Nucleosome core particle containing an 8-oxoG damage site
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8vx5
Q-score: 0.493
You Q, Feng X, Cai Y, Baylin SB, Li H
Commun Biol (2024) 7 pp. 1202-1202 [ Pubmed: 39341999 DOI: doi:10.1038/s42003-024-06919-7 ]
- Complex of human ogg1 with a 35 bp dna duplex containing 8-oxog (Complex from Homo sapiens)
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (18 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Structure of Acidothermus cellulolyticus Cas9 ternary complex (Cleavage Intermediate 1)
Resolution: 2.21 Å
EM Method: Single-particle
Fitted PDBs: 8d2l
Q-score: 0.661
Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H
Nat Catal (2023) 6 pp. 969-977 [ DOI: doi:10.1038/s41929-023-01031-1 Pubmed: 38348449 ]
- Dna (Complex)
- Cryoem structure of acecas9 (cleavage intermediate 1) (Complex)
- Dna non-target strand (5'-d(p*tp*ap*tp*ap*cp*ap*cp*cp*ap*ap*gp*cp*t)-3') (3 kDa, DNA from synthetic construct)
- Single guide rna (106-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus 11B)
- Dna target strand (5'-d(*ap*gp*cp*tp*tp*gp*gp*tp*gp*tp*ap*tp*a)-3') (4 kDa, DNA from synthetic construct)
- Dna target strand (5'-d(p*cp*cp*ap*gp*gp*ap*tp*cp*tp*tp*gp*cp*cp*ap*tp*cp*cp*tp*ap*cp*cp*tp*cp*t)-3') (7 kDa, DNA from synthetic construct)
- Water (18 Da, Ligand)
- Dna non-target strand (5'-d(p*ap*gp*a)-3') (910 Da, DNA from synthetic construct)
Structure of Acidothermus cellulolyticus Cas9 ternary complex (Pre-cleavage)
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 8d2n
Q-score: 0.459
Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H
Nat Catal (2023) 6 pp. 969-977 [ DOI: doi:10.1038/s41929-023-01031-1 Pubmed: 38348449 ]
- Dna (Complex)
- Single guide rna (106-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Dna non-target strand (5'-d(p*tp*ap*cp*ap*cp*cp*ap*ap*gp*cp*t)-3') (3 kDa, DNA from synthetic construct)
- Dna target strand (25-mer) (7 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus 11B)
- Cryoem structure of acecas9 (pre-cleavage) (Complex)
Structure of Acidothermus cellulolyticus Cas9 ternary complex (Post-cleavage 2)
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8d2o
Q-score: 0.56
Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H
Nat Catal (2023) 6 pp. 969-977 [ DOI: doi:10.1038/s41929-023-01031-1 Pubmed: 38348449 ]
- Dna (Complex)
- Dna non-target strand (5'-d(p*ap*tp*ap*cp*ap*cp*cp*ap*ap*gp*cp*t)-3') (3 kDa, DNA from synthetic construct)
- Water (18 Da, Ligand)
- Cryoem structure of acecas9 (post-cleavage 2) (Complex)
- Single guide rna (106-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus 11B)
- Dna target strand (5'-d(*ap*gp*cp*tp*tp*gp*gp*tp*gp*tp*ap*tp*a)-3') (4 kDa, DNA from synthetic construct)
- Dna target strand (5'-d(p*cp*cp*ap*gp*gp*ap*tp*cp*tp*tp*g)-3') (3 kDa, DNA from synthetic construct)
Structure of Acidothermus cellulolyticus Cas9 ternary complex (Target bound)
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 8d2p
Q-score: 0.572
Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H
Nat Catal (2023) 6 pp. 969-977 [ DOI: doi:10.1038/s41929-023-01031-1 Pubmed: 38348449 ]
- Single guide rna (102-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Dna (Complex)
- Cryoem structure of acecas9 (target bound) (Complex)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus 11B)
- Dna target strand (5'-d(p*cp*cp*ap*gp*gp*ap*tp*cp*tp*tp*gp*cp*cp*ap*tp*cp*cp*tp*ap*cp*cp*tp*cp*t)-3') (7 kDa, DNA from synthetic construct)
- Water (18 Da, Ligand)
Structure of Acidothermus cellulolyticus Cas9 ternary complex (Post-cleavage 1)
Resolution: 2.58 Å
EM Method: Single-particle
Fitted PDBs: 8d2q
Q-score: 0.522
Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H
Nat Catal (2023) 6 pp. 969-977 [ DOI: doi:10.1038/s41929-023-01031-1 Pubmed: 38348449 ]
- Dna (Complex)
- Dna non-target strand (5'-d(p*ap*tp*ap*cp*ap*cp*cp*ap*ap*gp*cp*t)-3') (3 kDa, DNA from synthetic construct)
