4Y3O: Ribosomal oxygenase NO66

Crystal structure of Ribosomal oxygenase NO66 in complex with substrate Rpl8 peptide and Ni(II) and cofactor N-oxalyglycine. Determined by X-ray diffraction at 2.2 Å resolution. Released 7 Oct 2015.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,118
Mol. weight: 108.92 kDa
Ligands: OGA, NI
Released: 7 Oct 2015

Explore 4Y3O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y3O contains 54 α-helices and 56 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: 27 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	184-194	11
α-helix	198-210	13
α-helix	215-221	7
β-strand	228-230	3	1
α-helix	244-253	10
β-strand	257	1	2
β-strand	258	1	1
β-strand	262-268	7	1
β-strand	271-274	4	1
α-helix	276-277	2
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	323-330	8	1
β-strand	334	1	3
β-strand	335	1	1
β-strand	340	1	4
β-strand	345-353	9	1
β-strand	355-360	6	4
α-helix	365-367	3
α-helix	373-377	5
α-helix	379-381	3
β-strand	387-391	5	4
β-strand	396-399	4	1
β-strand	404-408	5	4
β-strand	409	1	3
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	529-530	2	7
β-strand	535-536	2	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	584-586	3	9
α-helix	589-591	3
α-helix	592-600	9
β-strand	606-607	2	8
α-helix	608-610	3
α-helix	616-628	13
β-strand	632-634	3	8

Chain B: 27 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	184-193	10
α-helix	198-210	13
α-helix	215-221	7
β-strand	228-230	3	10
α-helix	244-253	10
β-strand	257	1	11
β-strand	258	1	10
β-strand	262-267	6	10
β-strand	272-274	3	10
α-helix	276-277	2
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	323-330	8	10
β-strand	334	1	12
β-strand	335	1	10
β-strand	340	1	13
β-strand	345-353	9	10
β-strand	355-360	6	13
α-helix	365-367	3
α-helix	373-376	4
α-helix	379-381	3
β-strand	387-391	5	13
β-strand	396-399	4	10
β-strand	404-408	5	13
β-strand	409	1	12
β-strand	415-422	8	10
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	510-512	3
α-helix	516-520	5
α-helix	523-525	3
β-strand	529-530	2	14
β-strand	535-536	2	14
β-strand	547-550	4	15
β-strand	556-561	6	16
β-strand	564-569	6	16
α-helix	581-582	2
β-strand	584-586	3	16
α-helix	589-591	3
α-helix	592-600	9
β-strand	606-607	2	15
α-helix	608-610	3
α-helix	616-628	13
β-strand	632-634	3	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66	A, B	protein	466	Homo sapiens	Q9H6W3 (AlphaFold model)
Rpl8 peptide	C, D	protein	11	Homo sapiens	P62917 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4Y3O_1 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 (chains A, B)
GGEPAWDSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDH
TYYQGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCS
LRLLCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRK
LWRVYRPRVPTEELALTSSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHS
LHLTLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRT
AFMEKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEP
VNVGAQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAM
ELLLGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLALN

Sequence of entity 2 (C, D), FASTA

>4Y3O_2 Rpl8 peptide (chains C, D)
GGGNHQHIGKP

Ligands and cofactors

ID	Name	Formula	Copies
OGA	N-oxalylglycine	C4 H5 N O5	2
NI	Nickel (II) ion	Ni	2

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

Primary citation

Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8. Wang, C., Zhang, Q., Hang, T. et al. Acta Crystallogr D Biol Crystallogr (2015) 71:1955-1964. DOI 10.1107/S1399004715012948 · PubMed

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…
4CCN 2.23 Å, 60S ribosomal protein L8 histidine hydroxylase (NO66 L299C/C300S) in complex with…
4E4H 2.28 Å, Crystal structure of Histone Demethylase NO66
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

Browse structure collections

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