ISDA

Deposition Date 2020-03-26

Release Date 2020-08-26

Last Version Date 2023-10-18

Entry Detail

PDB ID:

6WAT

Keywords:

GENE REGULATION

Title:

complex structure of PHF1

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.80 Å

R-Value Free:

0.26

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 1 21 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3.1t peptide
Gene (Uniprot):H3-4
Chain IDs:EA (auth: A), FA (auth: B), GA (auth: C), HA (auth: D), IA (auth: E), JA (auth: F), KA (auth: G), LA (auth: H), MA (auth: I), NA (auth: J), OA (auth: K), PA (auth: L), QA (auth: M), RA (auth: N), SA (auth: O), TA (auth: P), UA (auth: Q), VA (auth: R), WA (auth: S), XA (auth: T), YA (auth: V), ZA (auth: Y), AB (auth: Z), BB (auth: a), CB (auth: b), DB (auth: c), EB (auth: d), FB (auth: e), GB (auth: f), HB (auth: g)
Chain Length:9
Number of Molecules:30
Biological Source:Homo sapiens

UniProt ID:Q16695

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PHD finger protein 1
Gene (Uniprot):PHF1
Chain IDs:A (auth: AA), B (auth: AC), C (auth: BA), D (auth: BC), E (auth: CA), F (auth: CC), G (auth: DA), H (auth: DC), I (auth: EA), J (auth: EC), K (auth: FA), L (auth: FC), M (auth: GA), N (auth: GC), O (auth: HA), P (auth: HC), Q (auth: IA), R (auth: IC), S (auth: JA), T (auth: JC), U (auth: KA), V (auth: KC), W (auth: LA), X (auth: LC), Y (auth: MA), Z (auth: MC), AA (auth: NA), BA (auth: NC), CA (auth: OA), DA (auth: OC)
Chain Length:61
Number of Molecules:30
Biological Source:Homo sapiens

UniProt ID:O43189 Pfam ID:PF18104

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
AYA	EA	ALA	modified residue
M3L	EA	LYS	modified residue

Ligand Molecules

UNX

Primary Citation

Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19.

Dong, C, Nakagawa, R, Oyama, K, Yamamoto, Y, Zhang, W, Dong, A, Li, Y, Yoshimura, Y, Kamiya, H, Nakayama, J.I, Ueda, J, Min, J.Show

Elife 9 ? ? (2020)

PMID: 32869745 DOI: 10.7554/eLife.58675

Abstact

The Polycomb repressive complex 2 (PRC2) is a multicomponent histone H3K27 methyltransferase complex, best known for silencing the Hox genes during embryonic development. The Polycomb-like proteins PHF1, MTF2, and PHF19 are critical components of PRC2 by stimulating its catalytic activity in embryonic stem cells. The Tudor domains of PHF1/19 have been previously shown to be readers of H3K36me3 in vitro. However, some other studies suggest that PHF1 and PHF19 co-localize with the H3K27me3 mark but not H3K36me3 in cells. Here, we provide further evidence that PHF1 co-localizes with H3t in testis and its Tudor domain preferentially binds to H3tK27me3 over canonical H3K27me3 in vitro. Our complex structures of the Tudor domains of PHF1 and PHF19 with H3tK27me3 shed light on the molecular basis for preferential recognition of H3tK27me3 by PHF1 and PHF19 over canonical H3K27me3, implicating that H3tK27me3 might be a physiological ligand of PHF1/19.

Legend

Protein

Chemical

Disease

Primary Citation of related structures