- Water (18 Da, Ligand)
- Single guide rna (86-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Cryoem structure of acecas9 (post-cleavage 1) (Complex)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus 11B)
- Dna target strand (5'-d(*ap*gp*cp*tp*tp*gp*gp*tp*gp*tp*ap*tp*a)-3') (4 kDa, DNA from synthetic construct)
- Dna target strand (5'-d(p*cp*cp*ap*gp*gp*ap*tp*cp*tp*tp*g)-3') (3 kDa, DNA from synthetic construct)
Cryo-EM structure of GIPR splice variant 1 (SV1) in complex with Gs protein
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8itl
Q-score: 0.477
Zhao F, Hang K, Zhou Q, Shao L, Li H, Li W, Lin S, Dai A, Cai X, Liu Y, Xu Y, Feng W, Yang D, Wang MW
PNAS (2023) 120 pp. e2306145120-e2306145120 [ DOI: doi:10.1073/pnas.2306145120 Pubmed: 37792509 ]
- Gastric inhibitory polypeptide receptor (42 kDa, Protein from Homo sapiens)
- Cryo-em structure of a splice variant of the gipr(sv1) in complex with gs protein (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (40 kDa, Protein from Rattus norvegicus)
- Nanobody-35 (13 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Guanine nucleotide-binding protein g(s) subunit alpha isoforms short (45 kDa, Protein from Bos taurus)
Cryo-EM structure of GIPR splice variant 2 (SV2) in complex with Gs protein
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8itm
Q-score: 0.479
Zhao F, Hang K, Zhou Q, Shao L, Li H, Li W, Lin S, Dai A, Cai X, Liu Y, Xu Y, Feng W, Yang D, Wang MW
PNAS (2023) 120 pp. e2306145120-e2306145120 [ DOI: doi:10.1073/pnas.2306145120 Pubmed: 37792509 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (40 kDa, Protein from Rattus norvegicus)
- Cryo-em structure of a splice variant of the gipr(sv2) in complex with gs protein (Complex from Homo sapiens)
- Nanobody-35 (13 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Gastric inhibitory polypeptide receptor (41 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(s) subunit alpha isoforms short (45 kDa, Protein from Bos taurus)
Cryo-EM structure of the alpha-MSH-bound human melanocortin receptor 5 (MC5R)-Gs complex
Resolution: 2.73 Å
EM Method: Single-particle
Fitted PDBs: 8inr
Q-score: 0.49
Feng W, Zhou Q, Chen X, Dai A, Cai X, Liu X, Zhao F, Chen Y, Ye C, Xu Y, Cong Z, Li H, Lin S, Yang D, Wang MW
Cell Discov (2023) 9 pp. 81- [ DOI: doi:10.1107/S0907444909042073 Pubmed: 37524700 ]
- Calcium ion (40 Da, Ligand)
- Alpha-melanocyte-stimulating hormone (1 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i) subunit alpha-1,guanine nucleotide-binding protein g(s) subunit alpha isoforms short (41 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1,hibit (40 kDa, Protein from Homo sapiens)
- Ha signal peptide,melanocortin receptor 5,lgbit subunit (56 kDa, Protein from Homo sapiens)
- Cryo-em structure of alpha-msh-bound human melanocortin receptor 5 in complex with g protein (Complex from Homo sapiens)
Cryo-EM structure of the gamma-MSH-bound human melanocortin receptor 3 (MC3R)-Gs complex
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 8ioc
Q-score: 0.459
Feng W, Zhou Q, Chen X, Dai A, Cai X, Liu X, Zhao F, Chen Y, Ye C, Xu Y, Cong Z, Li H, Lin S, Yang D, Wang MW
Cell Discov (2023) 9 pp. 81- [ DOI: doi:10.1107/S0907444909042073 Pubmed: 37524700 ]
- Nanobody-35 (17 kDa, Protein from Homo sapiens)
- Ha signal peptide,melanocortin receptor 3,lgbit subunit (56 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Guanine nucleotide-binding protein g(i) subunit alpha-1,guanine nucleotide-binding protein g(s) subunit alpha isoforms short (41 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1,hibit (40 kDa, Protein from Homo sapiens)
- Cryo-em structure of gamma-msh-bound human melanocortin receptor 3 in complex with g protein (Complex from Homo sapiens)
- Gamma-melanocyte-stimulating hormone (1 kDa, Protein from synthetic construct)