6WAV: PHF1

Crystal structure of PHF1 in complex with H3K36me3 substitution. Determined by X-ray diffraction at 1.7 Å resolution. Released 26 Aug 2020.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 8
Atoms: 2,355
Mol. weight: 33.36 kDa
Released: 26 Aug 2020

Explore 6WAV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WAV contains 4 α-helices and 26 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	36-40	5	1
β-strand	46-55	10	1
β-strand	60-65	6	1
β-strand	70-74	5	1
α-helix	75-77	3
β-strand	78-80	3	1
β-strand	82	1	2

Chains B and D: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	36-40	5	3
β-strand	45	1	4
β-strand	46-55	10	3
β-strand	60-65	6	3
β-strand	70-74	5	3
α-helix	75-77	3
β-strand	78-80	3	3
β-strand	82	1	5

Chain C: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	36-40	5	6
β-strand	45	1	2
β-strand	46-55	10	6
β-strand	60-65	6	6
β-strand	70-74	5	6
α-helix	75-77	3
β-strand	78-80	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PHD finger protein 1	A, B, C, D	protein	61	Homo sapiens	O43189 (AlphaFold model)
Histone H3.1	E, F, G, H	protein	12	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6WAV_1 PHD finger protein 1 (chains A, B, C, D)
GRPRLWEGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAALPGE
E

Sequence of entity 2 (E, F, G, H), FASTA

>6WAV_2 Histone H3.1 (chains E, F, G, H)
ATGGVKKPVRYR

Primary citation

Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19. Dong, C., Nakagawa, R., Oyama, K. et al. Elife (2020) 9. DOI 10.7554/eLife.58675 · PubMed

Other PDB entries of the same protein (UniProt O43189 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WAT 1.8 Å, complex structure of PHF1
4HCZ 1.85 Å, PHF1 Tudor in complex with H3K36me3
7LKY 1.85 Å, Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641
5XFN 1.9 Å, Structure of the N-terminal domains of PHF1
5XFO 1.9 Å, Structure of the N-terminal domains of PHF1
5XFP 2.3 Å, Binary complex of PHF1 and a double stranded DNA
8H43 2.3 Å, Crystal structure of PHF1 Tudor domain in complex with hit 1
2E5P Solution structure of the TUDOR domain of PHD finger protein 1 (PHF1 protein)
2M0O The solution structure of human PHF1 in complex with H3K36me3

Browse structure collections

About this viewer

MolViewer shows 6WAV directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.