2YBP: JMJD2A

JMJD2A complexed with R-2-hydroxyglutarate and histone H3K36me3 peptide (30-41). Determined by X-ray diffraction at 2.02 Å resolution. Released 30 Mar 2011.

Method: X-ray diffraction
Resolution: 2.02 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 6,556
Mol. weight: 92 kDa
Ligands: 2HG, ZN, NI
Released: 30 Mar 2011

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

Secondary structure: helices and β-sheets

2YBP contains 47 α-helices and 38 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: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
β-strand	15-17	3	1
α-helix	21-24	4
α-helix	27-36	10
α-helix	39-42	4
β-strand	44-47	4	1
α-helix	48-50	3
β-strand	66-67	2	2
β-strand	71-78	8	3
β-strand	81-88	8	3
β-strand	92-93	2	2
α-helix	94-102	9
α-helix	108-110	3
α-helix	114-124	11
β-strand	131-132	2	3
β-strand	133-137	5	1
α-helix	156-158	3
α-helix	159-164	6
β-strand	175-179	5	1
β-strand	184-188	5	4
α-helix	191-193	3
β-strand	195-203	9	1
β-strand	206-211	6	4
α-helix	213-215	3
α-helix	216-226	11
α-helix	228-233	6
α-helix	237-240	4
β-strand	243-245	3	3
α-helix	247-252	6
β-strand	258-262	5	4
β-strand	267-270	4	1
β-strand	275-280	6	4
β-strand	284-291	8	1
α-helix	296-302	7
β-strand	314	1	5
α-helix	318-324	7
α-helix	329-333	5
α-helix	346-347	2
α-helix	348-353	6

Chain B: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	13-14	2
β-strand	15-17	3	6
α-helix	21-24	4
α-helix	27-36	10
α-helix	39-42	4
β-strand	44-47	4	6
α-helix	48-50	3
β-strand	66-67	2	7
β-strand	71-78	8	8
β-strand	81-88	8	8
β-strand	92-93	2	7
α-helix	94-102	9
α-helix	108-110	3
α-helix	114-124	11
β-strand	131-132	2	8
β-strand	133-137	5	6
α-helix	156-158	3
α-helix	159-164	6
β-strand	175-179	5	6
β-strand	184-188	5	9
α-helix	191-193	3
β-strand	195-203	9	6
β-strand	206-211	6	9
α-helix	213-215	3
α-helix	216-226	11
α-helix	228-233	6
α-helix	237-240	4
β-strand	243-245	3	8
α-helix	247-252	6
β-strand	258-262	5	9
α-helix	263	1
β-strand	267-270	4	6
β-strand	275-280	6	9
β-strand	284-291	8	6
α-helix	296-302	7
β-strand	314	1	10
α-helix	318-324	7
α-helix	326-328	3
α-helix	329-333	5
α-helix	345-347	3
α-helix	348-353	6

Chains C and D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	33	1	5
α-helix	38-40	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 4A	A, B	protein	381	HOMO SAPIENS	O75164 (AlphaFold model)
Histone H3.1T	C, D	protein	12	HOMO SAPIENS	Q16695 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2YBP_1 LYSINE-SPECIFIC DEMETHYLASE 4A (chains A, B)
MHHHHHHSSGVDLGTENLYFQSMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQG
AHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFR
KIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILD
LVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKR
LERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAG
FNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDN
TVIDHTLPTPEAAEFLKESEL

Sequence of entity 2 (C, D), FASTA

>2YBP_2 HISTONE H3.1T (chains C, D)
PATGGVKKPHRY

Ligands and cofactors

ID	Name	Formula	Copies
2HG	(2R)-2-hydroxypentanedioic acid	C5 H8 O5	2
ZN	Zinc ion	Zn	2
NI	Nickel (II) ion	Ni	2

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

Primary citation

The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. Chowdhury, R., Yeoh, K.K., Tian, Y.M. et al. EMBO Rep (2011) 12:463-469. DOI 10.1038/embor.2011.43 · PubMed

Other PDB entries of the same protein (UniProt O75164 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GP4 1.59 Å, Jumonji domain-containing protein 2A with crystallization epitope mutations Q953E:A958D
9GII 1.7 Å, Jumonji domain-containing protein 2A with crystallization epitope mutation R913A
6G5X 1.78 Å, Crystal Structure of KDM4A with compound YP-02-145
2QQR 1.8 Å, JMJD2A hybrid tudor domains
4V2W 1.81 Å, JMJD2A complexed with ni(ii), nog and histone H3K27me3 peptide (16-35)
5VAR 1.83 Å, Crystal structure of KDM4A tandem TUDOR domain in complex with a tri-methyl lysine…
6G5W 1.83 Å, Crystal Structure of KDM4A with compound YP-03-038
9GLE 1.88 Å, Jumonji domain-containing protein 2A with crystallization epitope mutations A91T:T93S
2OX0 1.95 Å, Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9
6H8P 1.98 Å, JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)
3PDQ 1.99 Å, Crystal structure of JMJD2A complexed with bipyridyl inhibitor
2P5B 1.99 Å, The complex structure of JMJD2A and trimethylated H3K36 peptide

Browse structure collections

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