cryo-EM structure of Gs-coupled zebrafish GPR4 at pH 6.5
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8zfz
Q-score: 0.41
Ma Y, Wang Y, Tang M, Weng Y, Chen Y, Xu Y, An S, Wu Y, Zhao S, Xu H, Li D, Liu M, Lu W, Ru H, Song G
Nat Commun (2025) 16 pp. 605-605 [ DOI: doi:10.1038/s41467-025-55901-2 Pubmed: 39799123 ]
- Zgpr4-gs complex (Complex from Danio rerio)
- Guanine nucleotide-binding protein g(s) subunit alpha isoforms short (28 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Scfv16 (30 kDa, Protein from Mus musculus)
- Soluble cytochrome b562,g-protein coupled receptor 4,lgbit (72 kDa, Protein from synthetic construct)
cryo-EM structure of zebrafish GPR4-Gs complex at pH 8.5
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 9j31
Q-score: 0.467
Ma Y, Wang Y, Tang M, Weng Y, Chen Y, Xu Y, An S, Wu Y, Zhao S, Xu H, Li D, Liu M, Lu W, Ru H, Song G
Nat Commun (2025) 16 pp. 605-605 [ Pubmed: 39799123 DOI: doi:10.1038/s41467-025-55901-2 ]
- Soluble cytochrome b562,g-protein coupled receptor 4,lgbit (72 kDa, Protein from synthetic construct)
- Scfv16 (31 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(s) subunit alpha isoforms short (28 kDa, Protein from Homo sapiens)
- Zgpr4-gs complex (Complex from Danio rerio)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
MPOX E5 hexamer 2ATP, 2ADP, and ssDNA binding comformation
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8wh2
Q-score: 0.516
Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C
Sci Adv (2024) 10 pp. eadl1150-eadl1150 [ DOI: doi:10.1126/sciadv.adl1150 Pubmed: 39167653 ]
- Uncoating factor opg117 (90 kDa, Protein from Monkeypox virus)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*cp*cp*cp*cp*c)-3') (1 kDa, DNA from Spodoptera frugiperda)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Mpox helicase (Complex from Monkeypox virus)
MPOX E5 hexamer AMP-PNP and ssDNA bound form with clear primase domain
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 8wgy
Q-score: 0.494
Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C
Sci Adv (2024) 10 pp. eadl1150-eadl1150 [ DOI: doi:10.1126/sciadv.adl1150 Pubmed: 39167653 ]
- Uncoating factor opg117 (90 kDa, Protein from Monkeypox virus)
- Magnesium ion (24 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Mpox helicase (Complex from Monkeypox virus)
- Dna (5'-d(p*cp*cp*c)-3') (822 Da, DNA from Spodoptera frugiperda)
MPOX E5 double hexamer ssDNA bound conformation
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 8wgz
Q-score: 0.273
Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C
Sci Adv (2024) 10 pp. eadl1150-eadl1150 [ DOI: doi:10.1126/sciadv.adl1150 Pubmed: 39167653 ]
- Uncoating factor opg117 (90 kDa, Protein from Monkeypox virus)
- Mpox helicase (Complex from Monkeypox virus)
- Dna (5'-d(p*cp*cp*cp*cp*c)-3') (1 kDa, DNA from Spodoptera frugiperda)
MPOX E5 hexamer ssDNA and AMP-PNP bound conformation
Resolution: 2.51 Å
EM Method: Single-particle
Fitted PDBs: 8wh0
Q-score: 0.589
Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C
Sci Adv (2024) 10 pp. eadl1150-eadl1150 [ DOI: doi:10.1126/sciadv.adl1150 Pubmed: 39167653 ]
- Uncoating factor opg117 (90 kDa, Protein from Monkeypox virus)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*cp*cp*cp*cp*c)-3') (1 kDa, DNA from Spodoptera frugiperda)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Mpox helicase (Complex from Monkeypox virus)
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 8wh3
Q-score: 0.425
Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C
Sci Adv (2024) 10 pp. eadl1150-eadl1150 [ Pubmed: 39167653 DOI: doi:10.1126/sciadv.adl1150 ]
- Mpox helicase (Complex from Monkeypox virus)
- Uncoating factor opg117 (90 kDa, Protein from Monkeypox virus)
MPOX E5 hexamer ssDNA bound apo conformation
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 8wh4
Q-score: 0.404
Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C
Sci Adv (2024) 10 pp. eadl1150-eadl1150 [ DOI: doi:10.1126/sciadv.adl1150 Pubmed: 39167653 ]
- Uncoating factor opg117 (90 kDa, Protein from Monkeypox virus)
- Mpox helicase (Complex from Monkeypox virus)
- Dna (5'-d(p*cp*cp*cp*c)-3') (1 kDa, DNA from Spodoptera frugiperda)
MPOX E5 hexamer ADP and ssDNA bound and clear primase domain conformation
Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 8wh6
Q-score: 0.462
Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C
Sci Adv (2024) 10 pp. eadl1150-eadl1150 [ Pubmed: 39167653 DOI: doi:10.1126/sciadv.adl1150 ]
- Zinc ion (65 Da, Ligand)
- Mpox helicase (Complex from Monkeypox virus)
- Dna (5'-d(p*cp*cp*c)-3') (822 Da, DNA from Spodoptera frugiperda)
- Uncoating factor opg117 (90 kDa, Protein from Monkeypox virus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Monkeypox virus DNA replication holoenzyme F8, A22 and E4 in complex with a DNA duplex and dCTP
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8j8f
Q-score: 0.45
Xu Y, Wu Y, Wu X, Zhang Y, Yang Y, Li D, Yang B, Gao K, Zhang Z, Dong C
Int J Biol Macromol (2024) 270 pp. 132231-132231 [ DOI: doi:10.1016/j.ijbiomac.2024.132231 Pubmed: 38735603 ]
- Dna (5'-d(p*gp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*gp*ap*tp*ap*ap*cp*tp*tp*ap*ap*tp*cp*tp*cp*ap*cp*ap*tp*ap*gp*cp*ap*gp*cp*t)-3') (11 kDa, DNA from DNA molecule)
- Dna (5'-d(p*ap*gp*cp*tp*gp*cp*tp*ap*tp*gp*ap*gp*ap*tp*tp*ap*ap*gp*tp*tp*ap*t)-3') (7 kDa, DNA from DNA molecule)
- Monkeypox virus replication holoenzyme f8-a22-e4 in complex with a dna duplex and dctp (191 MDa, Complex from Monkeypox virus)
- E4r (27 kDa, Protein from Monkeypox virus)
- Dna polymerase processivity factor component a20 (49 kDa, Protein from Monkeypox virus)
- 2'-deoxycytidine-5'-triphosphate (467 Da, Ligand)
- Dna polymerase (120 kDa, Protein from Monkeypox virus)
- Calcium ion (40 Da, Ligand)