9GLE: Lysine-specific demethylase 4A

Jumonji domain-containing protein 2A with crystallization epitope mutations A91T:T93S. Determined by X-ray diffraction at 1.88 Å resolution. Released 18 Sept 2024.

Method: X-ray diffraction
Resolution: 1.88 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,084
Mol. weight: 84.84 kDa
Ligands: ZN, NI
Released: 18 Sept 2024

Explore 9GLE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GLE contains 47 α-helices and 34 β-strands across 2 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: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	14-15	2
β-strand	16-18	3	1
α-helix	22-25	4
α-helix	28-37	10
α-helix	40-43	4
β-strand	45-48	4	1
β-strand	67-68	2	2
β-strand	72-79	8	3
β-strand	82-89	8	3
β-strand	93-94	2	2
α-helix	95-103	9
α-helix	109-111	3
α-helix	115-125	11
β-strand	132-133	2	3
β-strand	134-138	5	1
α-helix	157-160	4
β-strand	176-180	5	1
β-strand	185-189	5	4
α-helix	192-194	3
β-strand	196-204	9	1
β-strand	207-212	6	4
α-helix	214-216	3
α-helix	217-227	11
α-helix	229-234	6
α-helix	238-241	4
β-strand	244-246	3	3
α-helix	248-253	6
β-strand	259-263	5	4
α-helix	264	1
β-strand	268-271	4	1
β-strand	276-281	6	4
β-strand	285-292	8	1
α-helix	297-303	7
α-helix	304-307	4
α-helix	319-325	7
α-helix	327-329	3
α-helix	330-334	5
α-helix	347-348	2
α-helix	349-354	6

Chain B: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
β-strand	17-18	2	5
α-helix	22-25	4
α-helix	28-37	10
α-helix	40-43	4
β-strand	45-48	4	5
α-helix	49-51	3
α-helix	63-65	3
β-strand	67-68	2	6
β-strand	72-79	8	7
β-strand	82-89	8	7
β-strand	93-94	2	6
α-helix	95-103	9
α-helix	109-111	3
α-helix	115-125	11
α-helix	130-131	2
β-strand	132-133	2	7
β-strand	134-138	5	5
α-helix	157-161	5
β-strand	176-180	5	5
β-strand	185-189	5	8
α-helix	192-194	3
β-strand	196-204	9	5
β-strand	207-212	6	8
α-helix	214-216	3
α-helix	217-227	11
α-helix	229-234	6
α-helix	238-241	4
β-strand	244-246	3	7
α-helix	248-253	6
β-strand	259-263	5	8
α-helix	264	1
β-strand	268-271	4	5
β-strand	276-281	6	8
β-strand	285-292	8	5
α-helix	297-303	7
α-helix	304-307	4
α-helix	319-325	7
α-helix	327-329	3
α-helix	330-334	5
α-helix	347-348	2
α-helix	349-354	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 4A	A, B	protein	360	Homo sapiens	O75164 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9GLE_1 Lysine-specific demethylase 4A (chains A, B)
SMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASY
DDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKTMSVREFRKIANSDKYCTPRYSEFEELER
KYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFG
MWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLR
HKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEY
GKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
NI	Nickel (II) ion	Ni	2

Water and common crystallization additives (EDO, SO4) are not listed.

Primary citation

A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants. Fairhead, M., Strain-Damerell, C., Ye, M. et al. To be published.

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
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
5D6W 1.99 Å, Crystal structure of double tudor domain of human lysine demethylase KDM4A

Browse structure collections

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