8F8Y: PHF2

PHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide. Determined by X-ray diffraction at 3.06 Å resolution. Released 18 Jan 2023.

Method: X-ray diffraction
Resolution: 3.06 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,893
Mol. weight: 108.6 kDa
Ligands: ZN
Released: 18 Jan 2023

Explore 8F8Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F8Y contains 49 α-helices and 49 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: 24 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
β-strand	7	1	2
β-strand	12	1	2
β-strand	20-22	3	3
β-strand	29-31	3	3
α-helix	42-44	3
β-strand	47	1	4
α-helix	51-57	7
β-strand	61	1	4
α-helix	87-94	8
α-helix	98-99	2
β-strand	100	1	5
α-helix	101-103	3
β-strand	106-107	2	6
α-helix	115-121	7
β-strand	127-129	3	6
β-strand	138	1	7
α-helix	146-153	8
β-strand	158-163	6	6
β-strand	168-173	6	6
α-helix	174-181	8
β-strand	190-194	5	6
β-strand	196	1	6
α-helix	201-205	5
β-strand	207	1	7
α-helix	210-215	6
α-helix	217-221	5
α-helix	229-230	2
β-strand	236-240	5	6
β-strand	244-249	6	5
α-helix	252-254	3
β-strand	256-263	8	6
β-strand	266-271	6	5
α-helix	275-286	12
α-helix	290-292	3
α-helix	295-297	3
β-strand	303-307	5	5
β-strand	312-315	4	6
β-strand	320-325	6	5
β-strand	329-336	8	6
α-helix	339-341	3
α-helix	342-355	14
α-helix	366-387	22
α-helix	390-392	3
α-helix	393-409	17
α-helix	415-418	4
α-helix	423	1
α-helix	428-441	14

Chain B: 25 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	1-4	4	1
β-strand	6-7	2	8
β-strand	12-13	2	8
β-strand	20-22	3	9
β-strand	29-31	3	9
α-helix	42-44	3
β-strand	45-47	3	10
α-helix	51-57	7
β-strand	61-62	2	10
α-helix	87-95	9
β-strand	100	1	11
α-helix	101-103	3
β-strand	106-107	2	12
α-helix	110-112	3
α-helix	115-121	7
β-strand	127-129	3	12
β-strand	138	1	13
α-helix	146-153	8
β-strand	158-163	6	12
β-strand	168-173	6	12
α-helix	174-181	8
β-strand	190-196	7	12
α-helix	201-205	5
β-strand	207	1	13
α-helix	210-215	6
α-helix	217-221	5
α-helix	229-231	3
β-strand	236-240	5	12
β-strand	244-249	6	11
α-helix	252-254	3
β-strand	256-263	8	12
β-strand	266-271	6	11
α-helix	275-286	12
α-helix	290-292	3
α-helix	295-298	4
β-strand	303-307	5	11
β-strand	312-315	4	12
β-strand	320-325	6	11
β-strand	329-336	8	12
α-helix	339-341	3
α-helix	342-355	14
α-helix	366-387	22
α-helix	390-392	3
α-helix	393-410	18
α-helix	415-418	4
α-helix	419-421	3
α-helix	423	1
α-helix	428-443	16

Chains E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase PHF2	A, B	protein	455	Homo sapiens	O75151 (AlphaFold model)
Serine/threonine-protein kinase VRK1 N-terminus peptide	E, F	protein	12	Homo sapiens	Q99986 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8F8Y_1 Lysine-specific demethylase PHF2 (chains A, B)
GSINMATVPVYCVCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKT
HGKSTLKKKRTWHKHGPGQAPDVKPVQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLG
YMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKE
FVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKY
CLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFA
DQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLK
LGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALA
EHEDELPEHFKPSQLIKDLAKEIRLSENASKAVRP

Sequence of entity 2 (E, F), FASTA

>8F8Y_2 Serine/threonine-protein kinase VRK1 N-terminus peptide (chains E, F)
PRVKAAQAGRQS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (SO4, EDO) are not listed.

Primary citation

A complete methyl-lysine binding aromatic cage constructed by two domains of PHF2. Horton, J.R., Zhou, J., Chen, Q. et al. J Biol Chem (2022) 299:102862-102862. DOI 10.1016/j.jbc.2022.102862 · PubMed

Other PDB entries of the same protein (UniProt O75151 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M10 1.15 Å, PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1
3KQI 1.78 Å, crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide
3PUA 1.89 Å, PHF2 Jumonji-NOG-Ni(II)
3PU8 1.94 Å, PHF2 Jumonji-NOG-Fe(II) complex
3PU3 1.95 Å, PHF2 Jumonji domain-NOG complex
3PTR 1.95 Å, PHF2 Jumonji domain
3PUS 2.08 Å, PHF2 Jumonji-NOG-Ni(II)
8F8Z 3.3 Å, PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide

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