9EOZ: Human OGG1

Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0. Determined by electron microscopy at 3.1 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, synthetic construct
Chains: 11
Atoms: 14,100
Mol. weight: 238.23 kDa
Released: 6 Nov 2024

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

Secondary structure: helices and β-sheets

9EOZ contains 54 α-helices and 27 β-strands across 9 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: 16 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	1
α-helix	30-32	3
α-helix	35-38	4
β-strand	48-51	4	1
β-strand	54-59	6	1
β-strand	62-68	7	1
β-strand	73-77	5	1
α-helix	90-100	11
α-helix	107-109	3
α-helix	110-116	7
α-helix	118-126	9
α-helix	137-145	9
α-helix	152-165	14
β-strand	169	1	2
β-strand	179	1	2
α-helix	194-197	4
α-helix	204-217	14
α-helix	221-229	9
α-helix	233-241	9
α-helix	248-256	9
α-helix	269-278	10
α-helix	293-307	15
α-helix	311-319	9

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	3
α-helix	50-75	26
β-strand	80-81	2	4
α-helix	83-92	10
β-strand	97-98	2	5

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	6
α-helix	86-113	28
β-strand	118-119	2	7
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	7
α-helix	50-75	26
β-strand	80-81	2	6
α-helix	83-92	10
β-strand	97-98	2	8

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	47-72	26
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	93-96	4
β-strand	101-102	2	5
α-helix	113-115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	102-119	18

Chain K: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	4
α-helix	86-113	28
β-strand	118-119	2	3
α-helix	121-131	11

Chain L: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	11
α-helix	46-72	27
β-strand	77-78	2	12
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	8
α-helix	113-115	3

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-glycosylase/DNA lyase	A	protein	356	Homo sapiens	O15527 (AlphaFold model)
Histone H4	B, F	protein	102	Homo sapiens	P62805 (AlphaFold model)
Histone H3.3	E, K	protein	135	Homo sapiens	P84243 (AlphaFold model)
Histone H2A type 1-C	G, L	protein	129	Homo sapiens	Q93077 (AlphaFold model)
Histone H2B type 1-C/E/F/G/I	H, M	protein	125	Homo sapiens	P62807
Widom 601 DNA (145-MER)	Y	DNA	145	synthetic construct
Widom 601 DNA (145-MER)	Z	DNA	145	synthetic construct

Sequence of entity 1 (A), FASTA

>9EOZ_1 N-glycosylase/DNA lyase (chains A)
GSSHHHHHHSQDPARALLPRRMGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWRE
QSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQL
YHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPR
LIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLR
ESSYEEAHKALCILPGVGTQVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAK
GPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQSRHAQEPPAKRRKGSKGPEG

Sequence of entity 2 (B, F), FASTA

>9EOZ_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (E, K), FASTA

>9EOZ_3 Histone H3.3 (chains E, K)
ARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 4 (G, L), FASTA

>9EOZ_4 Histone H2A type 1-C (chains G, L)
SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK

Sequence of entity 5 (H, M), FASTA

>9EOZ_5 Histone H2B type 1-C/E/F/G/I (chains H, M)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK

Sequence of entity 6 (Y), FASTA

>9EOZ_6 Widom 601 DNA (145-MER) (chains Y)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT

Sequence of entity 7 (Z), FASTA

>9EOZ_7 Widom 601 DNA (145-MER) (chains Z)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT

Primary citation

Structural basis for human OGG1 processing 8-oxodGuo within nucleosome core particles. Ren, M., Gut, F., Fan, Y. et al. Nat Commun (2024) 15:9407-9407. DOI 10.1038/s41467-024-53811-3 · PubMed

Other PDB entries of the same protein (UniProt O15527 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8XWC 1.45 Å, Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the substrate…
2XHI 1.55 Å, Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA…
5AN4 1.6 Å, Crystal structure of the human 8-oxoguanine glycosylase (OGG1) processed with the…
8XWU 1.68 Å, Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction…
8XXK 1.7 Å, Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction…
8XXG 1.82 Å, Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction…
9NZ8 1.85 Å, Crystal structure of human OGG1 in a DNA-free state
1M3Q 1.9 Å, Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine
6RLW 2.0 Å, Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487
7AYY 2.0 Å, Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator…
9NZ9 2.0 Å, Crystal structure of product-bound human OGG1(WT)
1LWY 2.01 Å, hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine

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