4E4H: Histone Demethylase NO66

Crystal structure of Histone Demethylase NO66. Determined by X-ray diffraction at 2.28 Å resolution. Released 30 Jan 2013.

Method: X-ray diffraction
Resolution: 2.28 Å
Organism: Homo sapiens
Chains: 4
Atoms: 15,448
Mol. weight: 211.11 kDa
Ligands: FE
Released: 30 Jan 2013

Explore 4E4H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4E4H contains 106 α-helices and 105 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: 28 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	184-192	9
α-helix	198-210	13
α-helix	215-217	3
α-helix	218-222	5
β-strand	228-230	3	1
α-helix	244-253	10
β-strand	257	1	2
β-strand	258	1	1
β-strand	262-266	5	1
β-strand	273-274	2	1
β-strand	280	1	2
α-helix	283-291	9
β-strand	295-298	4	1
α-helix	301-304	4
α-helix	306-319	14
β-strand	324-330	7	1
α-helix	334-339	6
β-strand	340	1	3
β-strand	345-353	9	1
β-strand	355-360	6	3
α-helix	365-367	3
α-helix	373-376	4
α-helix	379-381	3
β-strand	387-391	5	3
β-strand	396-399	4	1
β-strand	404-409	6	3
β-strand	410	1	4
β-strand	413	1	4
β-strand	415-422	8	1
β-strand	427	1	5
α-helix	428-446	19
α-helix	448-451	4
β-strand	453	1	6
α-helix	454-455	2
α-helix	458-460	3
α-helix	464-466	3
α-helix	472-487	16
α-helix	488-491	4
α-helix	494-508	15
α-helix	510-512	3
α-helix	516-520	5
α-helix	523-525	3
β-strand	529-531	3	7
β-strand	534-536	3	7
β-strand	547-550	4	8
β-strand	556-561	6	9
β-strand	564-569	6	9
α-helix	581-582	2
β-strand	584-587	4	9
α-helix	589-591	3
α-helix	592-601	10
β-strand	606-607	2	8
α-helix	608-610	3
α-helix	616-628	13
β-strand	632-634	3	8

Chain B: 26 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	184-193	10
α-helix	198-210	13
α-helix	215-217	3
α-helix	218-222	5
β-strand	228-230	3	10
α-helix	244-253	10
β-strand	257	1	11
β-strand	258	1	10
β-strand	262-268	7	10
β-strand	271-274	4	10
β-strand	280	1	11
α-helix	283-291	9
β-strand	295-298	4	10
α-helix	301-304	4
α-helix	306-319	14
β-strand	324-330	7	10
β-strand	340	1	12
β-strand	345-353	9	10
β-strand	355-360	6	12
α-helix	365-367	3
α-helix	373-376	4
α-helix	379-381	3
β-strand	387-391	5	12
β-strand	396-399	4	10
β-strand	404-408	5	12
β-strand	415-422	8	10
β-strand	427	1	13
α-helix	428-446	19
α-helix	448-450	3
β-strand	453	1	14
α-helix	454-455	2
α-helix	458-460	3
α-helix	464-466	3
α-helix	472-487	16
α-helix	488-491	4
α-helix	494-508	15
α-helix	509-512	4
α-helix	516-520	5
α-helix	523-525	3
β-strand	529-531	3	15
β-strand	534-536	3	15
β-strand	547-550	4	16
β-strand	556-561	6	17
β-strand	564-569	6	17
α-helix	581-582	2
β-strand	583-587	5	17
α-helix	589-600	12
β-strand	606-607	2	16
α-helix	608-610	3
α-helix	617-629	13
β-strand	632-634	3	16

