8OO9 | pdb_00008oo9

CryoEM Structure INO80core Hexasome complex ATPase-DNA refinement state1

PDB DOI: https://doi.org/10.2210/pdb8OO9/pdb
EM Map EMD-17007: EMDB EMDataResource
NAKB: 8OO9

Classification: DNA BINDING PROTEIN
Organism(s): Thermochaetoides thermophila, synthetic construct
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2023-04-04 Released: 2023-07-26
Deposition Author(s): Zhang, M., Jungblut, A., Hoffmann, T., Eustermann, S.
Funding Organization(s): EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND, European Research Council (ERC), German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8OO9

Literature

Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling.

Zhang, M., Jungblut, A., Kunert, F., Hauptmann, L., Hoffmann, T., Kolesnikova, O., Metzner, F., Moldt, M., Weis, F., DiMaio, F., Hopfner, K.P., Eustermann, S.

(2023) Science 381: 313-319

PubMed: 37384673 Search on PubMed
DOI: https://doi.org/10.1126/science.adf6287
Primary Citation Related Structures:
8OO7, 8OO9, 8OOA, 8OOC, 8OOF, 8OOK, 8OOP, 8OOR, 8OOS, 8OOT

PubMed Abstract:
Loss of H2A-H2B histone dimers is a hallmark of actively transcribed genes, but how the cellular machinery functions in the context of noncanonical nucleosomal particles remains largely elusive. In this work, we report the structural mechanism for adenosine 5'-triphosphate-dependent chromatin remodeling of hexasomes by the INO80 complex. We show how INO80 recognizes noncanonical DNA and histone features of hexasomes that emerge from the loss of H2A-H2B. A large structural rearrangement switches the catalytic core of INO80 into a distinct, spin-rotated mode of remodeling while its nuclear actin module remains tethered to long stretches of unwrapped linker DNA. Direct sensing of an exposed H3-H4 histone interface activates INO80, independently of the H2A-H2B acidic patch. Our findings reveal how the loss of H2A-H2B grants remodelers access to a different, yet unexplored layer of energy-driven chromatin regulation.

Organizational Affiliation

Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

Macromolecule Content

Total Structure Weight: 271.01 kDa
Atom Count: 4,516
Modeled Residue Count: 481
Deposited Residue Count: 1,586
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin-remodeling ATPase INO80	A [auth G]	1,134	Thermochaetoides thermophila	Mutation(s): 0 Gene Names: TT172_LOCUS3790

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
DNA strand 1	B [auth K]	226	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
DNA strand 2	C [auth L]	226	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain D [auth G] MOL2 format, chain D [auth G] mmCIF format, chain D [auth G]	D [auth G]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth G] Interactions & Density Focus chain D [auth G]
ALF (Subject of Investigation/LOI) Query on ALF Download:Ideal Coordinates CCD File SDF format, chain F [auth G] MOL2 format, chain F [auth G] mmCIF format, chain F [auth G]	F [auth G]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain F [auth G] Interactions & Density Focus chain F [auth G]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth G] MOL2 format, chain E [auth G] mmCIF format, chain E [auth G]	E [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth G] Interactions & Density Focus chain E [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-26

Deposition Author(s):

Funding Organization	Location	Grant Number
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND	Germany	847543
European Research Council (ERC)	European Union	833613
German Research Foundation (DFG)	Germany	CRC136
German Research Foundation (DFG)	Germany	CRC1064