Cryo-EM structure of MraY in complex with analogue 2
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 9b70
Q-score: 0.561
Yamamoto K, Sato T, Hao A, Asao K, Kaguchi R, Kusaka S, Ruddarraju RR, Kazamori D, Seo K, Takahashi S, Horiuchi M, Yokota SI, Lee SY, Ichikawa S
Nat Commun (2024) 15 pp. 5085-5085 [ Pubmed: 38877016 DOI: doi:10.1038/s41467-024-49484-7 ]
- Complex of mray aa dimer with nanobody bound (200 kDa, Complex from Aquifex aeolicus VF5)
- Water (18 Da, Ligand)
- Phospho-n-acetylmuramoyl-pentapeptide-transferase (40 kDa, Protein from Aquifex aeolicus VF5)
- Mrayaa nanobody (15 kDa, Protein from Lama glama)
- (2~{s},3~{s})-3-[(2~{s},3~{r},4~{s},5~{r})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-2-[[3-[[[(2~{s})-6-azanyl-2-(hexadecanoylamino)hexanoyl]amino]methyl]phenyl]methylamino]-3-[(2~{s},3~{s},4~{r},5~{r})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propanoic acid (934 Da, Ligand)
Cryo-EM structure of MraY in complex with analogue 3
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9b71
Q-score: 0.585
Yamamoto K, Sato T, Hao A, Asao K, Kaguchi R, Kusaka S, Ruddarraju RR, Kazamori D, Seo K, Takahashi S, Horiuchi M, Yokota SI, Lee SY, Ichikawa S
Nat Commun (2024) 15 pp. 5085-5085 [ Pubmed: 38877016 DOI: doi:10.1038/s41467-024-49484-7 ]
- Complex of mray aa dimer with nanobody bound (200 kDa, Complex from Aquifex aeolicus VF5)
- Water (18 Da, Ligand)
- Phospho-n-acetylmuramoyl-pentapeptide-transferase (40 kDa, Protein from Aquifex aeolicus VF5)
- Mrayaa nanobody (15 kDa, Protein from Lama glama)
- (2~{s},3~{s})-3-[(2~{s},3~{r},4~{s},5~{r})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-[(2~{s},3~{s},4~{r},5~{r})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]-2-[[4-[[[(2~{s})-5-carbamimidamido-2-(hexadecanoylamino)pentanoyl]amino]methyl]phenyl]methylamino]propanoic acid (962 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)/g(s)/g(t) subunit beta-1 (Complex from Rattus norvegicus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (Complex from Bos taurus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Human gpr34-gi complex bound to s3e-lysops (Complex)
- (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)
- Scfv16 (Complex from Mus musculus)
- Scfv16 (27 kDa, Protein from Mus musculus)
- 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) subunit alpha-1 (Complex from Homo sapiens)
- 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 (Complex 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 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Rattus norvegicus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (Complex from Bos taurus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Probable g-protein coupled receptor 34 (45 kDa, Protein from Homo sapiens)
- Human gpr34-gi complex bound to m1 (Complex)
- Scfv16 (Complex from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- 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(t) subunit beta-1 (37 kDa, Protein from Rattus norvegicus)
- (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)
- Probable g-protein coupled receptor 34 (Complex from Homo sapiens)
Human GPR34 -Gi complex bound to M1, receptor focused
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8xbi
Q-score: 0.457
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)
- Probable g-protein coupled receptor 34 (45 kDa, Protein from Homo sapiens)
- Human gpr34-gi complex bound to m1,receptor focused (Complex from Homo sapiens)
CryoEM structure of SARS-CoV-2 spike monomer in complex with neutralising antibody P008_60
Resolution: 4.31 Å
EM Method: Single-particle
Fitted PDBs: 7zbu
Q-score: 0.209
Seow J, Khan H, Rosa A, Calvaresi V, Graham C, Pickering S, Pye VE, Cronin NB, Huettner I, Malim MH, Politis A, Cherepanov P, Doores KJ
Cell Rep (2022) 40 pp. 111276-111276 [ Pubmed: 35981534 DOI: doi:10.1016/j.celrep.2022.111276 ]
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- P008_60 antibody, heavy chain (25 kDa, Protein from Homo sapiens)
- 3-[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-2-[[5-[(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1h-pyrrol-2-yl]methyl]-4-methyl-1h-pyrrol-3-yl]propanoic acid (588 Da, Ligand)
- Monomeric spike glycoprotein ectodomain from sars-cov-2 in complex with a neutralising antibody p008_60 (125 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- P008_60 antibody, light chain (23 kDa, Protein from Homo sapiens)