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)
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)
Cryo-EM structure of the Pyrobaculum calidifontis 50S ribosomal subunit in complex with Dri
Resolution: 1.95 Å
EM Method: Single-particle
Fitted PDBs: 9e6q
Q-score: 0.726
Nissley AJ, Shulgina Y, Kivimae RW, Downing BE, Penev PI, Banfield JF, Nayak DD, Cate JHD
To Be Published
- Large ribosomal subunit protein ul29 (9 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Parep1 domain containing protein (10 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el32 (18 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el30 (10 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Spermine (202 Da, Ligand)
- Large ribosomal subunit protein el18 (13 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el24 (7 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul30 (20 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- El42 (10 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- 50s ribosomal protein l15e (22 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el21 (11 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul24 (14 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein el8 (16 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el34 (9 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul23 (9 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul16 (19 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Putative signal-transduction protein with cbs domains (72 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Lsu ribosomal protein l38e (7 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el31 (10 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul3 (37 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul6 (21 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul18 (23 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el39 (6 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Dj-1/pfpi domain-containing protein (20 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- 50s ribosomal subunit (Complex from Pyrobaculum calidifontis JCM 11548)
- Zinc ion (65 Da, Ligand)
- 5s rrna (41 kDa, RNA from Pyrobaculum calidifontis JCM 11548)
- El14 (11 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el13 (17 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el43 (11 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein ul15 (17 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul14 (15 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- 23s rrna (984 kDa, RNA from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el20 (8 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el40 (6 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul22 (21 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul13 (21 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul2 (26 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el37 (6 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein ul4 (31 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
- Large ribosomal subunit protein el19 (17 kDa, Protein from Pyrobaculum calidifontis JCM 11548)
Non-translating S. pombe ribosome large subunit
Resolution: 1.94 Å
EM Method: Single-particle
Fitted PDBs: 9axu
Q-score: 0.661
Gemin O, Gluc M, Rosa H, Purdy M, Niemann M, Peskova Y, Mattei S, Jomaa A
Nat Commun (2024) 15 pp. 8666-8666 [ DOI: doi:10.1038/s41467-024-52911-4 Pubmed: 39379376 ]
- Large ribosomal subunit protein el21b (18 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul13a (22 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el33a (12 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el32a (14 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul15b (16 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el27a (15 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el18b (21 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el8 (28 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el13 (23 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul16a (25 kDa, Protein from Schizosaccharomyces pombe)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal rna (1 MDa, RNA from Schizosaccharomyces pombe)
- 5.8s ribosomal rna (52 kDa, RNA from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul4a (39 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul30c (28 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul14b (14 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el37b (10 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul24 (14 kDa, Protein from Schizosaccharomyces pombe)
- 5s ribosomal rna (78 kDa, RNA from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul22a (20 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el31 (13 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul29 (14 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el36b (11 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el15b (23 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el20a (20 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el42 (12 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul3a (43 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul6b (21 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul23a (15 kDa, Protein from Schizosaccharomyces pombe)
- Zinc ion (65 Da, Ligand)
- Non-translating s. pombe ribosome large subunit (3 MDa, Complex from Schizosaccharomyces pombe 972h-)
- Large ribosomal subunit protein ul2c (27 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el30a (11 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el6 (21 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el14 (15 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el38a (8 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el43a (10 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el19b (22 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el39 (6 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el24b (16 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el34b (12 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el22 (13 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul18b (33 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el28 (14 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein ul5a (19 kDa, Protein from Schizosaccharomyces pombe)
- Large ribosomal subunit protein el29 (7 kDa, Protein from Schizosaccharomyces pombe)
Orf virus scaffolding protein Orfv075
Resolution: 1.9 Å
EM Method: Single-particle
Fitted PDBs: 9ikc
Q-score: 0.763
Kim S, Ko S, Kim M, Jang Y, Hyun J
Biochem Biophys Res Commun (2024) 728 pp. 150334-150334 [ Pubmed: 38968773 DOI: doi:10.1016/j.bbrc.2024.150334 ]
- Orfv075 trimer (190 kDa, Complex from Orf virus (strain NZ2))
- Water (18 Da, Ligand)
- 62 kda protein (63 kDa, Protein from Orf virus (strain NZ2))
Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
Resolution: 1.99 Å
EM Method: Single-particle
Fitted PDBs: 8xn9
Q-score: 0.666
To Be Published
- Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1d6 (Complex from Henipavirus nipahense)
- 1d6 vh (22 kDa, Protein from Macaca)
- 1d6 fab (Complex from Macaca)
- Fusion glycoprotein f0 (55 kDa, Protein from Henipavirus nipahense)
- Nipah virus fusion glycoprotein (Complex from Henipavirus nipahense)
- 1d6 vl (25 kDa, Protein from Macaca)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 1.97 Å
EM Method: Single-particle
Fitted PDBs: 8sr7
Q-score: 0.603
Huang Y, Kumar S, Lee J, Lu W, Du J
Nat Struct Mol Biol (2024) 31 pp. 1509-1521 [ DOI: doi:10.1038/s41594-024-01316-4 Pubmed: 38773335 ]
- Magnesium ion (24 Da, Ligand)
- Adenosine monophosphate (347 Da, Ligand)
- Water (18 Da, Ligand)
- Trpm2 chanzyme (168 kDa, Protein from Salpingoeca rosetta)
- Trpm2 chanzyme in the presence of magnesium, adenosine monophosphate, and ribose-5-phosphate (Complex from Salpingoeca rosetta)
- Cholesterol (386 Da, Ligand)
- 5-o-phosphono-beta-d-ribofuranose (230 Da, Ligand)
Cryo-EM structure of the ClpC1:ClpP1P2 degradation complex in Streptomyces hawaiiensis
Resolution: 1.96 Å
EM Method: Single-particle
Fitted PDBs: 8xon
Q-score: 0.503
Xu X, Wang Y, Huang W, Li D, Deng Z, Long F
Mbio (2024) 15 pp. e0003124-e0003124 [ Pubmed: 38501868 DOI: doi:10.1128/mbio.00031-24 ]
- Clpp1,clpp2,clpc1,casein (Complex from Streptomyces hawaiiensis)
- Atp-dependent clp protease proteolytic subunit (24 kDa, Protein from Streptomyces hawaiiensis)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Ndp-hexose 4-ketoreductase (77 kDa, Protein from Streptomyces hawaiiensis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp-dependent clp protease proteolytic subunit (22 kDa, Protein from Streptomyces hawaiiensis)
- Casein (2 kDa, Protein from Bos taurus)
Cryo-EM structure of the ClpC1:ClpP1P2 degradation complex in Streptomyces hawaiiensis
Resolution: 1.84 Å
EM Method: Single-particle
Fitted PDBs: 8xoo
Q-score: 0.514
Xu X, Wang Y, Huang W, Li D, Deng Z, Long F
Mbio (2024) 15 pp. e0003124-e0003124 [ Pubmed: 38501868 DOI: doi:10.1128/mbio.00031-24 ]
- Clpp1,clpp2,clpc1,casein (Complex from Streptomyces hawaiiensis)
- Atp-dependent clp protease proteolytic subunit (24 kDa, Protein from Streptomyces hawaiiensis)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Ndp-hexose 4-ketoreductase (77 kDa, Protein from Streptomyces hawaiiensis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp-dependent clp protease proteolytic subunit (22 kDa, Protein from Streptomyces hawaiiensis)
- Casein (2 kDa, Protein from Bos taurus)