PSI-FCPI-L in Thalassiosira pseudonana
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 8zeh
Q-score: 0.566
Feng Y, Li Z, Yang Y, Shen L, Li X, Liu X, Zhang X, Zhang J, Ren F, Wang Y, Liu C, Han G, Wang X, Kuang T, Shen JR, Wang W
J Integr Plant Biol (2024) [ Pubmed: 39670505 DOI: doi:10.1111/jipb.13816 ]
- Pt17531-like protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (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)
- Chlorophyll a (893 Da, Ligand)
- Tp-lhcr18 (16 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-psar (9 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Chlorophyll c1 (610 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 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)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Fucoxanthin chl a/c light-harvesting protein, major type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-lhcr20 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c light-harvesting protein (23 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Beta-carotene (536 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Tp-psi-fcpi-l (Complex from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein, lhcr type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c light-harvesting protein (19 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit psa29 (13 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Phylloquinone (450 Da, Ligand)
- Tp-redcap (20 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (19 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Tp-PSI-FCPI-S in Thalassiosira pseudonana
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8zet
Q-score: 0.485
Feng Y, Li Z, Yang Y, Shen L, Li X, Liu X, Zhang X, Zhang J, Ren F, Wang Y, Liu C, Han G, Wang X, Kuang T, Shen JR, Wang W
J Integr Plant Biol (2024) [ Pubmed: 39670505 DOI: doi:10.1111/jipb.13816 ]
- Pt17531-like protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (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)
- Chlorophyll a (893 Da, Ligand)
- Tp-psar (9 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Chlorophyll c1 (610 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 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)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein, major type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Beta-carotene (536 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit psa29 (13 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-psi-fcpi-s (Complex from Thalassiosira pseudonana CCMP1335)
- Phylloquinone (450 Da, Ligand)
- Tp-redcap (20 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Composite cryo-EM map of PhiKZ capsid after applying the "block-based" reconstruction method
Yang Y, Shao Q, Guo M, Han L, Zhao X, Wang A, Li X, Wang B, Pan JA, Chen Z, Fokine A, Sun L, Fang Q
Nat Commun (2024) 15 pp. 6551-6551 [ Pubmed: 39095371 DOI: doi:10.1038/s41467-024-50811-1 ]
- Gp86 (48 kDa, Protein from Phikzvirus phiKZ)
- Gp120 (83 kDa, Protein from Phikzvirus phiKZ)
- Gp28 (36 kDa, Protein from Phikzvirus phiKZ)
- Gp244 (13 kDa, Protein from Phikzvirus phiKZ)
- Gp35 (29 kDa, Protein from Phikzvirus phiKZ)
- Gp162 (57 kDa, Protein from Phikzvirus phiKZ)
- Gp91 (20 kDa, Protein from Phikzvirus phiKZ)
- Gp184 (25 kDa, Protein from Phikzvirus phiKZ)
- Gp93 (47 kDa, Protein from Phikzvirus phiKZ)
- Gp85 (16 kDa, Protein from Phikzvirus phiKZ)
- Gp119 (20 kDa, Protein from Phikzvirus phiKZ)
- Phikzvirus phikz (Virus from Phikzvirus phiKZ)
Structure of PSII-ACPII supercomplex from cryptophyte algae
Resolution: 2.47 Å
EM Method: Single-particle
Fitted PDBs: 8wb4
Q-score: 0.539
Mao Z, Li X, Li Z, Shen L, Li X, Yang Y, Wang W, Kuang T, Shen JR, Han G
Nat Commun (2024) 15 pp. 4535-4535 [ Pubmed: 38806516 DOI: doi:10.1038/s41467-024-48878-x ]
- Acpii-6 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center x protein (4 kDa, Protein from Chroomonas placoidea)
- Chlorophyll a (893 Da, Ligand)
- Acpii-5 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem ii d2 protein (39 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chroomonas placoidea)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chroomonas placoidea)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii cp43 reaction center protein (50 kDa, Protein from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(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-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol (564 Da, Ligand)
- Acpii-3 (24 kDa, Protein from Chroomonas placoidea)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Acpii-2 (23 kDa, Protein from Chroomonas placoidea)
- 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)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem ii reaction center protein r (2 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chroomonas placoidea)
- Acpii-4 (23 kDa, Protein from Chroomonas placoidea)
- Ccpii-s (30 kDa, Protein from Chroomonas placoidea)
- Structure of psii-acpii supercomplex from cryptophyte algae (Complex from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (550 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chroomonas placoidea)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chroomonas placoidea)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein w (11 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein j (3 kDa, Protein from Chroomonas placoidea)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Acpii-1 (25 kDa, Protein from Chroomonas placoidea)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chroomonas placoidea)
- Photosystem ii cytochrome c550 (17 kDa, Protein from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein k (5 kDa, Protein from Chroomonas placoidea)
- Chlorophyll c2 (608 Da, Ligand)
- Photosystem ii reaction center protein o (34 kDa, Protein from Chroomonas placoidea)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein q (1 kDa, Protein from Chroomonas placoidea)
- Photosystem ii protein d1 (39 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein g (5 kDa, Protein from Chroomonas placoidea)
- Chloride ion (35 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii reaction center m (11 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein u (15 kDa, Protein from Chroomonas placoidea)
Structure of ACPII-CCPII from cryptophyte algae
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 8xkl
Q-score: 0.49
Mao Z, Li X, Li Z, Shen L, Li X, Yang Y, Wang W, Kuang T, Shen JR, Han G
Nat Commun (2024) 15 pp. 4535-4535 [ Pubmed: 38806516 DOI: doi:10.1038/s41467-024-48878-x ]
- Acpii-6 (23 kDa, Protein from Chroomonas placoidea)
- Acpii-1 (25 kDa, Protein from Chroomonas placoidea)
- Acpii-4 (23 kDa, Protein from Chroomonas placoidea)
- Chlorophyll a (893 Da, Ligand)
- Acpii-5 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein g (5 kDa, Protein from Chroomonas placoidea)
- Ccpii-s (30 kDa, Protein from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (550 Da, Ligand)
- (1~{r})-3,5,5-trimethyl-4-[(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-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol (564 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- Structure of acpii-ccpii from cryptophyte algae (Complex from Chroomonas placoidea)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll c2 (608 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Acpii-3 (24 kDa, Protein from Chroomonas placoidea)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Acpii-2 (23 kDa, Protein from Chroomonas placoidea)
Structure of African swine fever virus topoisomerase II
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8kgl
Q-score: 0.303
Cong J, Xin Y, Kang H, Yang Y, Wang C, Zhao D, Li X, Rao Z, Chen Y
Nat Commun (2024) 15 pp. 4607-4607 [ Pubmed: 38816407 DOI: doi:10.1038/s41467-024-49047-w ]
- Dna topoisomerase 2 (138 kDa, Protein from African swine fever virus LIS57)
- Pp1192r (Complex from African swine fever virus)
Structure of African swine fever virus topoisomerase II in complex with dsDNA
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 8kgm
Q-score: 0.157
Cong J, Xin Y, Kang H, Yang Y, Wang C, Zhao D, Li X, Rao Z, Chen Y
Nat Commun (2024) 15 pp. 4607-4607 [ Pubmed: 38816407 DOI: doi:10.1038/s41467-024-49047-w ]
- Dna (38-mer) (16 kDa, DNA from DNA molecule)
- Dna (38-mer) (15 kDa, DNA from DNA molecule)
- Dna topoisomerase 2 (138 kDa, Protein from African swine fever virus)
- Pp1192r (Complex from African swine fever virus)