7AYY: Human 8-oxoguanine DNA Glycosylase hOGG1

Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator TH10785. Determined by X-ray diffraction at 2.0 Å resolution. Released 1 Jun 2022.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 13,010
Mol. weight: 191.72 kDa
Ligands: SEQ
Released: 1 Jun 2022

Explore 7AYY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7AYY contains 100 α-helices and 35 β-strands across 5 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 AAA: 19 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	24-27	4	1
α-helix	35-38	4
β-strand	47-51	5	1
β-strand	54-59	6	1
β-strand	62-68	7	1
β-strand	72-78	7	1
α-helix	92-99	8
α-helix	106-116	11
α-helix	118-124	7
α-helix	131-133	3
α-helix	137-145	9
α-helix	152-166	15
β-strand	169-173	5	2
β-strand	176-179	4	2
α-helix	180-183	4
α-helix	184-187	4
α-helix	192-198	7
α-helix	204-214	11
α-helix	215-219	5
α-helix	222-230	9
α-helix	233-240	8
α-helix	248-258	11
α-helix	270-279	10
α-helix	293-307	15
α-helix	311-323	13

Chain BBB: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	24-27	4	3
α-helix	30-32	3
α-helix	35-37	3
β-strand	48-51	4	3
β-strand	54-59	6	3
β-strand	62-68	7	3
β-strand	72-78	7	3
α-helix	87-89	3
α-helix	90-99	10
α-helix	106-116	11
α-helix	118-126	9
α-helix	131-133	3
α-helix	137-145	9
α-helix	152-166	15
β-strand	169-173	5	4
β-strand	176-179	4	4
α-helix	180-183	4
α-helix	184-187	4
α-helix	192-198	7
α-helix	204-214	11
α-helix	215-219	5
α-helix	222-230	9
α-helix	233-240	8
α-helix	248-258	11
α-helix	269-278	10
α-helix	293-307	15
α-helix	311-323	13

Chain CCC: 18 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	24-27	4	5
α-helix	35-38	4
β-strand	47-51	5	5
β-strand	54-59	6	5
β-strand	62-68	7	5
β-strand	72-78	7	5
α-helix	83-85	3
α-helix	90-99	10
α-helix	106-116	11
α-helix	118-126	9
α-helix	137-145	9
α-helix	152-166	15
β-strand	169-173	5	6
β-strand	176-179	4	6
α-helix	180-183	4
α-helix	184-187	4
α-helix	192-198	7
α-helix	204-217	14
α-helix	223-230	8
α-helix	233-240	8
α-helix	248-258	11
α-helix	269-279	11
α-helix	293-307	15
α-helix	311-323	13

Chain DDD: 20 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	24-27	4	7
α-helix	35-38	4
β-strand	47-51	5	7
β-strand	54-59	6	7
β-strand	62-68	7	7
β-strand	72-78	7	7
α-helix	87-89	3
α-helix	90-99	10
α-helix	106-116	11
α-helix	118-126	9
α-helix	131-133	3
α-helix	137-145	9
α-helix	152-166	15
α-helix	168	1
β-strand	169-173	5	8
β-strand	176-179	4	8
α-helix	180-183	4
α-helix	184-187	4
α-helix	192-198	7
α-helix	204-218	15
α-helix	222-229	8
α-helix	233-240	8
α-helix	248-258	11
α-helix	269-279	11
α-helix	293-307	15
α-helix	311-323	13

Chain EEE: 22 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	20-22	3
β-strand	24-27	4	9
α-helix	35-38	4
β-strand	47-51	5	9
β-strand	54-59	6	9
β-strand	62-68	7	9
β-strand	72-78	7	9
α-helix	87-89	3
α-helix	90-99	10
α-helix	106-115	10
α-helix	118-126	9
α-helix	131-133	3
α-helix	137-145	9
α-helix	152-166	15
α-helix	168	1
β-strand	169-173	5	10
β-strand	176-179	4	10
α-helix	180-183	4
α-helix	184-187	4
α-helix	192-198	7
α-helix	204-214	11
α-helix	215-219	5
α-helix	222-230	9
α-helix	233-240	8
α-helix	248-258	11
α-helix	269-279	11
α-helix	293-307	15
α-helix	311-322	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-glycosylase/DNA lyase	AAA, BBB, CCC, DDD, EEE	protein	337	Homo sapiens	O15527 (AlphaFold model)

Sequence of entity 1 (AAA, BBB, CCC, DDD, EEE), FASTA

>7AYY_1 N-glycosylase/DNA lyase (chains AAA, BBB, CCC, DDD, EEE)
MGSSHHHHHHSSGLVPRGSHMGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQ
SPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLY
HHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRL
IQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRE
SSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKG
PSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQSR

Ligands and cofactors

ID	Name	Formula	Copies
SEQ	~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine	C17 H21 N3	5

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

Primary citation

Small-molecule activation of OGG1 increases oxidative DNA damage repair by gaining a new function. Michel, M., Benitez-Buelga, C., Calvo, P.A. et al. Science (2022) 376:1471-1476. DOI 10.1126/science.abf8980 · 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
9NZ9 2.0 Å, Crystal structure of product-bound human OGG1(WT)
1LWY 2.01 Å, hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine
2NOH 2.01 Å, Structure of catalytically inactive Q315A human 8-oxoguanine glycosylase complexed to…

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