Photosynthetic LH2-LH1 complex from the purple bacterium Halorhodospira halophila
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8z81
Q-score: 0.682
Tani K, Nagashima KVP, Kojima R, Kondo M, Kanno R, Satoh I, Kawakami M, Hiwatashi N, Nakata K, Nagashima S, Inoue K, Isawa Y, Morishita R, Takaichi S, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Humbel BM, Kimura Y, Nagasawa Y, Dewa T, Wang-Otomo ZY
Nat Commun (2025) 16 pp. 1410-1410 [ DOI: doi:10.1038/s41467-024-55811-9 Pubmed: 39915441 ]
- Antenna complex, alpha/beta subunit (7 kDa, Protein from Halorhodospira halophila)
- Antenna complex, alpha/beta subunit (8 kDa, Protein from Halorhodospira halophila)
- Bacteriochlorophyll a (911 Da, Ligand)
- Photosynthetic lh2-lh1 complex from the purple phototrophic bacterium halorhodospira halophila (Complex from Halorhodospira halophila)
- Antenna complex, alpha/beta subunit (6 kDa, Protein from Halorhodospira halophila)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Lh2-lh1 complex of halorhodospira halophila (Complex from Halorhodospira halophila)
- Antenna complex, alpha/beta subunit (7 kDa, Protein from Halorhodospira halophila)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Antenna complex, alpha/beta subunit (7 kDa, Protein from Halorhodospira halophila)
- Spirilloxanthin (596 Da, Ligand)
- Antenna complex, alpha/beta subunit (7 kDa, Protein from Halorhodospira halophila)
Structure of LAT1-CD98hc-Fab170 in complex with BCH, consensus map
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 8kdg
Q-score: 0.424
Lee Y, Jin C, Ohgaki R, Xu M, Ogasawara S, Warshamanage R, Yamashita K, Murshudov G, Nureki O, Murata T, Kanai Y
Nat Commun (2025) 16 pp. 1635-1635 [ Pubmed: 39952931 DOI: doi:10.1038/s41467-025-56903-w ]
- Fab170 (Complex from Mus musculus)
- Fab170 light chain (24 kDa, Protein from Mus musculus)
- (1~{s},2~{r},4~{r})-2-azanylbicyclo[2.2.1]heptane-2-carboxylic acid (155 Da, Ligand)
- 4f2 cell-surface antigen heavy chain (68 kDa, Protein from Homo sapiens)
- Lat1-cd98hc-fab170 (173 kDa, Complex)
- Fab170 heavy chain (24 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Lat1-cd98hc (Complex from Homo sapiens)
- Large neutral amino acids transporter small subunit 1 (56 kDa, Protein from Homo sapiens)
Structure of LAT1-CD98hc in complex with BCH, focused on TMD
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 8kdh
Q-score: 0.45
Lee Y, Jin C, Ohgaki R, Xu M, Ogasawara S, Warshamanage R, Yamashita K, Murshudov G, Nureki O, Murata T, Kanai Y
Nat Commun (2025) 16 pp. 1635-1635 [ Pubmed: 39952931 DOI: doi:10.1038/s41467-025-56903-w ]
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- (1~{s},2~{r},4~{r})-2-azanylbicyclo[2.2.1]heptane-2-carboxylic acid (155 Da, Ligand)
- 4f2 cell-surface antigen heavy chain (68 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Large neutral amino acids transporter small subunit 1 (56 kDa, Protein from Homo sapiens)
- Lat1-cd98hc-fab170 (173 kDa, Complex from Homo sapiens)
CryoEM structure of influenza A RNP-like particle single-stranded assembled with a 12-mer RNA.
Resolution: 3.32 Å
EM Method: Helical reconstruction
Fitted PDBs: 9gan
Q-score: 0.493
Chenavier F, Zarkadas E, Freslon LL, Stelfox AJ, Schoehn G, Ruigrok RWH, Ballandras-Colas A, Crepin T
Nucleic Acids Res (2025) 53 [ DOI: doi:10.1093/nar/gkae1211 Pubmed: 39673795 ]
- Rna (5'-p(uc)6-fam3') (3 kDa, RNA from synthetic construct)
- Complex np-rna (Complex from Influenza A virus)
- Nucleoprotein (56 kDa, Protein from Influenza A virus)
- 2-[3,6-bis(oxidanylidene)-4,5-dihydroxanthen-9-yl]-4-[3-[(2r)-2-oxidanylpropoxy]propylcarbamoyl]benzoic acid (493 Da, Ligand)
CryoEM structure of influenza A RNP-like particle double-stranded assembled with a 12-mer RNA.
