PSI-LHCI supercomplex binding with 10 Lhcas from C. subellipsoidea
Resolution: 1.92 Å
EM Method: Single-particle
Fitted PDBs: 9kqp
Q-score: 0.723
Tsai PC, Kato K, Shen JR, Akita F
Biochim Biophys Acta Bioenerg (2025) 1866 pp. 149543-149543 [ Pubmed: 39947506 DOI: doi:10.1016/j.bbabio.2025.149543 ]
- Photosystem i reaction center subunit v, chloroplastic (14 kDa, Protein from Coccomyxa subellipsoidea C-169)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Coccomyxa subellipsoidea C-169)
- [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate-oxy)-ethyl]-trimethylammonium (440 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Coccomyxa subellipsoidea C-169)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a-b binding protein, chloroplastic (26 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Photosystem i reaction center subunit ii, chloroplastic (20 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll b (907 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a-b binding protein, chloroplastic (26 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Unknown ligand (254 Da, Ligand)
- Photosystem i psao (15 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Phylloquinone (450 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Coccomyxa subellipsoidea C-169)
- (3~{e},5~{e},7~{e})-6-methyl-8-[(6~{r})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one (260 Da, Ligand)
- Green alga photosystem i lhci supercomplex binding with 10 lhcas (Complex from Coccomyxa subellipsoidea C-169)
- Photosystem i iron-sulfur center (8 kDa, Protein from Coccomyxa subellipsoidea C-169)
- 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 reaction center subunit iii (25 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a-b binding protein, chloroplastic/lhca2 (29 kDa, Protein from Coccomyxa subellipsoidea C-169)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem i reaction centre subunit vi (14 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Psi subunit v (21 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Astaxanthin (596 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction centre subunit iv/psae (8 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Psi-k (13 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Coccomyxa subellipsoidea C-169)
Resolution: 1.97 Å
EM Method: Single-particle
Fitted PDBs: 9eh5
Q-score: 0.703
Flesher DA, Shin J, Debus RJ, Brudvig GW
J Biol Chem (2025) pp. 108272-108272 [ Pubmed: 39922494 DOI: doi:10.1016/j.jbc.2025.108272 ]
- Cytochrome c-550 (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii reaction center protein h (7 kDa, Protein from Synechocystis sp. PCC 6803)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii (Complex from Synechocystis sp. PCC 6803)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Synechocystis sp. PCC 6803)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosystem ii protein d1 2 (38 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii cp47 reaction center protein (55 kDa, Protein from Synechocystis sp. PCC 6803)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein k (5 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii reaction center protein l (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii reaction center x protein (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii reaction center protein t (3 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii cp43 reaction center protein (50 kDa, Protein from Synechocystis sp. PCC 6803)
- Sll1638 protein (16 kDa, Protein from Synechocystis sp. PCC 6803)
- Pheophytin a (871 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii reaction center protein j (3 kDa, Protein from Synechocystis sp. PCC 6803)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii protein y (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii manganese-stabilizing polypeptide (29 kDa, Protein from Synechocystis sp. PCC 6803)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Cytochrome b559 subunit beta (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
- 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)
- Photosystem ii 12 kda extrinsic protein (14 kDa, Protein from Synechocystis sp. PCC 6803)
- Chloride ion (35 Da, Ligand)
- Photosystem ii d2 protein (39 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii reaction center protein ycf12 (4 kDa, Protein from Synechocystis sp. PCC 6803)
Cryo-EM structure of coproheme decarboxylase from Corynebacterium diphtheriae in complex with heme b
Resolution: 1.94 Å
EM Method: Single-particle
Fitted PDBs: 8quo
Q-score: 0.327
Patil G, Alonso de Armino DJ, Guo Y, Furtmuller PG, Borek D, Estrin DA, Hofbauer S
Protein Sci (2025) 34 pp. e70027-e70027 [ Pubmed: 39865384 DOI: doi:10.1002/pro.70027 ]
- Coproheme decarboxylase (27 kDa, Protein from Corynebacterium diphtheriae)
- Coproheme decarboxylase from corynebacterium diphteriae in complex with heme b (132 MDa, Complex from Corynebacterium diphtheriae)
- Water (18 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
Canine parvovirus subtype 2a empty capsid in complex with Fab fragments of Mab 2C5
Adu OF, Lee H, Fruh SP, Schoenle MV, Weichert WS, Flyak AI, Hafenstein SL, Parrish CR
PNAS (2025) 122 pp. e2423460122-e2423460122 [ Pubmed: 39951487 DOI: doi:10.1073/pnas.2423460122 ]
- Capsid protein 2 (64 kDa, Protein from Canine parvovirus 2a)
- Canine parvovirus 2a (Virus from Canine parvovirus 2a)
E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)
Resolution: 1.95 Å
EM Method: Single-particle
Fitted PDBs: 9d89
Q-score: 0.692
Panteleev PV, Pichkur EB, Kruglikov RN, Paleskava A, Shulenina OV, Bolosov IA, Bogdanov IV, Safronova VN, Balandin SV, Marina VI, Kombarova TI, Korobova OV, Shamova OV, Myasnikov AG, Borzilov AI, Osterman IA, Sergiev PV, Bogdanov AA, Dontsova OA, Konevega AL, Ovchinnikova TV
Nat Commun (2024) 15 pp. 8925-8925 [ Pubmed: 39414793 DOI: doi:10.1038/s41467-024-53309-y ]
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- Potassium ion (39 Da, Ligand)
- 50s ribosomal protein l9 (4 kDa, Protein from Escherichia coli)
- E. coli 70s ribosome in complex with pramp rumicidin-2 (Complex from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- Rumicidin-2 (12-27) (2 kDa, Protein from Beatragus hunteri)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 23s rrna (885 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- (2s)-2-amino-4-(methylsulfanyl)butane-1-thiol (151 Da, Ligand)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
Beta-galactosidase (LacZ) in complex with glycosyrin from Pseudomonas syringae.
