3KV4: PHF8

Structure of PHF8 in complex with histone H3. Determined by X-ray diffraction at 2.19 Å resolution. Released 22 Dec 2009.

Method: X-ray diffraction
Resolution: 2.19 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,871
Mol. weight: 55.43 kDa
Ligands: OGA, NI, FE2, ZN
Released: 22 Dec 2009

Explore 3KV4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KV4 contains 25 α-helices and 23 β-strands across 2 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: 25 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	1
β-strand	12-13	2	1
β-strand	20-22	3	2
β-strand	29-31	3	2
α-helix	32-35	4
α-helix	39-42	4
β-strand	45-47	3	3
α-helix	51-57	7
β-strand	61-62	2	3
α-helix	79-81	3
α-helix	85-92	8
β-strand	97-98	2	4
α-helix	99-101	3
β-strand	104	1	5
α-helix	113-118	6
β-strand	125-127	3	5
β-strand	136	1	6
α-helix	144-151	8
β-strand	156-161	6	5
β-strand	166-171	6	5
α-helix	172-180	9
β-strand	188-194	7	5
α-helix	199-203	5
β-strand	205	1	6
α-helix	208-213	6
α-helix	215-219	5
α-helix	227-229	3
β-strand	234-238	5	5
β-strand	242-247	6	4
α-helix	250-252	3
β-strand	254-261	8	5
β-strand	263-269	7	4
α-helix	273-283	11
α-helix	288-290	3
α-helix	293-296	4
β-strand	301-306	6	4
β-strand	310-313	4	5
α-helix	314	1
β-strand	318-323	6	4
β-strand	327-334	8	5
α-helix	340-352	13
α-helix	357-359	3
α-helix	364-384	21
α-helix	391-407	17
α-helix	413-415	3
α-helix	417-419	3
α-helix	426-446	21

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PHD finger protein 8	A	protein	447	Homo sapiens	Q9UPP1 (AlphaFold model)
Histone H3-like	B	protein	24		Q6NXT2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3KV4_1 PHD finger protein 8 (chains A)
MASVPVYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLHGPS
IMKKRRGSSKGHDTHKGKPVKTGSPTFVRELRSRTFDSSDEVILKPTGNQLTVEFLEENS
FSVPILVLKKDGLGMTLPSPSFTVRDVEHYVGSDKEIDVIDVTRQADCKMKLGDFVKYYY
SGKREKVLNVISLEFSDTRLSNLVETPKIVRKLSWVENLWPEECVFERPNVQKYCLMSVR
DSYTDFHIDFGGTSVWYHVLKGEKIFYLIRPTNANLTLFECWSSSSNQNEMFFGDQVDKC
YKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNFLHSLNIEMQLKAYEIEKRLSTADLFR
FPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTRKEALPDHEDEI
PETVRTVQLIKDLAREIRLVEDIFQQN

Sequence of entity 2 (B), FASTA

>3KV4_2 Histone H3-like (chains B)
ARTKQTARKSTGGKAPRKQLATKA

Ligands and cofactors

ID	Name	Formula	Copies
OGA	N-oxalylglycine	C4 H5 N O5	1
NI	Nickel (II) ion	Ni	1
FE2	FE (II) ion	Fe	1
ZN	Zinc ion	Zn	2

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

Primary citation

Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Horton, J.R., Upadhyay, A.K., Qi, H.H. et al. Nat Struct Mol Biol (2010) 17:38-43. DOI 10.1038/nsmb.1753 · PubMed

Other PDB entries of the same protein (UniProt Q9UPP1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7CMZ 1.7 Å, Crystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8
3K3O 2.1 Å, Crystal structure of the catalytic core domain of human PHF8 complexed with…
2WWU 2.15 Å, Crystal structure of the catalytic domain of PHD finger protein 8
3K3N 2.4 Å, Crystal structure of the catalytic core domain of human PHF8
4DO0 2.55 Å, Crystal Structure of human PHF8 in complex with Daminozide

Browse structure collections

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