Resolution: 4.0 Å
EM Method: Helical reconstruction
Fitted PDBs: 9gap
Q-score: 0.303
Chenavier F, Zarkadas E, Freslon LL, Stelfox AJ, Schoehn G, Ruigrok RWH, Ballandras-Colas A, Crepin T
Nucleic Acids Res (2025) 53 [ DOI: doi:10.1093/nar/gkae1211 Pubmed: 39673795 ]
- Complex np-rna (Complex)
- Nucleoprotein (56 kDa, Protein from Influenza A virus)
- Rna (5'-p(uc)6-fam3') (3 kDa, RNA from synthetic construct)
- Rna (Complex from synthetic construct)
- 2-[3,6-bis(oxidanylidene)-4,5-dihydroxanthen-9-yl]-4-[3-[(2r)-2-oxidanylpropoxy]propylcarbamoyl]benzoic acid (493 Da, Ligand)
- Nucleoprotein (Complex from Influenza A virus)
Resolution: 3.08 Å
EM Method: Helical reconstruction
Fitted PDBs: 9gas
Q-score: 0.531
Chenavier F, Zarkadas E, Freslon LL, Stelfox AJ, Schoehn G, Ruigrok RWH, Ballandras-Colas A, Crepin T
Nucleic Acids Res (2025) 53 [ DOI: doi:10.1093/nar/gkae1211 Pubmed: 39673795 ]
- Complex np-rna (Complex)
- Nucleoprotein (56 kDa, Protein from Influenza A virus)
- Rna (Complex from synthetic construct)
- 2-[3,6-bis(oxidanylidene)-4,5-dihydroxanthen-9-yl]-4-[3-[(2r)-2-oxidanylpropoxy]propylcarbamoyl]benzoic acid (493 Da, Ligand)
- Rna (5'-p(uc)9-fam3') (5 kDa, RNA from synthetic construct)
- Nucleoprotein (Complex from Influenza A virus)
Resolution: 3.2 Å
EM Method: Helical reconstruction
Fitted PDBs: 9gat
Q-score: 0.437
Chenavier F, Zarkadas E, Freslon LL, Stelfox AJ, Schoehn G, Ruigrok RWH, Ballandras-Colas A, Crepin T
Nucleic Acids Res (2025) 53 [ DOI: doi:10.1093/nar/gkae1211 Pubmed: 39673795 ]
- Complex np-rna (Complex)
- Nucleoprotein (56 kDa, Protein from Influenza A virus)
- Rna (Complex from synthetic construct)
- 2-[3,6-bis(oxidanylidene)-4,5-dihydroxanthen-9-yl]-4-[3-[(2r)-2-oxidanylpropoxy]propylcarbamoyl]benzoic acid (493 Da, Ligand)
- Rna (5'-p(uc)9-fam3') (5 kDa, RNA from synthetic construct)
- Nucleoprotein (Complex from Influenza A virus)
Resolution: 3.04 Å
EM Method: Helical reconstruction
Fitted PDBs: 9gav
Q-score: 0.518
Chenavier F, Zarkadas E, Freslon LL, Stelfox AJ, Schoehn G, Ruigrok RWH, Ballandras-Colas A, Crepin T
Nucleic Acids Res (2025) 53 [ DOI: doi:10.1093/nar/gkae1211 Pubmed: 39673795 ]
- Complex np-rna (Complex)
- Nucleoprotein (56 kDa, Protein from Influenza A virus)
- Rna (Complex from synthetic construct)
- 2-[3,6-bis(oxidanylidene)-4,5-dihydroxanthen-9-yl]-4-[3-[(2r)-2-oxidanylpropoxy]propylcarbamoyl]benzoic acid (493 Da, Ligand)
- Rna (5'-p(uc)9-fam3') (5 kDa, RNA from synthetic construct)
- Nucleoprotein (Complex from Influenza A virus)
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 ]
- Fucoxanthin chl a/c light-harvesting protein (19 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-psar (9 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Beta-carotene (536 Da, Ligand)
- Fucoxanthin chlorophyll a/c light-harvesting protein (23 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Pt17531-like protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit xii (3 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)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Tp-redcap (20 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein, major type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-lhcr20 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Tp-lhcr18 (16 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit psa29 (13 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-psi-fcpi-l (Complex from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (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)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Phylloquinone (450 Da, Ligand)
- Fucoxanthin chl a/c light-harvesting protein, lhcr type (18 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 xi (15 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 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)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll c1 (610 Da, Ligand)
- Photosystem i reaction center subunit iii (17 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 ]
- Tp-psar (9 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-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 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)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (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)
- Tp-redcap (20 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein, major type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit psa29 (13 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Phylloquinone (450 Da, Ligand)
- Tp-psi-fcpi-s (Complex from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit xi (15 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)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Iron/sulfur cluster (351 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)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thalassiosira pseudonana CCMP1335)