrupts the H2A-DNA contacts and is poised to pump entry DNA into the nucleosome. Arp5 and Ies6 bind superhelical locations -2 and -3 to act as a counter grip for the motor, on the other side of the H2A-H2B dimer. The Arp5 insertion domain forms a grappler element that binds the nucleosome dyad, connects the Arp5 actin-fold and entry DNA over a distance of about 90 Å and packs against histone H2A-H2B near the 'acidic patch'. Our structure together with biochemical data suggests a unified mechanism for nucleosome sliding and histone editing by INO80. The motor is part of a macromolecular ratchet, persistently pumping entry DNA across the H2A-H2B dimer against the Arp5 grip until a large nucleosome translocation step occurs. The transient exposure of H2A-H2B by motor activity as well as differential recognition of H2A.Z and H2A may regulate histone exchange. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 637.9 KB | Display | ![]() |
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PDB format | ![]() | 502.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4264MC ![]() 4277C ![]() 4278C ![]() 4280C ![]() 6fmlC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 6 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 50451.848 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Cell line: High Five Cells (BTI-TN-5B1-4) / Gene: CTHT_0006820 Cell line (production host): High Five Cells (BTI-TN-5B1-4) Production host: ![]() #2: Protein | Mass: 53212.746 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0006170 / Production host: ![]() #3: Protein | | Mass: 127529.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal double FlagTag Source: (gene. exp.) ![]() Production host: ![]() #4: Protein | | Mass: 53258.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0004910 / Production host: ![]() #5: Protein | | Mass: 23127.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0032670 / Production host: ![]() #6: Protein | | Mass: 87773.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0032660 / Production host: ![]() |
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-Non-polymers , 2 types, 7 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/ATP.gif)
#7: Chemical | ChemComp-ADP / #8: Chemical | ChemComp-ATP / | |
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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 |
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Sample preparation
Component | Name: INO80core masked reconstruction / Type: COMPLEX Details: 3xRvb1, 3x Rvb2, Ino80insert, Arp5, Ies2, Ies6 other parts of complex are masked out Entity ID: #1-#6 / Source: RECOMBINANT |
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Molecular weight | Value: 0.6 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 Details: 20 mM HEPES pH 8, 60 mM KCl, 0.5% glycerol, 0.25 mM CaCl2, 20 uM ZnCl2, 0.25 mM DTT, 0.05% Octyl-beta-glucoside |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Monodisperse sample: INO80core complex reconstituted with nucleosomal substrate was purified by gelfiltration. Addition of nucleotides or crosslinking was not required. |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Calibrated defocus min: 1300 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 59.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3992 Details: Images were collected in movie mode with 4 frames per second and 10s total aquisition |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
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Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 1 Å / B: 1 Å / C: 1 Å / Space group name: P1 / Space group num: 1 | ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 251692 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.754 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144278 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
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