Resolution: 2.11 Å
EM Method: Single-particle
Fitted PDBs: 8z8z
Q-score: 0.589
Xiong Q, Zhu Z, Li T, Li X, Zhou Z, Chao Y, Yang C, Feng S, Qu Q, Li D
Nat Struct Mol Biol (2025) [ DOI: doi:10.1038/s41594-024-01474-5 Pubmed: 39824977 ]
- Lychos (127 kDa, Complex from Homo sapiens)
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (717 Da, Ligand)
- Water (18 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (4~{z},7~{z},10~{z},13~{z},16~{z},19~{z})-docosa-4,7,10,13,16,19-hexaenoate (764 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Lysosomal cholesterol signaling protein,fluorescent protein (127 kDa, Protein from synthetic construct)
FCP tetramer in Chaetoceros gracilis
Resolution: 2.71 Å
EM Method: Single-particle
Fitted PDBs: 8wck
Q-score: 0.586
Zhou C, Feng Y, Li Z, Shen L, Li X, Wang Y, Han G, Kuang T, Liu C, Shen JR, Wang W
Plant Commun. (2024) 5 pp. 101041-101041 [ Pubmed: 39030906 DOI: doi:10.1016/j.xplc.2024.101041 ]
- Chlorophyll c2 (608 Da, Ligand)
- Fcp tetramer (Complex from Chaetoceros neogracilis)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Chlorophyll c1 (610 Da, Ligand)
- Chlorophyll a/b-binding protein (22 kDa, Protein from Chaetoceros neogracilis)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
FCP pentamer in Chaetoceros gracilis
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 8wcl
Q-score: 0.585
Zhou C, Feng Y, Li Z, Shen L, Li X, Wang Y, Han G, Kuang T, Liu C, Shen JR, Wang W
Plant Commun. (2024) 5 pp. 101041-101041 [ Pubmed: 39030906 DOI: doi:10.1016/j.xplc.2024.101041 ]
- Fcp pentamer in chaetoceros gracilis (Complex from Chaetoceros neogracilis)
- Chlorophyll a/c-binding protein lhcf6 (22 kDa, Protein from Chaetoceros neogracilis)
- Chlorophyll c2 (608 Da, Ligand)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Chlorophyll c1 (610 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll a/b-binding protein (22 kDa, Protein from Chaetoceros neogracilis)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Fucoxanthin-chlorophyll a/c protein (21 kDa, Protein from Chaetoceros neogracilis)
- Chlorophyll a/c-binding protein lhcf7 (22 kDa, Protein from Chaetoceros neogracilis)
- Chlorophyll a (893 Da, Ligand)
A neutralizing nanobody VHH60 against wt SARS-CoV-2
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8xki
Q-score: 0.441
Liu Q, Lu Y, Cai C, Huang Y, Zhou L, Guan Y, Fu S, Lin Y, Yan H, Zhang Z, Li X, Yang X, Yang H, Guo H, Lan K, Chen Y, Hou SC, Xiong Y
Cell Death Dis (2024) 15 pp. 458-458 [ Pubmed: 38937437 DOI: doi:10.1038/s41419-024-06802-7 ]
- Nanobody vhh60 (13 kDa, Protein from synthetic construct)
- Spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike glycoprotein complex with vhh60 nanobody (Complex)
- Nanobody (Complex from synthetic construct)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
FCP trimer in diatom Thalassiosira pseudonana
Resolution: 2.73 Å
EM Method: Single-particle
Fitted PDBs: 8jp3
Q-score: 0.575
Zhou C, Feng Y, Li Z, Shen L, Li X, Wang Y, Han G, Kuang T, Liu C, Shen JR, Wang W
Plant Commun. (2024) 5 pp. 101041-101041 [ Pubmed: 39030906 DOI: doi:10.1016/j.xplc.2024.101041 ]
- Chlorophyll c2 (608 Da, Ligand)
- Fucoxanthin chlorophyll a/c protein 8 (19 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Fcp trimer (Complex from Thalassiosira pseudonana CCMP1335)
- Chlorophyll c1 (610 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
V gamma9 V delta2 TCR and CD3 complex in LMNG
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8jc0
Q-score: 0.438
Xin W, Huang B, Chi X, Liu Y, Xu M, Zhang Y, Li X, Su Q, Zhou Q
Nature (2024) 630 pp. 222-229 [ Pubmed: 38657677 DOI: doi:10.1038/s41586-024-07439-4 ]
- T-cell surface glycoprotein cd3 epsilon chain (23 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 gamma chain (20 kDa, Protein from Homo sapiens)
- T cell receptor gamma variable 9,t cell receptor gamma constant 1 (37 kDa, Protein from Homo sapiens)
- T cell receptor delta variable 2,t cell receptor delta constant (34 kDa, Protein from Homo sapiens)
- V gamma9 v delta2 t cell receptor in complex with cd3 (Complex from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- T-cell surface glycoprotein cd3 delta chain (18 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 zeta chain (21 kDa, Protein from Homo sapiens)
Vgamma5Vdelta1 EH TCR-CD3 complex
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8wxe
Q-score: 0.329
Xin W, Huang B, Chi X, Liu Y, Xu M, Zhang Y, Li X, Su Q, Zhou Q
Nature (2024) 630 pp. 222-229 [ Pubmed: 38657677 DOI: doi:10.1038/s41586-024-07439-4 ]
- T-cell surface glycoprotein cd3 epsilon chain (23 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 gamma chain (20 kDa, Protein from Homo sapiens)
- T cell receptor delta 1 gamma 5 eh mutant (Complex from Homo sapiens)
- Signal peptide,flag tag,t cell receptor gamma variable 5,t cell receptor gamma constant 1 (37 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- T-cell surface glycoprotein cd3 delta chain (18 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 zeta chain (21 kDa, Protein from Homo sapiens)
