Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural mechanism of extranucleosomal DNA readout by the INO80 complex.
Journal, issue, pages	Sci Adv, Vol. 8, Issue 49, Page eadd3189, Year 2022
Publish date	Dec 9, 2022
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 /
PubMed 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.
External links	Sci Adv / PubMed:36490333 / PubMed Central
Methods	EM (single particle)
Resolution	2.9 - 7.7 Å
Structure data	15163 8a5a EMDB-15163: Cryo-EM reconstruction of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80 PDB-8a5a: Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80 Method: EM (single particle) / Resolution: 3.3 Å EMDB-15164: Human Ino80 A-module + YY1 Method: EM (single particle) / Resolution: 7.5 Å 15165 8a5d EMDB-15165, PDB-8a5d: Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of Chaetomium thermophilum INO80 Method: EM (single particle) / Resolution: 2.9 Å EMDB-15177: Cryo-EM reconstruction of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80 Method: EM (single particle) / Resolution: 3.2 Å 15179 8a5o EMDB-15179: Cryo-EM reconstruction of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80 PDB-8a5o: Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80 Method: EM (single particle) / Resolution: 3.2 Å 15180 8a5p EMDB-15180, PDB-8a5p: Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of Chaetomium thermophilum INO80 on curved DNA Method: EM (single particle) / Resolution: 3.4 Å 15184 8a5q EMDB-15184, PDB-8a5q: Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of Chaetomium thermophilum INO80 on straight DNA Method: EM (single particle) / Resolution: 3.3 Å EMDB-15186: Cryo-EM reconstruction of DNA bound Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80 Method: EM (single particle) / Resolution: 7.5 Å EMDB-15187: A-module of Chaetomium thermophilum INO80 bound to curved DNA Method: EM (single particle) / Resolution: 3.7 Å EMDB-15188: Nucleosome bound Chaetomium thermophilum INO80 (ADP-BeF3 state) core complex with Arp5 grappler in parallel conformation Method: EM (single particle) / Resolution: 3.5 Å EMDB-15211: Ino80 core complex with A-module on nucleosome Method: EM (single particle) / Resolution: 7.7 Å 15647 8atf EMDB-15647, PDB-8atf: Nucleosome-bound Ino80 ATPase Method: EM (single particle) / Resolution: 3.45 Å EMDB-15688: CryoEM structure of INO80 core nucleosome complex in closed grappler conformation (ADP-BeFx state) Method: EM (single particle) / Resolution: 3.8 Å PDB-8av6: CryoEM structure of INO80 core nucleosome complex in closed grappler conformation Method: ELECTRON MICROSCOPY / Resolution: 4.68 Å
Chemicals	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogueYM ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM
Source	saccharomyces cerevisiae s288c (yeast) homo sapiens (human) thermochaetoides thermophila (fungus) synthetic construct (others) dna molecule (others)
Keywords	DNA BINDING PROTEIN / chromatin remodeler / INO80 / Actin-related protein