2YU1: HJHDM1A

Crystal structure of hJHDM1A complexed with a-ketoglutarate. Determined by X-ray diffraction at 2.7 Å resolution. Released 24 Apr 2007.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,255
Mol. weight: 53.12 kDa
Ligands: AKG, FE2
Released: 24 Apr 2007

Explore 2YU1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YU1 contains 20 α-helices and 17 β-strands across 1 chain. 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: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	40-45	6
β-strand	50	1	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	95-101	7
β-strand	111-112	2	2
α-helix	123-130	8
β-strand	141-146	6	2
α-helix	154-156	3
β-strand	158	1	3
α-helix	161-166	6
α-helix	168-172	5
α-helix	175-177	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	229-234	6	1
α-helix	238-249	12
α-helix	258-261	4
β-strand	266-270	5	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	326	1
α-helix	329-345	17
β-strand	350	1	4
α-helix	352-362	11
α-helix	455-469	15
α-helix	473-475	3
β-strand	482	1	4
α-helix	485-498	14
α-helix	504-507	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
JmjC domain-containing histone demethylation protein 1A	A	protein	451	Homo sapiens	Q9Y2K7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2YU1_1 JmjC domain-containing histone demethylation protein 1A (chains A)
MEPEEERIRYSQRLRGTMRRRYEDDGISDDEIEGKRTFDLEEKLHTNKYNANFVTFMEGK
DFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIE
MTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKES
QTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHN
LELYENWLLSGSQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFL
HSFNIPMQLKIYNIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKEFQKESLS
MDLELNGLESGNGDEEAVDREPRQVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDED
ALIADVKILLEELANSDPKLALTGVPIVQWP

Ligands and cofactors

ID	Name	Formula	Copies
AKG	2-oxoglutaric acid	C5 H6 O5	1
FE2	FE (II) ion	Fe	1

Primary citation

Structural basis for histone demethylation by JHDM1. Han, Z., Liu, P., Gu, L. et al. To be published.

Other PDB entries of the same protein (UniProt Q9Y2K7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PHV 2.16 Å, Crystal structure of human KDM2A with substrate competitive inhibitor 183c
4BBQ 2.24 Å, Crystal structure of the CXXC and PHD domain of Human Lysine-specific Demethylase 2A…
6BYH 2.61 Å, Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex.
2YU2 2.7 Å, Crystal structure of hJHDM1A without a-ketoglutarate
7UV9 3.2 Å, KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate
6C16 3.27 Å, Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex.

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