4QX7: Histone demethylase kdm2a-h3k36me2 with alpha-kg

Crystal structure of histone demethylase kdm2a-h3k36me2 with alpha-kg. Determined by X-ray diffraction at 2.34 Å resolution. Released 5 Nov 2014.

Method: X-ray diffraction
Resolution: 2.34 Å
Organism: Mus musculus
Chains: 6
Atoms: 7,027
Mol. weight: 96.88 kDa
Ligands: NI, AKG
Released: 5 Nov 2014

Explore 4QX7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4QX7 contains 43 α-helices and 40 β-strands across 6 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: 18 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	175-180	6
β-strand	187	1	4
β-strand	199-203	5	2
β-strand	207-212	6	1
α-helix	215-217	3
β-strand	219-226	8	2
β-strand	229-234	6	1
α-helix	238-250	13
α-helix	258-260	3
β-strand	266-270	5	1
β-strand	275-278	4	2
β-strand	283-288	6	1
β-strand	292-299	8	2
α-helix	305-318	14
α-helix	322-324	3
α-helix	329-345	17
β-strand	350	1	5
α-helix	352-363	12

Chain B: 3 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

Chain C: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	40-45	6
β-strand	50	1	6
α-helix	54	1
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
β-strand	187	1	9
α-helix	188-190	3
β-strand	199-203	5	7
β-strand	207-212	6	6
α-helix	215-217	3
β-strand	219-226	8	7
β-strand	229-234	6	6
α-helix	238-250	13
α-helix	258-260	3
β-strand	266-270	5	6
β-strand	275-278	4	7
β-strand	283-288	6	6
β-strand	292-299	8	7
α-helix	305-318	14
α-helix	322-324	3
α-helix	329-345	17
β-strand	350	1	10
α-helix	352-363	12

Chain D: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	455-469	15
α-helix	473-475	3
β-strand	482	1	10
α-helix	485-499	15

Chains E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	32	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 2A	A, C	protein	329	Mus musculus	P59997 (AlphaFold model)
Lysine-specific demethylase 2A	B, D	protein	68	Mus musculus	P59997 (AlphaFold model)
Histone H3.2	E, F	protein	15	Mus musculus	P84228 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4QX7_1 Lysine-specific demethylase 2A (chains A, C)
RTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTV
NDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLEN
MVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDF
GGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYT
FVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCWY
VLERYVYCITNRSHLTKDFQKESLSMDME

Sequence of entity 2 (B, D), FASTA

>4QX7_2 Lysine-specific demethylase 2A (chains B, D)
QVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKILLEELASSDPKLALT
GVPIVQWP

Sequence of entity 3 (E, F), FASTA

>4QX7_3 Histone H3.2 (chains E, F)
APATGGVKKPHRYRP

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	2
AKG	2-oxoglutaric acid	C5 H6 O5	2

Primary citation

A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36. Cheng, Z., Cheung, P., Kuo, A.J. et al. Genes Dev (2014) 28:1758-1771. DOI 10.1101/gad.246561.114 · 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
7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
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
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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