Chain C: 26 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	184-192	9
α-helix	198-210	13
α-helix	215-217	3
α-helix	218-222	5
β-strand	228-230	3	18
α-helix	244-253	10
β-strand	257	1	19
β-strand	258	1	18
β-strand	262-266	5	18
β-strand	273-274	2	18
α-helix	276-277	2
β-strand	280	1	19
α-helix	283-291	9
β-strand	295-298	4	18
α-helix	301-304	4
α-helix	306-319	14
β-strand	324-330	7	18
α-helix	334-339	6
β-strand	340	1	20
β-strand	345-353	9	18
β-strand	355-360	6	20
α-helix	365-367	3
α-helix	376-378	3
β-strand	387-391	5	20
β-strand	396-399	4	18
β-strand	404-409	6	20
β-strand	415-422	8	18
β-strand	427	1	14
α-helix	428-446	19
α-helix	448-450	3
β-strand	453	1	13
α-helix	454-455	2
α-helix	458-460	3
α-helix	464-466	3
α-helix	472-491	20
α-helix	494-508	15
α-helix	510-512	3
α-helix	516-520	5
α-helix	523-525	3
β-strand	529-531	3	21
β-strand	534-536	3	21
β-strand	547-550	4	22
β-strand	556-561	6	23
β-strand	564-569	6	23
β-strand	584-587	4	23
α-helix	589-591	3
α-helix	592-601	10
β-strand	606-607	2	22
α-helix	608-610	3
α-helix	616-629	14
β-strand	632-634	3	22

Chain D: 26 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	184-193	10
α-helix	198-210	13
α-helix	215-217	3
α-helix	218-222	5
β-strand	228-230	3	24
α-helix	244-253	10
β-strand	257	1	25
β-strand	258	1	24
β-strand	262-268	7	24
β-strand	271-274	4	24
β-strand	280	1	25
α-helix	283-291	9
β-strand	295-298	4	24
α-helix	301-304	4
α-helix	306-319	14
β-strand	324-330	7	24
β-strand	334	1	26
β-strand	340	1	27
β-strand	345-353	9	24
β-strand	355-360	6	27
α-helix	365-367	3
α-helix	373-378	6
α-helix	379-381	3
β-strand	387-391	5	27
β-strand	396-399	4	24
β-strand	404-408	5	27
β-strand	409	1	26
β-strand	415-422	8	24
β-strand	427	1	6
α-helix	428-446	19
α-helix	448-450	3
β-strand	453	1	5
α-helix	454-455	2
α-helix	458-460	3
α-helix	464-466	3
α-helix	472-487	16
α-helix	488-491	4
α-helix	494-508	15
α-helix	509-512	4
α-helix	516-520	5
β-strand	522	1	28
α-helix	523-525	3
β-strand	529-530	2	29
β-strand	535-536	2	29
β-strand	547-550	4	28
β-strand	556-561	6	30
β-strand	564-569	6	30
α-helix	581-582	2
β-strand	583-586	4	30
α-helix	592-601	10
β-strand	606-607	2	28
α-helix	608-610	3
α-helix	616-629	14
β-strand	632-634	3	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase NO66	A, B, C, D	protein	463	Homo sapiens	Q9H6W3 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>4E4H_1 Lysine-specific demethylase NO66 (chains A, B, C, D)
HMGSSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYY
QGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRL
LCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWR
VYRPRAPTEELALTSSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHL
TLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFM
EKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEPVNV
GAQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELL
LGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLALN

Ligands and cofactors

ID	Name	Formula	Copies
FE	FE (III) ion	Fe	4

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

Primary citation

tructural Basis for Tetramerization-dependent Gene Repression by Histone Demethylase NO66. Tao, Y., Wu, M., Sinha, K.M. et al. To be published.

Other PDB entries of the same protein (UniProt Q9H6W3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4CCJ 2.15 Å, 60S ribosomal protein L8 histidine hydroxylase (NO66) in apo form
4CCK 2.15 Å, 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II) and…
4Y3O 2.2 Å, Crystal structure of Ribosomal oxygenase NO66 in complex with substrate Rpl8 peptide and…
4CCN 2.23 Å, 60S ribosomal protein L8 histidine hydroxylase (NO66 L299C/C300S) in complex with…
4CCO 2.3 Å, 60S ribosomal protein L8 histidine hydroxylase (NO66 S373C) in complex with Mn(II),…
4DIQ 2.4 Å, Crystal Structure of human NO66
4CCM 2.51 Å, 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II),…
4Y33 2.7 Å, Crystal of NO66 in complex with Ni(II)and N-oxalylglycine (NOG)
4Y4R 3.3 Å, Crystal structure of ribosomal oxygenase NO66 dimer mutant

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