- Signal peptide,flag tag,t cell receptor delta variable 1,t cell receptor delta constant (34 kDa, Protein from Homo sapiens)
T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8wy0
Q-score: 0.402
Xin W, Huang B, Chi X, Liu Y, Xu M, Zhang Y, Li X, Su Q, Zhou Q
Nature (2024) 630 pp. 222-229 [ Pubmed: 38657677 DOI: doi:10.1038/s41586-024-07439-4 ]
- T-cell surface glycoprotein cd3 epsilon chain (23 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 gamma chain (20 kDa, Protein from Homo sapiens)
- T cell receptor delta 2 gamma 9 with f283a, f290a, f291a (Cell from Homo sapiens)
- Signal peptide,flag tag,t cell receptor gamma variable 9,t cell receptor gamma constant 1 (37 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Signal peptide,flag tag,t cell receptor delta variable 2,t cell receptor delta constant (34 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 delta chain (18 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 zeta chain (21 kDa, Protein from Homo sapiens)
T cell receptor V delta2 V gamma9 in GDN
Resolution: 4.12 Å
EM Method: Single-particle
Fitted PDBs: 8yc0
Q-score: 0.349
Xin W, Huang B, Chi X, Liu Y, Xu M, Zhang Y, Li X, Su Q, Zhou Q
Nature (2024) 630 pp. 222-229 [ Pubmed: 38657677 DOI: doi:10.1038/s41586-024-07439-4 ]
- T-cell surface glycoprotein cd3 epsilon chain (23 kDa, Protein from Homo sapiens)
- Tcr v delta2 v gamma 9 in complex with cd3 in gdn (Cell from Homo sapiens)
- T-cell surface glycoprotein cd3 gamma chain (20 kDa, Protein from Homo sapiens)
- T cell receptor gamma variable 9,t cell receptor gamma constant 1 (37 kDa, Protein from Homo sapiens)
- T cell receptor delta variable 2,t cell receptor delta constant (34 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- T-cell surface glycoprotein cd3 delta chain (18 kDa, Protein from Homo sapiens)
- T-cell surface glycoprotein cd3 zeta chain (21 kDa, Protein from Homo sapiens)
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8j5k
Q-score: 0.504
Zhao S, Shen L, Li X, Tao Q, Li Z, Xu C, Zhou C, Yang Y, Sang M, Han G, Yu LJ, Kuang T, Shen JR, Wang W
Nat Commun (2023) 14 pp. 8164-8164 [ DOI: doi:10.1038/s41467-023-44055-8 Pubmed: 38071196 ]
- Psbe (8 kDa, Protein from Stephanocyclus meneghinianus)
- Psbu (10 kDa, Protein from Stephanocyclus meneghinianus)
- Psbm (4 kDa, Protein from Stephanocyclus meneghinianus)
- Beta-carotene (536 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- (1~{r})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- Psbf (3 kDa, Protein from Stephanocyclus meneghinianus)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Fcpii-j, fucoxanthin chlorophyll a/c binding protein (17 kDa, Protein from Stephanocyclus meneghinianus)
- Psby (3 kDa, Protein from Stephanocyclus meneghinianus)
- Psbt (3 kDa, Protein from Stephanocyclus meneghinianus)
- Psbb (53 kDa, Protein from Stephanocyclus meneghinianus)
- Fcpii-i, fucoxanthin chlorophyll a/c binding protein (23 kDa, Protein from Stephanocyclus meneghinianus)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Psbd (37 kDa, Protein from Stephanocyclus meneghinianus)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Psbx (3 kDa, Protein from Stephanocyclus meneghinianus)
- Psbo (26 kDa, Protein from Stephanocyclus meneghinianus)
- Psbz (6 kDa, Protein from Stephanocyclus meneghinianus)
- Fcpii-g, fucoxanthin chlorophyll a/c binding protein (18 kDa, Protein from Stephanocyclus meneghinianus)
- Pheophytin a (871 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Fcpii-h2, fucoxanthin chlorophyll a/c binding protein (18 kDa, Protein from Stephanocyclus meneghinianus)
- Psbk (4 kDa, Protein from Stephanocyclus meneghinianus)
- Psbw (5 kDa, Protein from Stephanocyclus meneghinianus)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Psbh (7 kDa, Protein from Stephanocyclus meneghinianus)
- Psb34 (2 kDa, Protein from Stephanocyclus meneghinianus)
- Fcpii-k, fucoxanthin chlorophyll a/c binding protein (13 kDa, Protein from Stephanocyclus meneghinianus)
- Cm-psii-fcpii (Complex from Stephanocyclus meneghinianus)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Psbc (49 kDa, Protein from Stephanocyclus meneghinianus)
- Fcpii-h1, fucoxanthin chlorophyll a/c binding protein (18 kDa, Protein from Stephanocyclus meneghinianus)
- Psbj (3 kDa, Protein from Stephanocyclus meneghinianus)
- Chlorophyll a (893 Da, Ligand)
- Psbl (4 kDa, Protein from Stephanocyclus meneghinianus)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Psbv (14 kDa, Protein from Stephanocyclus meneghinianus)
- Chloride ion (35 Da, Ligand)
- Psbq' (16 kDa, Protein from Stephanocyclus meneghinianus)
- Psba (36 kDa, Protein from Stephanocyclus meneghinianus)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Psbi (3 kDa, Protein from Stephanocyclus meneghinianus)