Resolution: 1.93 Å
EM Method: Single-particle
Fitted PDBs: 8ri7
Q-score: 0.792
Hardenbrook NJ, Sheng Y, Sanguankiattichai N, Zhang P, Preston G, van der Hoorn R
To Be Published
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Beta-galactosidase (117 kDa, Protein from Escherichia coli)
- Beta-galactosidase (Complex from Escherichia coli)
- Sodium ion (22 Da, Ligand)
- (2s,3r,4s)-2-[bis(oxidanyl)methyl]pyrrolidine-3,4-diol (149 Da, Ligand)
Beta-galactosidase (LacZ) in complex with synthetic glycosyrin.
Resolution: 1.42 Å
EM Method: Single-particle
Fitted PDBs: 8ri8
Q-score: 0.82
Hardenbrook NJ, Sheng Y, Sanguankiattichai N, Zhang P, Preston G, van der Hoorn R
To Be Published
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Beta-galactosidase (117 kDa, Protein from Escherichia coli)
- Beta-galactosidase (Complex from Escherichia coli)
- Sodium ion (22 Da, Ligand)
- (2s,3r,4s)-2-[bis(oxidanyl)methyl]pyrrolidine-3,4-diol (149 Da, Ligand)
LH2 complex from Ectothiorhodospira haloalkaliphila at near-atomic resolution
Resolution: 1.7 Å
EM Method: Single-particle
Fitted PDBs: 8z4v
Q-score: 0.823
Burtseva AD, Baymukhametov TN, Bolshakov MA, Makhneva ZK, Mardanov AV, Tsedilin AM, Zhang H, Popov VO, Ashikhmin AA, Boyko KM
Structure (2025) 33 pp. 311-320.e3 [ Pubmed: 39694041 DOI: doi:10.1016/j.str.2024.11.015 ]
- Light-harvesting protein b:800-850 subunit beta (5 kDa, Protein from Ectothiorhodospira haloalkaliphila ATCC 51935)
- Light-harvesting protein b-800/850 alpha chain (7 kDa, Protein from Ectothiorhodospira haloalkaliphila ATCC 51935)
- Water (18 Da, Ligand)
- Lh2 complex from ectothiorhodospira haloalkaliphila (Complex from Ectothiorhodospira haloalkaliphila)
- Bacteriochlorophyll a (911 Da, Ligand)
- Anhydrorhodovibrin (566 Da, Ligand)
Cryo-EM structure of the N2-4N2C402 complex at a resolution of 1.9 angstrom
Resolution: 1.9 Å
EM Method: Single-particle
Fitted PDBs: 8zr4
Q-score: 0.793
Wang X, Yang Q, Chu BX, Wu XD, Zhang ZL
Cell Host Microbe (2024) [ ]
- Neuraminidase (43 kDa, Protein from Influenza A virus)
- 4n2c402_fab_h (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 4n2c402_fab_l (12 kDa, Protein from Homo sapiens)
- A complex of n2 with 4n2c402-fab (500 kDa, Complex from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Structure of an STK19-containing TC-NER complex
Resolution: 1.9 Å
EM Method: Single-particle
Fitted PDBs: 9bz0
Q-score: 0.448
Mevissen TET, Kummecke M, Schmid EW, Farnung L, Walter JC
Cell (2024) 187 pp. 7091-7106.e24 [ DOI: doi:10.1016/j.cell.2024.10.020 Pubmed: 39547228 ]
- Dna (49-mer) (27 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna (35-mer) (27 kDa, DNA from synthetic construct)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Det1- and ddb1-associated protein 1 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Transcription-coupled nucleotide excision repair complex (Complex from Homo sapiens)
- Rna (5'-r(p*ap*up*cp*gp*ap*gp*ap*gp*gp*a)-3') (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Water (18 Da, Ligand)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)