PSI-LHCI supercomplex binding with 8 Lhcas from C. subellipsoidea
Resolution: 2.06 Å
EM Method: Single-particle
Fitted PDBs: 9kqq
Q-score: 0.668
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 iron-sulfur center (8 kDa, Protein from Coccomyxa subellipsoidea C-169)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit ii, chloroplastic (20 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (26 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Photosystem i reaction centre subunit iv/psae (8 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Phylloquinone (450 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a-b binding protein, chloroplastic (24 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)
- (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 reaction center subunit ix (4 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Green alga photosystem i lhci supercomplex binding with 8 lhcas (Complex from Coccomyxa subellipsoidea C-169)
- Beta-carotene (536 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (26 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Psi subunit v (21 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Astaxanthin (596 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit iii (25 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Diacyl glycerol (625 Da, Ligand)
- Photosystem i reaction center subunit v, chloroplastic (14 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Unknown ligand (254 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Psi-k (13 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Water (18 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Coccomyxa subellipsoidea C-169)
- Iron/sulfur cluster (351 Da, Ligand)
Resolution: 2.71 Å
EM Method: Single-particle
Fitted PDBs: 9fzy
Q-score: 0.673
Yin MD, Lemaire ON, Rosas Jimenez JG, Belhamri M, Shevchenko A, Hummer G, Wagner T, Murphy BJ
Science (2025) 387 pp. 498-504 [ DOI: doi:10.1126/science.adr9672 Pubmed: 39883773 ]
- Carbon monoxide dehydrogenase/acetyl-coa synthase beta subunit (67 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Nickel (ii) ion (58 Da, Ligand)
- Corrinoid iron-sulfur protein large subunit (49 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Fe(3)-ni(1)-s(4) cluster (410 Da, Ligand)
- Co-methylating acetyl-coa synthase (76 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Cobalamin (1 kDa, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Acetyl-coa decarbonylase/synthase complex subunit delta (34 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Carbon monoxide dehydrogenase/acetyl-coa synthase in complex with corrinoid/iron-sulfur protein (Complex from Clostridium autoethanogenum DSM 10061)
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 9fzz
Q-score: 0.675
Yin MD, Lemaire ON, Rosas Jimenez JG, Belhamri M, Shevchenko A, Hummer G, Wagner T, Murphy BJ
Science (2025) 387 pp. 498-504 [ DOI: doi:10.1126/science.adr9672 Pubmed: 39883773 ]
- Carbon monoxide dehydrogenase/acetyl-coa synthase beta subunit (67 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Nickel (ii) ion (58 Da, Ligand)
- Corrinoid iron-sulfur protein large subunit (49 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Fe(3)-ni(1)-s(4) cluster (410 Da, Ligand)
- Co-methylating acetyl-coa synthase (76 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Cobalamin (1 kDa, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Acetyl-coa decarbonylase/synthase complex subunit delta (34 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Carbon monoxide dehydrogenase/acetyl-coa synthase in complex with corrinoid/iron-sulfur protein (Complex from Clostridium autoethanogenum DSM 10061)
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 9g00
Q-score: 0.663
Yin MD, Lemaire ON, Rosas Jimenez JG, Belhamri M, Shevchenko A, Hummer G, Wagner T, Murphy BJ
Science (2025) 387 pp. 498-504 [ DOI: doi:10.1126/science.adr9672 Pubmed: 39883773 ]
- Carbon monoxide dehydrogenase/acetyl-coa synthase beta subunit (67 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Nickel (ii) ion (58 Da, Ligand)
- Corrinoid iron-sulfur protein large subunit (49 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Fe(3)-ni(1)-s(4) cluster (410 Da, Ligand)
- Co-methylating acetyl-coa synthase (76 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Cobalamin (1 kDa, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Acetyl-coa decarbonylase/synthase complex subunit delta (34 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Carbon monoxide dehydrogenase/acetyl-coa synthase in complex with corrinoid/iron-sulfur protein (Complex from Clostridium autoethanogenum DSM 10061)
