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)
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 ]
- Segment polarity protein dishevelled homolog dvl-2 (79 kDa, Protein from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Frizzled-4 (60 kDa, Protein from Homo sapiens)
- Gpcr complex (450 kDa, Complex from Homo sapiens)
Cryo-EM structure of the ISFba1 TnpB-reRNA-dsDNA complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8iaz
Q-score: 0.548
Ren K, Zhou F, Zhang F, Yin M, Zhu Y, Wang S, Chen Y, Huang T, Wu Z, He J, Zhang A, Guo C, Huang Z
Cell Res (2024) 34 pp. 370-385 [ DOI: doi:10.1038/s41422-024-00952-1 Pubmed: 38575718 ]
- Rna (207-mer) (66 kDa, RNA from Firmicutes bacterium AM43-11BH)
- Transposase (44 kDa, Protein from Firmicutes bacterium AM43-11BH)
- Dna (5'-d(p*cp*cp*ap*tp*tp*ap*gp*gp*ap*gp*cp*tp*gp*ap*tp*g)-3') (4 kDa, DNA from Firmicutes bacterium AM43-11BH)
- The complex of protein with grna and target dna (Complex from Firmicutes bacterium AM43-11BH)
- Dna (5'-d(p*ap*cp*ap*tp*gp*gp*ap*cp*cp*ap*tp*cp*ap*gp*cp*tp*cp*cp*tp*ap*ap*tp*gp*g)-3') (7 kDa, DNA from Firmicutes bacterium AM43-11BH)
- Zinc ion (65 Da, Ligand)
Histamine-bound H4R/Gi complex
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8jxt
Q-score: 0.472
Xia R, Shi S, Xu Z, Vischer HF, Windhorst AD, Qian Y, Duan Y, Liang J, Chen K, Zhang A, Guo C, Leurs R, He Y
Nat Commun (2024) 15 pp. 2493-2493 [ Pubmed: 38509098 DOI: doi:10.1038/s41467-024-46840-5 ]
- Scfv16 (26 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Gpcr/g-protein complex (130 MDa, Complex from Homo sapiens)
- Phosphate ion (94 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-1 (40 kDa, Protein from Homo sapiens)
- Histamine (111 Da, Ligand)
- Histamine h4 receptor (44 kDa, Protein from Homo sapiens)
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 7yub
Q-score: 0.513
Duan Y, Leong NCP, Zhao J, Zhang Y, Nguyen DT, Ha HTT, Wang N, Xia R, Xu Z, Ma Z, Qian Y, Yin H, Zhu X, Zhang A, Guo C, Xia Y, Nguyen LN, He Y
Cell Res (2024) 34 pp. 177-180 [ DOI: doi:10.1038/s41422-023-00913-0 Pubmed: 38123825 ]
- Nbfab-l-chain (23 kDa, Protein from synthetic construct)
- Nbfab-h-chain (26 kDa, Protein from synthetic construct)
- Sphingosine-1-phosphate transporter spns2 (58 kDa, Protein from Homo sapiens)
- Tc-nb8 (14 kDa, Protein from Lama glama)
- (2s,3r,4e)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate (379 Da, Ligand)
- Spns2 nanobody complex (Complex from Lama glama)
Resolution: 3.64 Å
EM Method: Single-particle
Fitted PDBs: 8jwf
Q-score: 0.354
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 8jwg
Q-score: 0.335
DHA-bound FFAR4 in complex with Gs
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8h4i
Q-score: 0.574
Yin H, Inoue A, Ma Z, Zhu X, Xia R, Xu Z, Wang N, Duan Y, Zhang A, Guo C, He Y
Cell Res (2023) 33 pp. 644-647 [ DOI: doi:10.1038/s41422-023-00835-x Pubmed: 37286793 ]
- Gpcr/g-protein complex (Complex 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 (37 kDa, Protein from Homo sapiens)
- Nb35 (17 kDa, Protein from Lama glama)
- Engineered mini galpha-s subunit (41 kDa, Protein from Homo sapiens)
- Docosa-4,7,10,13,16,19-hexaenoic acid (328 Da, Ligand)
- Free fatty acid receptor 4 (40 kDa, Protein from Homo sapiens)
GW9508-bound FFAR4 in complex with Gq
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8h4k
Q-score: 0.545
Yin H, Inoue A, Ma Z, Zhu X, Xia R, Xu Z, Wang N, Duan Y, Zhang A, Guo C, He Y
Cell Res (2023) 33 pp. 644-647 [ DOI: doi:10.1038/s41422-023-00835-x Pubmed: 37286793 ]
- Gpcr/g-protein complex (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Engineered mini galpha-q subunit (41 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Nb35 (17 kDa, Protein from Lama glama)
- 3-(4-{[(3-phenoxyphenyl)methyl]amino}phenyl)propanoic acid (347 Da, Ligand)
- Free fatty acid receptor 4 (40 kDa, Protein from Homo sapiens)