PDBsum entry 6hts

DNA binding protein

PDB id: 6hts

Contents

Protein chains

434 a.a.

429 a.a.

680 a.a.

326 a.a.

96 a.a.

82 a.a.

106 a.a.

96 a.a.

86 a.a.

72 a.a.

DNA/RNA

Ligands

ADP ×6

Metals

_ZN

PDB id:

6hts

Name:

DNA binding protein

Title:

Cryo-em structure of the human ino80 complex bound to nucleosome

Structure:

Ruvb-like 1. Chain: a, c, e. Synonym: 49 kda tata box-binding protein-interacting protein,49 kda tbp-interacting protein,54 kda erythrocyte cytosolic protein,ecp-54, ino80 complex subunit h,nuclear matrix protein 238,nmp 238,pontin 52, tip49a,tip60-associated protein 54-alpha,tap54-alpha. Engineered: yes. Ruvb-like 2. Chain: b, d, f.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ruvbl1, ino80h, nmp238, tip49, tip49a. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_variant: sf9. Gene: ruvbl2, ino80j, tip48, tip49b, cgi-46. Gene: ino80, ino80a, inoc1, kiaa1259.

Authors:

R.Ayala,O.Willhoft,R.J.Aramayo,M.Wilkinson,E.A.Mccormack,L.Ocloo, D.B.Wigley,X.Zhang

Key ref:

R.Ayala et al. (2018). Structure and regulation of the human INO80-nucleosome complex. Nature, 556, 391-395. PubMed id: 29643506 DOI: 10.1038/s41586-018-0021-6

Date:

04-Oct-18 Release date: 07-Nov-18

Supersedes:

6etx

Protein chains

Q9Y265  (RUVB1_HUMAN) -  RuvB-like 1 from Homo sapiens

Seq: 456 a.a.

Struc: 434 a.a.

Protein chains

Q9Y230  (RUVB2_HUMAN) -  RuvB-like 2 from Homo sapiens

Seq: 463 a.a.

Struc: 429 a.a.

Protein chain

Q9ULG1  (INO80_HUMAN) -  Chromatin-remodeling ATPase INO80 from Homo sapiens

Seq: 1556 a.a.

Struc: 680 a.a.

Protein chain

Q9H9F9  (ARP5_HUMAN) -  Actin-related protein 5 from Homo sapiens

Seq: 607 a.a.

Struc: 326 a.a.

Protein chains

P68431  (H31_HUMAN) -  Histone H3.1 from Homo sapiens

Seq: 136 a.a.

Struc: 96 a.a.

Protein chain

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 82 a.a.

Protein chains

P04908  (H2A1B_HUMAN) -  Histone H2A type 1-B/E from Homo sapiens

Seq: 130 a.a.

Struc: 106 a.a.

Protein chains

P06899  (H2B1J_HUMAN) -  Histone H2B type 1-J from Homo sapiens

Seq: 126 a.a.

Struc: 96 a.a.

Protein chain

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 86 a.a.

Protein chain

Q9C086  (IN80B_HUMAN) -  INO80 complex subunit B from Homo sapiens

Seq: 356 a.a.

Struc: 72 a.a.

DNA/RNA chains

C-C-G-A-G-T-A-C-A-T-G-C-A-C-A-G-G-A-T-G-T-A-T-A-T-A-T-C-T-G-A-C-A-C-G-T-G-C-C- 150 bases

C-C-C-G-G-T-G-C-C-G-A-G-G-C-C-G-C-T-C-A-A-T-T-G-G-T-C-G-T-A-G-A-C-A-G-C-T-C-T- 150 bases

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D, E, F: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + H(+)

• Enzyme class 2: Chain G: E.C.3.6.4.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/s41586-018-0021-6

Nature 556:391-395 (2018)

PubMed id: 29643506

Structure and regulation of the human INO80-nucleosome complex.

R.Ayala, O.Willhoft, R.J.Aramayo, M.Wilkinson, E.A.McCormack, L.Ocloo, D.B.Wigley, X.Zhang.

ABSTRACT

Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines ¹ . Biochemical studies^2-4 have placed the motor domains of several chromatin remodellers in the superhelical location 2 region of the nucleosome. Structural studies of yeast Chd1 and Snf2-a subunit in the complex with the capacity to remodel the structure of chromatin (RSC)-in complex with nucleosomes^5-7 have provided insights into the basic mechanism of nucleosome sliding performed by these complexes. However, how larger, multi-subunit remodelling complexes such as INO80 interact with nucleosomes and how remodellers carry out functions such as nucleosome sliding ⁸ , histone exchange ⁹ and nucleosome spacing^10-12 remain poorly understood. Although some remodellers work as monomers ¹³ , others work as highly cooperative dimers^{11, 14, 15}. Here we present the structure of the human INO80 chromatin remodeller with a bound nucleosome, which reveals that INO80 interacts with nucleosomes in a previously undescribed manner: the motor domains are located on the DNA at the entry point to the nucleosome, rather than at superhelical location 2. The ARP5-IES6 module of INO80 makes additional contacts on the opposite side of the nucleosome. This arrangement enables the histone H3 tails of the nucleosome to have a role in the regulation of the activities of the INO80 motor domain-unlike in other characterized remodellers, for which H4 tails have been shown to regulate the motor domains.