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 9g01
Q-score: 0.706
Yin MD, Lemaire ON, Rosas Jimenez JG, Belhamri M, Shevchenko A, Hummer G, Wagner T, Murphy BJ
Science (2025) 387 pp. 498-504 [ DOI: doi:10.1126/science.adr9672 Pubmed: 39883773 ]
- Carbon monoxide dehydrogenase/acetyl-coa synthase beta subunit (67 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Nickel (ii) ion (58 Da, Ligand)
- Fe(3)-ni(1)-s(4) cluster (410 Da, Ligand)
- Co-methylating acetyl-coa synthase (76 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Carbon monoxide (28 Da, Ligand)
- Carbon monoxide dehydrogenase/acetyl-coa synthase (Complex from Clostridium autoethanogenum DSM 10061)
- Iron/sulfur cluster (351 Da, Ligand)
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 9g03
Q-score: 0.712
Yin MD, Lemaire ON, Rosas Jimenez JG, Belhamri M, Shevchenko A, Hummer G, Wagner T, Murphy BJ
Science (2025) 387 pp. 498-504 [ DOI: doi:10.1126/science.adr9672 Pubmed: 39883773 ]
- Carbon monoxide dehydrogenase/acetyl-coa synthase beta subunit (67 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Fe(3)-ni(1)-s(4) cluster (410 Da, Ligand)
- Carbon monoxide dehydrogenase/acetyl-coa synthase in complex with ferredoxin (Complex from Clostridium autoethanogenum DSM 10061)
- Co-methylating acetyl-coa synthase (76 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Ferredoxin (5 kDa, Protein from Clostridium autoethanogenum DSM 10061)
- Iron/sulfur cluster (351 Da, Ligand)
SIRT7-H3K36MTUnucleosome complex
Carlos MY, Babatunde E, Polina F, Esther S, Dongchun N, Henning S, Beat F
To Be Published
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- [[(2~{r},3~{a}~{r},5~{r},6~{r},6~{a}~{r})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{r},3~{s},4~{r},5~{r})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate (673 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- K36 structure (Complex from Homo sapiens)
- Histone h2a type 2-a (13 kDa, Protein from Homo sapiens)
- Dna (149-mer) (46 kDa, DNA from Homo sapiens)
- Nad-dependent protein deacetylase sirtuin-7 (45 kDa, Protein from Homo sapiens)
- Dna (149-mer) (45 kDa, DNA from Homo sapiens)
Native human GABAA receptor of beta2-alpha1-beta2-alpha1-gamma2 assembly
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9crs
Q-score: 0.509
Zhou J, Noviello CM, Teng J, Moore H, Lega B, Hibbs RE
Nature (2025) 638 pp. 562-568 [ Pubmed: 39843743 DOI: doi:10.1038/s41586-024-08454-1 ]
- Kappa fab_1f4 light chain (23 kDa, Protein from Mus musculus)
- Gamma-aminobutyric acid receptor subunit gamma-2 (50 kDa, Protein from Homo sapiens)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit beta-2 (56 kDa, Protein from Homo sapiens)
- Native gabaa receptor from human brain (Complex from Homo sapiens)
- Gamma-aminobutyric acid receptor subunit alpha-1 (48 kDa, Protein from Homo sapiens)
- Igg2b fab_1f4 heavy chain (49 kDa, Protein from Mus musculus)
The structure of type III CRISPR-associated deaminase in complex cA4
Resolution: 2.28 Å
EM Method: Single-particle
Fitted PDBs: 8z3r
Q-score: 0.605
Li Y, Li Z, Yan P, Hua C, Kong J, Wu W, Cui Y, Duan Y, Li S, Li G, Ji S, Chen Y, Zhao Y, Yang P, Hu C, Lu M, Chen M, Xiao Y
Science (2024) pp. eadr0393-eadr0393 [ DOI: doi:10.1126/science.adr0393 Pubmed: 39666823 ]
- Crispr-associated adenosine deaminase (Complex from Limisphaera ngatamarikiensis)
- Zinc ion (65 Da, Ligand)
- Adenosine deaminase domain-containing protein (70 kDa, Protein from Limisphaera ngatamarikiensis)
- 3'-o-[(r)-{[(2s,3as,4s,6s,6as)-6-(6-amino-9h-purin-9-yl)-2-hydroxy-2-oxotetrahydro-2h-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]adenosine (658 Da, Ligand)
Leukotriene C4-bound Multidrug Resistance-associated Protein 2 (MRP2)
Resolution: 2.75 Å
EM Method: Single-particle
Fitted PDBs: 9c12
Q-score: 0.53
Koide E, Pietz HL, Beltran J, Chen J
Nat Commun (2025) 16 pp. 484-484 [ Pubmed: 39779684 DOI: doi:10.1038/s41467-024-55810-w ]
- Wild type mrp2 bound to its substrate, leukotriene c4 (Cell from Homo sapiens)
- (5~{s},6~{r},7~{e},9~{e},11~{z},14~{z})-6-[(2~{r})-2-[[(4~{s})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-3-( 2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid (625 Da, Ligand)
- Atp-binding cassette sub-family c member 2 (174 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Unknown ligand (790 Da, Ligand)