7UVA: KDM2A histone demethylase catalytic domain

Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015. Determined by X-ray diffraction at 1.98 Å resolution. Released 22 Feb 2023.

Method: X-ray diffraction
Resolution: 1.98 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 7,117
Mol. weight: 96.92 kDa
Ligands: OH0, FE
Released: 22 Feb 2023

Explore 7UVA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UVA contains 45 α-helices and 38 β-strands across 5 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: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	40-45	6
β-strand	50	1	1
α-helix	54	1
β-strand	55-56	2	2
α-helix	59-61	3
α-helix	64-70	7
β-strand	76-78	3	2
β-strand	87	1	3
α-helix	95-102	8
β-strand	107-112	6	2
β-strand	117-122	6	2
α-helix	123-131	9
α-helix	134-136	3
β-strand	141-147	7	2
α-helix	152-156	5
β-strand	158	1	3
α-helix	161-166	6
α-helix	168-172	5
α-helix	175-178	4
β-strand	187	1	4
α-helix	188-190	3
β-strand	199-203	5	2
β-strand	208-212	5	1
α-helix	215-217	3
β-strand	219-226	8	2
β-strand	228-234	7	1
α-helix	238-250	13
α-helix	258-261	4
β-strand	266-271	6	1
β-strand	275-278	4	2
β-strand	283-287	5	1
β-strand	292-299	8	2
α-helix	305-317	13
α-helix	322-324	3
α-helix	329-345	17
β-strand	350	1	5
α-helix	352-362	11

Chain B: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	455-469	15
α-helix	473-476	4
β-strand	482	1	5
α-helix	485-499	15
α-helix	504-507	4

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	32	1	4

Chain D: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	40-45	6
β-strand	50	1	6
β-strand	55-56	2	7
α-helix	59-61	3
α-helix	64-70	7
β-strand	76-78	3	7
β-strand	87	1	8
α-helix	95-102	8
β-strand	107-112	6	7
β-strand	117-122	6	7
α-helix	123-131	9
α-helix	134-136	3
β-strand	141-147	7	7
α-helix	152-156	5
β-strand	158	1	8
α-helix	161-166	6
α-helix	168-172	5
α-helix	175-180	6
α-helix	188-190	3
β-strand	199-203	5	7
β-strand	208-213	6	6
α-helix	215-217	3
β-strand	219-226	8	7
β-strand	228-234	7	6
α-helix	238-250	13
α-helix	258-261	4
β-strand	266-271	6	6
β-strand	275-278	4	7
β-strand	283-287	5	6
β-strand	292-299	8	7
α-helix	305-317	13
α-helix	322-324	3
α-helix	329-345	17
β-strand	350	1	9
α-helix	352-363	12

Chain E: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	455-470	16
α-helix	473-475	3
β-strand	482	1	9
α-helix	485-499	15
α-helix	504-507	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 2A	A, D	protein	330	Mus musculus	P59997 (AlphaFold model)
Lysine-specific demethylase 2A	B, E	protein	69	Mus musculus	P59997 (AlphaFold model)
Histone H3.2	C, F	protein	13	Homo sapiens	Q71DI3 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>7UVA_1 Lysine-specific demethylase 2A (chains A, D)
MRTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFT
VNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLE
NMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVD
FGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGY
TFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCW
YVLERYVYCITNRSHLTKDFQKESLSMDME

Sequence of entity 2 (B, E), FASTA

>7UVA_2 Lysine-specific demethylase 2A (chains B, E)
MQVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKILLEELASSDPKLAL
TGVPIVQWP

Sequence of entity 3 (C, F), FASTA

>7UVA_3 Histone H3.2 (chains C, F)
APATGGVCKPHRY

Ligands and cofactors

ID	Name	Formula	Copies
OH0	N-heptanoyl-N-hydroxy-beta-alanine	C10 H19 N O4	2
FE	FE (III) ion	Fe	2

Primary citation

Structural basis of paralog-specific KDM2A/B nucleosome recognition. Spangler, C.J., Skrajna, A., Foley, C.A. et al. Nat Chem Biol (2023) 19:624-632. DOI 10.1038/s41589-023-01256-y · PubMed

Other PDB entries of the same protein (UniProt P59997 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4QXB 1.6 Å, crystal structure of histone demethylase KDM2A-H3K36ME3 with NOG
4QX8 1.65 Å, Crystal structure of histone demethylase kdm2a-h3k36me3 complex with alpha-kg
4QXC 1.75 Å, Crystal structure of histone demethylase KDM2A-H3K36ME2 with NOG
4QWN 2.1 Å, Histone demethylase KDM2A-H3K36ME1-alpha-KG complex structure
4QXH 2.2 Å, Crystal structure of histone demethylase KDM2A-H3K36ME1 with NOG
4TN7 2.2 Å, Crystal structure of mouse KDM2A-H3K36ME-NO complex
4QX7 2.34 Å, Crystal structure of histone demethylase kdm2a-h3k36me2 with alpha-kg
9WSR 2.79 Å, Structure of mouse NLRP14-KDM2A-SKP1 complex
9WSQ 3.35 Å, Structure of dimeric mouse NLRP14-KDM2A-SKP1 complex

Browse structure collections

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