cryo-EM structure of a nanobody bound heliorhodopsin
Xia R, Sun M, Lu Y, Wang N, Zhang A, Guo C, Xu Z, Cai X, He Y
Biochem Biophys Res Commun (2025) 750 pp. 151398-151398 [ DOI: doi:10.1016/j.bbrc.2025.151398 Pubmed: 39889627 ]
- Nanobody b4 (13 kDa, Protein from Vicugna pacos)
- 1,2-dilauroyl-sn-glycero-3-phosphate (535 Da, Ligand)
- Heliorhodopsin (28 kDa, Protein from Escherichia coli)
- Palmitic acid (256 Da, Ligand)
- Retinal (284 Da, Ligand)
- Dimer complex (Complex from Escherichia coli)
- Acetate ion (59 Da, Ligand)
Integrin alpha-v beta-8 in complex with the Fab of 130H2
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 9ind
Q-score: 0.533
Guo C, Sun H, Du Y, Dai X, Pang Y, Han Z, Xiong X, Li S, Zhang J, Zheng Q, Gui X
J Exp Clin Cancer Res (2025) 44 pp. 1-1 [ Pubmed: 39743547 DOI: doi:10.1186/s13046-024-03250-1 ]
- 130h2-fab (Complex from Mus musculus)
- The heavy chain of 130h2-fab (13 kDa, Protein from Mus musculus)
- Integrin beta-8 (39 kDa, Protein from Homo sapiens)
- Integrin alpha-v beta-8 (Complex from Homo)
- Integrin alpha-v beta-8 complexed with antibody fab fragment of 130h2 (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Integrin alpha-v heavy chain (47 kDa, Protein from Homo sapiens)
- The light chain of 130h2-fab (11 kDa, Protein from Mus musculus)
LPA-bound LPAR6 in complex with miniGq
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 9itb
Q-score: 0.576
Duan Y, Xu Z, Hao B, Zhang A, Guo C, He Y
PNAS (2025) 122 pp. e2415426122-e2415426122 [ Pubmed: 39847322 DOI: doi:10.1073/pnas.2415426122 ]
- 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 (37 kDa, Protein from Homo sapiens)
- Palmitic acid (256 Da, Ligand)
- Engineered minigaq (41 kDa, Protein from Homo sapiens)
- Gpcr/g-protein complex (Complex from Homo sapiens)
- Nb35 (17 kDa, Protein from Lama glama)
- (2r)-2-hydroxy-3-(phosphonooxy)propyl (9e)-octadec-9-enoate (436 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Lysophosphatidic acid receptor 6 (33 kDa, Protein from Homo sapiens)
LPA-bound LPAR6 in complex with miniG13
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 9ite
Q-score: 0.558
Duan Y, Xu Z, Hao B, Zhang A, Guo C, He Y
PNAS (2025) 122 pp. e2415426122-e2415426122 [ Pubmed: 39847322 DOI: doi:10.1073/pnas.2415426122 ]
- Engineered miniga13 (26 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Palmitic acid (256 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Gpcr/g-protein complex (Complex from Homo sapiens)
- (2r)-2-hydroxy-3-(phosphonooxy)propyl (9e)-octadec-9-enoate (436 Da, Ligand)
- Scfv16 (26 kDa, Protein from Homo sapiens)
- Lysophosphatidic acid receptor 6 (34 kDa, Protein from Homo sapiens)
Qian Y, Ma Z, Xu Z, Duan Y, Xiong Y, Xia R, Zhu X, Zhang Z, Tian X, Yin H, Liu J, Song J, Lu Y, Zhang A, Guo C, Jin L, Kim WJ, Ke J, Xu F, Huang Z, He Y
Nat Commun (2024) 15 pp. 7644-7644 [ Pubmed: 39223191 DOI: doi:10.1038/s41467-024-52174-z ]
- Cholesterol hemisuccinate (486 Da, Ligand)
- Frizzled-4 (60 kDa, Protein from Homo sapiens)
- Gpcr complex (450 kDa, Complex from Homo sapiens)
- Segment polarity protein dishevelled homolog dvl-2 (79 kDa, Protein from Homo sapiens)
