Pfr conformer of Arabidopsis thaliana phytochrome B in complex with phytochrome-interacting factor 6
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8yb4
Q-score: 0.522
Wang Z, Wang W, Zhao D, Song Y, Lin X, Shen M, Chi C, Xu B, Zhao J, Deng XW, Wang J
Cell (2024) 187 pp. 6235-6250.e19 [ DOI: doi:10.1016/j.cell.2024.09.005 Pubmed: 39317197 ]
- Complex of atphyb-pfr homodimer (Complex from Arabidopsis thaliana)
- Phytochrome-interacting factor 6 (11 kDa, Protein from Arabidopsis thaliana)
- Pif6 monomer (Complex)
- Ternary complex of atphyb-pfr homodimer with atpif6 (120 kDa, Complex from Arabidopsis thaliana)
- 3-[5-[[(3~{r},4~{r})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{h}-pyrrol-2-yl]methyl]-4-methyl-1~{h}-pyrrol-3-yl]propanoic acid (586 Da, Ligand)
- Phytochrome b (129 kDa, Protein from Arabidopsis thaliana)
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 9iuz
Q-score: 0.473
Wang Z, Wang W, Zhao D, Song Y, Lin X, Shen M, Chi C, Xu B, Zhao J, Deng XW, Wang J
Cell (2024) 187 pp. 6235-6250.e19 [ DOI: doi:10.1016/j.cell.2024.09.005 Pubmed: 39317197 ]
- Phytochrome b (99 kDa, Protein from Arabidopsis thaliana)
- Complex of phyb mutant(y276h) homodimer (Complex from Arabidopsis thaliana)
- Ternary complex of phyb mutant(y276h) with pif6 (100 kDa, Complex from Arabidopsis thaliana)
- Phytochrome-interacting factor 6 (11 kDa, Protein from Arabidopsis thaliana)
- Pif6 monomer (Complex)
- 3-[5-[[(3~{r},4~{r})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{h}-pyrrol-2-yl]methyl]-4-methyl-1~{h}-pyrrol-3-yl]propanoic acid (586 Da, Ligand)
Pr conformer of Arabidopsis thaliana phytochrome A - AtphyA-Pr
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8isj
Q-score: 0.43
Zhang Y, Lin X, Ma C, Zhao J, Shang X, Wang Z, Xu B, Gao N, Deng XW, Wang J
Cell Res (2023) 33 pp. 806-809 [ Pubmed: 37491602 DOI: doi:10.1038/s41422-023-00858-4 ]
- Phytochrome a (124 kDa, Protein from Arabidopsis thaliana)
- 3-[5-[[(3~{r},4~{r})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{h}-pyrrol-2-yl]methyl]-4-methyl-1~{h}-pyrrol-3-yl]propanoic acid (586 Da, Ligand)
- Pr conformer of arabidopsis thaliana phytochrome a - atphya-pr (Complex from Arabidopsis thaliana)
Pr conformer of Zea mays phytochrome A1 - ZmphyA1-Pr
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8isk
Q-score: 0.415
Zhang Y, Lin X, Ma C, Zhao J, Shang X, Wang Z, Xu B, Gao N, Deng XW, Wang J
Cell Res (2023) 33 pp. 806-809 [ Pubmed: 37491602 DOI: doi:10.1038/s41422-023-00858-4 ]
- 3-[5-[[(3~{r},4~{r})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{h}-pyrrol-2-yl]methyl]-4-methyl-1~{h}-pyrrol-3-yl]propanoic acid (586 Da, Ligand)
- Phytochrome (124 kDa, Protein from Zea mays)
- Zea mays phytochrome a1 (zmphya1-pr) (Complex from Arabidopsis thaliana)
Cryo-EM structure of Arabidopsis phytochrome A.
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8iff
Q-score: 0.405
Wang J, Zhou C, Guan Z, Wang Q, Zhao J, Wang L, Zhang L, Zhang D, Deng XW, Ma L, Yin P
Cell Res (2023) 33 pp. 802-805 [ Pubmed: 37402899 DOI: doi:10.1038/s41422-023-00847-7 ]
- 3-[5-[[(3~{r},4~{r})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{h}-pyrrol-2-yl]methyl]-4-methyl-1~{h}-pyrrol-3-yl]propanoic acid (586 Da, Ligand)
- Phytochrome a (Complex from Arabidopsis thaliana)
- Phytochrome a (124 kDa, Protein from Arabidopsis thaliana)
SARS-CoV-2 spike glycoprotein trimer in closed state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7wgv
Q-score: 0.513
Zhao MM, Zhu Y, Zhang L, Zhong G, Tai L, Liu S, Yin G, Lu J, He Q, Li MJ, Zhao RX, Wang H, Huang W, Fan C, Shuai L, Wen Z, Wang C, He X, Chen Q, Liu B, Xiong X, Bu Z, Wang Y, Sun F, Yang JK
Cell Discov (2022) 8 pp. 53- [ DOI: doi:10.1038/s41421-022-00419-w ]
- 3-[5-[(z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1h-pyrrol-2-yl]methyl]-4-methyl-1h-pyrrol-3-yl]propanoic acid (584 Da, Ligand)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 b.1.1.7 spike glycoprotein trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
- Linoleic acid (280 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 spike glycoprotein trimer in closed state after treatment with Cathepsin L
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7wgx
Q-score: 0.468
Zhao MM, Zhu Y, Zhang L, Zhong G, Tai L, Liu S, Yin G, Lu J, He Q, Li MJ, Zhao RX, Wang H, Huang W, Fan C, Shuai L, Wen Z, Wang C, He X, Chen Q, Liu B, Xiong X, Bu Z, Wang Y, Sun F, Yang JK
Cell Discov (2022) 8 pp. 53- [ DOI: doi:10.1038/s41421-022-00419-w ]
- 3-[5-[(z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1h-pyrrol-2-yl]methyl]-4-methyl-1h-pyrrol-3-yl]propanoic acid (584 Da, Ligand)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 b.1.1.7 spike glycoprotein trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7v6y
Q-score: 0.448
Luo Y, Wan G, Zhang X, Zhou X, Wang Q, Fan J, Cai H, Ma L, Wu H, Qu Q, Cong Y, Zhao Y, Li D
Structure (2021) 29 pp. 1286- [ Pubmed: 34174188 DOI: doi:10.1016/j.str.2021.06.004 ]
- Cholesterol (386 Da, Ligand)
- Protein patched homolog 1,protein patched homolog 1 (121 kDa, Protein from Mus musculus)
- Ptc1 in lipid nanodisc (160 MDa, Complex from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- (2s)-2-azanyl-3-[[(2s)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid (481 Da, Ligand)