Sarbecovirus YN2013 Spike Trimer in a Locked Conformation
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 8zy4
Q-score: 0.568
To Be Published
- The spike protein of yn2013 strain (450 kDa, Cellular component from BtRs-BetaCoV/YN2013)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 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 (137 kDa, Protein from BtRs-BetaCoV/YN2013)
Structure of chanoclavine synthase from Claviceps fusiformis in complex with prechanoclavine
Resolution: 2.33 Å
EM Method: Single-particle
Fitted PDBs: 9jdc
Q-score: 0.693
Liu ZW, Wang T, Li X, Shen PP, Huang J-W, Chen C-C, Guo R-T
To Be Published
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (2~{s})-2-(methylamino)-3-[4-[(1~{e})-3-methylbuta-1,3-dienyl]-1~{h}-indol-3-yl]propanoic acid (284 Da, Ligand)
- Catalase easc (54 kDa, Protein from Claviceps fusiformis)
- Ergot alkaloid synthesis protein c (Complex from Claviceps fusiformis)
Resolution: 2.37 Å
EM Method: Single-particle
Fitted PDBs: 8yak
Q-score: 0.652
Hu Y, Dai L, Xu Y, Niu D, Yang X, Xie Z, Shen P, Li X, Li H, Zhang L, Min J, Guo RT, Chen CC
Int J Biol Macromol (2024) 278 pp. 134831-134831 [ Pubmed: 39163957 DOI: doi:10.1016/j.ijbiomac.2024.134831 ]
- (2~{s})-2-[[(3~{r})-5-chloranyl-3-methyl-8-oxidanyl-1-oxidanylidene-3,4-dihydroisochromen-7-yl]carbonylamino]-3-phenyl-propanoic acid (403 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Imidazolonepropionase (43 kDa, Protein from Pseudoxanthomonas wuyuanensis)
- Pwadh-g88d-d344n (Complex from Pseudoxanthomonas wuyuanensis)
Cryo-EM structure of the GLP-1(9-36)-bound human GLP-1R-Gs complex in the presence of LSN3318839
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 9ivm
Q-score: 0.455
Li J, Li G, Mai Y, Liu X, Yang D, Zhou Q, Wang MW
Acta Pharm Sin B (2024) 14 pp. 5069-5073 [ Pubmed: 39664415 DOI: doi:10.1016/j.apsb.2024.09.002 ]
- Cryo-em structure of the glp-1(9-36)-bound human glp-1r-gs complex in the presence of lsn3318839 (Complex from Homo sapiens)
- Glp-1(9-36) (3 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Nanobody-35 (15 kDa, Protein from Homo sapiens)
- 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)
- Glucagon-like peptide 1 receptor (50 kDa, Protein from Homo sapiens)
- (2~{r})-2-[2-[1-[(1~{r})-1-[2,6-bis(chloranyl)-3-cyclopropyl-phenyl]ethyl]imidazo[4,5-c]pyridin-6-yl]phenyl]propanoic acid (480 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
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 [ Pubmed: 39317197 DOI: doi:10.1016/j.cell.2024.09.005 ]
- Complex of atphyb-pfr homodimer (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)
- Pif6 monomer (Complex)
- Phytochrome-interacting factor 6 (11 kDa, Protein from Arabidopsis thaliana)
- Phytochrome b (129 kDa, Protein from Arabidopsis thaliana)
- Ternary complex of atphyb-pfr homodimer with atpif6 (120 kDa, Complex 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 [ Pubmed: 39317197 DOI: doi:10.1016/j.cell.2024.09.005 ]
- Complex of phyb mutant(y276h) homodimer (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-interacting factor 6 (11 kDa, Protein from Arabidopsis thaliana)
- Pif6 monomer (Complex)
- Ternary complex of phyb mutant(y276h) with pif6 (100 kDa, Complex from Arabidopsis thaliana)
- Phytochrome b (99 kDa, Protein from Arabidopsis thaliana)
CryoEM structure of Deinococcus radiodurans BphP photosensory module in Pr state
To Be Published
- Bacteriophytochrome (84 kDa, Protein from Deinococcus radiodurans)
- Deinococcus radiodurans bphp (163 kDa, Complex from Deinococcus radiodurans)
- 3-[2-[(z)-[3-(2-carboxyethyl)-5-[(z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(z)-[(3e)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1h-pyrrol-3- yl]propanoic acid (585 Da, Ligand)
Human GPR34 -Gi complex bound to S3E-LysoPS
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8xbe
Q-score: 0.445
Izume T, Kawahara R, Uwamizu A, Chen L, Yaginuma S, Omi J, Kawana H, Hou F, Sano FK, Tanaka T, Kobayashi K, Okamoto HH, Kise Y, Ohwada T, Aoki J, Shihoya W, Nureki O
Nat Commun (2024) 15 pp. 902-902 [ DOI: doi:10.1038/s41467-024-45046-z Pubmed: 38326347 ]
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Human gpr34-gi complex bound to s3e-lysops (Complex)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Rattus norvegicus)
- Probable g-protein coupled receptor 34 (Complex from Homo sapiens)
- Scfv16 (27 kDa, Protein from Mus musculus)
- (2~{s})-2-azanyl-3-[[(2~{r})-1-ethoxy-3-[(~{z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid (551 Da, Ligand)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (Complex 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(o) subunit gamma-2 (Complex from Bos taurus)
- Scfv16 (Complex from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus norvegicus)
- Probable g-protein coupled receptor 34 (45 kDa, Protein from Homo sapiens)
Human GPR34 -Gi complex bound to S3E-LysoPS, receptor focused
Resolution: 3.43 Å
EM Method: Single-particle
Fitted PDBs: 8xbg
Q-score: 0.42
Izume T, Kawahara R, Uwamizu A, Chen L, Yaginuma S, Omi J, Kawana H, Hou F, Sano FK, Tanaka T, Kobayashi K, Okamoto HH, Kise Y, Ohwada T, Aoki J, Shihoya W, Nureki O
Nat Commun (2024) 15 pp. 902-902 [ DOI: doi:10.1038/s41467-024-45046-z Pubmed: 38326347 ]
- Human gpr34-gi complex bound to s3e-lysops, receptor focused (Complex from Homo sapiens)
- (2~{s})-2-azanyl-3-[[(2~{r})-1-ethoxy-3-[(~{z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid (551 Da, Ligand)
- Probable g-protein coupled receptor 34 (45 kDa, Protein from Homo sapiens)
Human GPR34 -Gi complex bound to M1
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 8xbh
Q-score: 0.473
Izume T, Kawahara R, Uwamizu A, Chen L, Yaginuma S, Omi J, Kawana H, Hou F, Sano FK, Tanaka T, Kobayashi K, Okamoto HH, Kise Y, Ohwada T, Aoki J, Shihoya W, Nureki O
Nat Commun (2024) 15 pp. 902-902 [ DOI: doi:10.1038/s41467-024-45046-z Pubmed: 38326347 ]
- (2~{s})-2-azanyl-3-[[(2~{r})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid (617 Da, Ligand)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Rattus norvegicus)
- Probable g-protein coupled receptor 34 (Complex from Homo sapiens)
- Human gpr34-gi complex bound to m1 (Complex)
- Scfv16 (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (Complex 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(o) subunit gamma-2 (Complex from Bos taurus)
- Scfv16 (Complex from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus norvegicus)
- Probable g-protein coupled receptor 34 (45 kDa, Protein from Homo sapiens)