2Q8C: PDB entry 2Q8C

Crystal structure of JMJD2A in ternary complex with an histone H3K9me3 peptide and 2-oxoglutarate. Determined by X-ray diffraction at 2.05 Å resolution. Released 3 Jul 2007.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,851
Mol. weight: 85.48 kDa
Ligands: NI, ZN, AKG
Released: 3 Jul 2007

Explore 2Q8C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Q8C contains 42 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: 23 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
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	169	1	4
β-strand	175-179	5	1
β-strand	184-188	5	5
α-helix	189-190	2
α-helix	191-193	3
β-strand	195-203	9	1
β-strand	206-211	6	5
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	5
α-helix	263	1
β-strand	267-270	4	1
β-strand	275-280	6	5
β-strand	284-291	8	1
α-helix	296-302	7
α-helix	303-306	4
α-helix	318-324	7
α-helix	329-333	5

Chain B: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
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	94-101	8
α-helix	108-110	3
α-helix	114-124	11
β-strand	131-132	2	8
β-strand	133-137	5	6
α-helix	158-164	7
β-strand	169	1	9
β-strand	175-179	5	6
β-strand	184-188	5	10
α-helix	189-190	2
α-helix	191-193	3
β-strand	195-203	9	6
β-strand	206-211	6	10
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	10
β-strand	267-270	4	6
β-strand	275-280	6	10
β-strand	284-291	8	6
α-helix	296-302	7
α-helix	303-306	4
α-helix	318-324	7
α-helix	329-333	5

Chains F and G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
JmjC domain-containing histone demethylation protein 3A	A, B	protein	352	Homo sapiens	O75164 (AlphaFold model)
Histone 3 peptide	F, G	protein	15

Sequence of entity 1 (A, B), FASTA

>2Q8C_1 JmjC domain-containing histone demethylation protein 3A (chains A, B)
GSMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRAS
YDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELE
RKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYF
GMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFL
RHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIE
YGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEA

Sequence of entity 2 (F, G), FASTA

>2Q8C_2 HISTONE 3 PEPTIDE (chains F, G)
ARTKQTARKSTGGKA

Ligands and cofactors

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

Primary citation

Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Couture, J.F., Collazo, E., Ortiz-Tello, P.A. et al. Nat Struct Mol Biol (2007) 14:689-695. DOI 10.1038/nsmb1273 · 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

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