Fzd4/DEP complex (local refined)
Qian Y, Ma Z, Xu Z, Duan Y, Xiong Y, Xia R, Zhu X, Zhang Z, Tian X, Yin H, Liu J, Song J, Lu Y, Zhang A, Guo C, Jin L, Kim WJ, Ke J, Xu F, Huang Z, He Y
Nat Commun (2024) 15 pp. 7644-7644 [ Pubmed: 39223191 DOI: doi:10.1038/s41467-024-52174-z ]
- Frizzled-4 (60 kDa, Protein from Homo sapiens)
- Gpcr complex (450 kDa, Complex from Homo sapiens)
- Segment polarity protein dishevelled homolog dvl-2 (79 kDa, Protein from Homo sapiens)
LPS-bound P2Y10 in complex with G13
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8kgg
Q-score: 0.518
Yin H, Kamakura N, Qian Y, Tatsumi M, Ikuta T, Liang J, Xu Z, Xia R, Zhang A, Guo C, Inoue A, He Y
Cell Chem Biol (2024) 31 pp. 1899-1908.e5 [ DOI: doi:10.1016/j.chembiol.2024.08.005 Pubmed: 39265572 ]
- Gpcr/g-protein complex (Complex from Homo sapiens)
- Putative p2y purinoceptor 10 (38 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Scfv16 (26 kDa, Protein from Homo sapiens)
- (2~{s})-2-$l^{4}-azanyl-3-[[(2~{r})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid (497 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-2,guanine nucleotide-binding protein subunit alpha-13 (26 kDa, Protein from Homo sapiens)
Structure of human TRPV4 with antagonist A1
Resolution: 3.74 Å
EM Method: Single-particle
Fitted PDBs: 8ju5
Q-score: 0.374
Fan J, Guo C, Liao D, Ke H, Lei J, Xie W, Tang Y, Tominaga M, Huang Z, Lei X
Adv Sci (2024) 11 pp. e2401583-e2401583 [ DOI: doi:10.1002/advs.202401583 Pubmed: 38659239 ]
- Transient receptor potential cation channel subfamily v member 4,3c-gfp (128 kDa, Protein from synthetic construct)
- Trpv4 (400 kDa, Complex from Homo sapiens)
- 4-[(3~{s},4~{s})-4-(aminomethyl)-1-(5-chloranylpyridin-2-yl)sulfonyl-4-oxidanyl-pyrrolidin-3-yl]oxy-2-fluoranyl-benzenecarbonitrile (426 Da, Ligand)
Structure of human TRPV4 with antagonist GSK279
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 8ju6
Q-score: 0.415
Fan J, Guo C, Liao D, Ke H, Lei J, Xie W, Tang Y, Tominaga M, Huang Z, Lei X
Adv Sci (2024) 11 pp. e2401583-e2401583 [ DOI: doi:10.1002/advs.202401583 Pubmed: 38659239 ]
- 1-({(5s,7s)-3-[5-(2-hydroxypropan-2-yl)pyrazin-2-yl]-7-methyl-2-oxo-1-oxa-3-azaspiro[4.5]decan-7-yl}methyl)-1h-benzimidazole-6-carbonitrile (460 Da, Ligand)
- Transient receptor potential cation channel subfamily v member 4,3c-gfp (128 kDa, Protein from synthetic construct)
- Trpv4 (400 kDa, Complex from Homo sapiens)
Structure of human TRPV4 with antagonist A2
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 8jvi
Q-score: 0.418
Fan J, Guo C, Liao D, Ke H, Lei J, Xie W, Tang Y, Tominaga M, Huang Z, Lei X
Adv Sci (2024) 11 pp. e2401583-e2401583 [ DOI: doi:10.1002/advs.202401583 Pubmed: 38659239 ]
- Transient receptor potential cation channel subfamily v member 4,3c-gfp (128 kDa, Protein from synthetic construct)
- Trpv4 (400 kDa, Complex from Homo sapiens)
- [6-[[4-(2,4-dimethyl-1,3-thiazol-5-yl)-1,3-thiazol-2-yl]amino]pyridin-3-yl]-[(1~{s},5~{r})-3-[5-(trifluoromethyl)pyrimidin-2-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]methanone (572 Da, Ligand)