4CCM: 60S ribosomal protein L8 histidine hydroxylase

60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1). Determined by X-ray diffraction at 2.51 Å resolution. Released 14 May 2014.

Method: X-ray diffraction
Resolution: 2.51 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 7,841
Mol. weight: 114.61 kDa
Ligands: OGA, MN
Released: 14 May 2014

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

Secondary structure: helices and β-sheets

4CCM contains 49 α-helices and 52 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: 24 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	244-252	9
β-strand	257	1	2
β-strand	258	1	1
β-strand	262-268	7	1
β-strand	271-274	4	1
β-strand	280	1	2
α-helix	283-292	10
β-strand	295-298	4	1
α-helix	301-304	4
α-helix	306-319	14
β-strand	324-330	7	1
β-strand	334	1	3
β-strand	340	1	4
β-strand	345-353	9	1
β-strand	355-359	5	4
α-helix	376-378	3
β-strand	387-391	5	4
β-strand	396-399	4	1
β-strand	405-408	4	4
β-strand	409	1	3
β-strand	415-422	8	1
β-strand	427	1	5
α-helix	428-446	19
α-helix	448-450	3
β-strand	453	1	6
α-helix	454-455	2
α-helix	458-460	3
α-helix	464-466	3
α-helix	472-486	15
α-helix	487-490	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
β-strand	584-587	4	9
α-helix	588	1
α-helix	589-600	12
β-strand	606-607	2	8
α-helix	608-610	3
α-helix	616-629	14
β-strand	632-634	3	8

Chain B: 25 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
α-helix	256	1
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	355-359	5	12
α-helix	365-367	3
α-helix	379-381	3
β-strand	387-391	5	12
β-strand	396-399	4	10
β-strand	405-408	4	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	488-490	3
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	13
β-strand	534-536	3	13
β-strand	547-550	4	14
β-strand	556-561	6	15
β-strand	564-569	6	15
β-strand	584-586	3	15
α-helix	589-601	13
β-strand	606-607	2	14
α-helix	608-610	3
α-helix	616-627	12
β-strand	632-634	3	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66	A, B	protein	467	HOMO SAPIENS	Q9H6W3 (AlphaFold model)
60S ribosomal protein L8	C, D	protein	35	HOMO SAPIENS	P62917 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4CCM_1 BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66 (chains A, B)
MSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYYQGL
FSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRLLCP
QAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWRVYR
PRVPTEELALTSSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHLTLS
TYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFMEKV
RVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEPVNVGAQ
LTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELLLGS
YPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLALNAENLYFQ

Sequence of entity 2 (C, D), FASTA

>4CCM_2 60S RIBOSOMAL PROTEIN L8 (chains C, D)
NPVEHPFGGGNHQHICKPSTIRRDAPAGRKVGLIA

Ligands and cofactors

ID	Name	Formula	Copies
OGA	N-oxalylglycine	C4 H5 N O5	2
MN	Manganese (II) ion	Mn	2

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

Primary citation

Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Chowdhury, R., Sekirnik, R., Brissett, N.C. et al. Nature (2014) 510:422-426. DOI 10.1038/nature13263 · 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…
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…
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
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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