Cryo-EM structure of human DNMT3B homo-tetramer (form I)
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8eih
Q-score: 0.493
Lu J, Fang J, Zhu H, Liang KL, Khudaverdyan N, Song J
Nucleic Acids Res (2023) 51 pp. 12476-12491 [ Pubmed: 37941146 DOI: doi:10.1093/nar/gkad972 ]
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Dna (cytosine-5)-methyltransferase 3b (Complex from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3b (73 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of human DNMT3B homo-tetramer (form II)
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 8eii
Q-score: 0.44
Lu J, Fang J, Zhu H, Liang KL, Khudaverdyan N, Song J
Nucleic Acids Res (2023) 51 pp. 12476-12491 [ Pubmed: 37941146 DOI: doi:10.1093/nar/gkad972 ]
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Dna (cytosine-5)-methyltransferase 3b (Complex from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3b (73 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of human DNMT3B homo-trimer
Resolution: 3.34 Å
EM Method: Single-particle
Fitted PDBs: 8eij
Q-score: 0.426
Lu J, Fang J, Zhu H, Liang KL, Khudaverdyan N, Song J
Nucleic Acids Res (2023) 51 pp. 12476-12491 [ Pubmed: 37941146 DOI: doi:10.1093/nar/gkad972 ]
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Dna (cytosine-5)-methyltransferase 3b (Complex from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3b (73 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of human DNMT3B homo-hexamer
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 8eik
Q-score: 0.383
Lu J, Fang J, Zhu H, Liang KL, Khudaverdyan N, Song J
Nucleic Acids Res (2023) 51 pp. 12476-12491 [ Pubmed: 37941146 DOI: doi:10.1093/nar/gkad972 ]
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Dna (cytosine-5)-methyltransferase 3b (Complex from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3b (73 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8foi
Q-score: 0.564
Sun C, Zhu H, Clark S, Gouaux E
Nature (2023) 622 pp. 195-201 [ Pubmed: 37730991 DOI: doi:10.1038/s41586-023-06556-w ]
- Native gabaa receptor isolated from mouse brain containing two alpha1 subunits, in complex with 8e3-fab, gaba, and allopregnanolone (350 kDa, Complex from Mus musculus)
- Heavy chain of 8e3 fab (24 kDa, Protein from Mus musculus)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- Dodecane (170 Da, Ligand)
- Light chain of 8e3-fab (23 kDa, Protein from Mus musculus)
- Allopregnanolone (318 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit gamma-2 (55 kDa, Protein from Mus musculus)
- Gamma-aminobutyric acid receptor subunit alpha-1 (51 kDa, Protein from Mus musculus)
- N-octane (114 Da, Ligand)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit beta-2 (59 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8g4o
Q-score: 0.423
Sun C, Zhu H, Clark S, Gouaux E
Nature (2023) 622 pp. 195-201 [ Pubmed: 37730991 DOI: doi:10.1038/s41586-023-06556-w ]
- Light chain of 8e3 fab (23 kDa, Protein from Mus musculus)
- Heavy chain of 8e3 fab (24 kDa, Protein from Mus musculus)
- Native gabaa receptor isolated from mouse brain containing two alpha1 subunits, in complex with 8e3-fab, didesethylflurazepam, and endogenous gaba (350 kDa, Complex from Mus musculus)
- (5m)-1-(2-aminoethyl)-7-chloro-5-(2-fluorophenyl)-1,3-dihydro-2h-1,4-benzodiazepin-2-one (331 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit gamma-2 (55 kDa, Protein from Mus musculus)
- Gamma-aminobutyric acid receptor subunit alpha-1 (51 kDa, Protein from Mus musculus)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit beta-2 (59 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 2.56 Å
EM Method: Single-particle
Fitted PDBs: 8g4x
Q-score: 0.504
Sun C, Zhu H, Clark S, Gouaux E
Nature (2023) 622 pp. 195-201 [ Pubmed: 37730991 DOI: doi:10.1038/s41586-023-06556-w ]
- Light chain of 8e3 fab (23 kDa, Protein from Mus musculus)
- Heavy chain of 8e3 fab (24 kDa, Protein from Mus musculus)
- Gamma-aminobutyric acid receptor subunit alpha-3 (55 kDa, Protein from Mus musculus)
- Allopregnanolone (318 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit gamma-2 (55 kDa, Protein from Mus musculus)
- Gamma-aminobutyric acid receptor subunit alpha-1 (51 kDa, Protein from Mus musculus)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit beta-2 (59 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Native gabaa receptor isolated from mouse brain containing one alpha1 subunit, in complex with 8e3-fab, gaba, and allopregnanolone (350 kDa, Complex from Mus musculus)
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8g5f
Q-score: 0.491
Sun C, Zhu H, Clark S, Gouaux E
Nature (2023) 622 pp. 195-201 [ Pubmed: 37730991 DOI: doi:10.1038/s41586-023-06556-w ]
- Light chain of 8e3 fab (23 kDa, Protein from Mus musculus)
- Heavy chain of 8e3 fab (24 kDa, Protein from Mus musculus)
- Gamma-aminobutyric acid receptor subunit alpha-3 (55 kDa, Protein from Mus musculus)
- Allopregnanolone (318 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit gamma-2 (55 kDa, Protein from Mus musculus)
- Gamma-aminobutyric acid receptor subunit alpha-1 (51 kDa, Protein from Mus musculus)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit beta-2 (59 kDa, Protein from Mus musculus)
- Native gabaa receptor isolated from mouse brain containing one alpha1 subunit, in complex with 8e3-fab, gaba, and allopregnanolone (350 kDa, Complex from Mus musculus)
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8g5g
Q-score: 0.435
Sun C, Zhu H, Clark S, Gouaux E
Nature (2023) 622 pp. 195-201 [ Pubmed: 37730991 DOI: doi:10.1038/s41586-023-06556-w ]
- Light chain of 8e3 fab (23 kDa, Protein from Mus musculus)
- Heavy chain of 8e3 fab (24 kDa, Protein from Mus musculus)
- Gamma-aminobutyric acid receptor subunit alpha-3 (55 kDa, Protein from Mus musculus)
- Allopregnanolone (318 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit gamma-2 (55 kDa, Protein from Mus musculus)
- Gamma-aminobutyric acid receptor subunit alpha-1 (51 kDa, Protein from Mus musculus)
- Zolpidem (307 Da, Ligand)
- Native gabaa receptor isolated from mouse brain containing one alpha1 subunit, in complex with 8e3-fab, gaba, zolpidem, and endogenous neurosteroid (350 kDa, Complex from Mus musculus)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit beta-2 (59 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8g5h
Q-score: 0.477
Sun C, Zhu H, Clark S, Gouaux E
Nature (2023) 622 pp. 195-201 [ Pubmed: 37730991 DOI: doi:10.1038/s41586-023-06556-w ]
- Light chain of 8e3 fab (23 kDa, Protein from Mus musculus)
- Heavy chain of 8e3 fab (24 kDa, Protein from Mus musculus)
- Gamma-aminobutyric acid receptor subunit alpha-3 (55 kDa, Protein from Mus musculus)
- Allopregnanolone (318 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit gamma-2 (55 kDa, Protein from Mus musculus)
- Gamma-aminobutyric acid receptor subunit alpha-1 (51 kDa, Protein from Mus musculus)
- Zolpidem (307 Da, Ligand)
- Native gabaa receptor isolated from mouse brain containing one alpha1 subunit, in complex with 8e3-fab, gaba, zolpidem, and endogenous neurosteroid (350 kDa, Complex from Mus musculus)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit beta-2 (59 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)