Structure of the E. coli clamp loader bound to the beta clamp in a Open-RNAp/t conformation
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8vat
Q-score: 0.465
Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA
J Biol Chem (2024) 300 pp. 107166-107166 [ DOI: doi:10.1016/j.jbc.2024.107166 Pubmed: 38490435 ]
- Structure of the e. coli clamp loader bound to the beta clamp in an open-rnap/t conformation (Complex from Escherichia coli)
- Rna (5'-r(p*ap*gp*up*gp*gp*up*gp*up*cp*up*g)-3') (3 kDa, RNA from synthetic construct)
- Beta sliding clamp (40 kDa, Protein from Escherichia coli)
- Dna polymerase iii subunit delta (38 kDa, Protein from Escherichia coli)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*tp*cp*ap*gp*ap*cp*ap*cp*cp*ap*cp*tp*gp*c)-3') (9 kDa, DNA from synthetic construct)
- Beryllium trifluoride ion (66 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna polymerase iii subunit delta' (37 kDa, Protein from Escherichia coli)
- Dna polymerase iii subunit tau (41 kDa, Protein from Escherichia coli)
cA4-bound Cami1 in complex with 70S ribosome
Resolution: 3.67 Å
EM Method: Single-particle
Fitted PDBs: 8phj
Q-score: 0.584
Mogila I, Tamulaitiene G, Keda K, Timinskas A, Ruksenaite A, Sasnauskas G, Venclovas C, Siksnys V, Tamulaitis G
Science (2023) 382 pp. 1036-1041 [ DOI: doi:10.1126/science.adj2107 Pubmed: 38033086 ]
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs16 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us7 (20 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
- Fmet-trna(fmet) (24 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs6, fully modified isoform (15 kDa, Protein from Escherichia coli)
- Cyclic tetraadenosine monophosphate (ca4) (1 kDa, RNA from Streptococcus thermophilus)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein bl12 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli)
- 23s rrna (2862-mer) (941 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli)
- Mrna (10 kDa, RNA from synthetic construct)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul10 (17 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
- Cami1 bound in 70s e.coli ribosome (Complex)
- Large ribosomal subunit protein bl28 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli)
- Ca4 (Complex from Streptococcus thermophilus)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul23 (11 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us2 (26 kDa, Protein from Escherichia coli)
- Crispr-associated protein cami1, ape2256 family (Complex from Allochromatium vinosum)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- 70s e.coli ribosome (Complex from Escherichia coli)
- Large ribosomal subunit protein bl31a (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Escherichia coli)
- Crispr-associated protein, ape2256 family (45 kDa, Protein from Allochromatium vinosum)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- Synthetic mrna (Complex from synthetic construct)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein ul11 (14 kDa, Protein from Escherichia coli)
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 8pvv
Q-score: 0.56
Manakova E, Golovinas E, Poceviciute R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaite E, Jurgelaitis E, Grybauskas A, Venclovas C, Zaremba M
Nucleic Acids Res (2024) 52 pp. 2530-2545 [ DOI: doi:10.1093/nar/gkad1241 Pubmed: 38197228 ]
- Archaeoglobus fulgidus afago-n protein (Complex from Archaeoglobus fulgidus DSM 8774)
- Afago and afago-n complex with 30 nt rna guide and 51 nt dna target (90 kDa, Complex)
- Rna (30-mer) (Complex from Escherichia coli)
- Piwi protein (49 kDa, Protein from Archaeoglobus fulgidus)
- Piwi protein (Complex from Archaeoglobus fulgidus)
- Archaeoglobus fulgidus afago-n protein (31 kDa, Protein from Archaeoglobus fulgidus DSM 8774)
- Water (18 Da, Ligand)
- Rna (30-mer) (9 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna (51-mer) (15 kDa, DNA from Escherichia coli)
- Dna (51-mer) (Complex from Escherichia coli)
Full-length APOBEC3G in complex with HIV-1 Vif, CBF-beta, and fork RNA
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 8e40
Q-score: 0.343
Ito F, Alvarez-Cabrera AL, Liu S, Yang H, Shiriaeva A, Zhou ZH, Chen XS
Sci Adv (2023) 9 pp. eade3168-eade3168 [ Pubmed: 36598981 DOI: doi:10.1126/sciadv.ade3168 ]
- Complex of apobec3g with hiv-1 vif and cbf-beta bound to fork rna (99 kDa, Complex from Human immunodeficiency virus 1)
- Virion infectivity factor (21 kDa, Protein from Human immunodeficiency virus 1)
- Core-binding factor subunit beta (18 kDa, Protein from Homo sapiens)
- Rna (6 kDa, RNA from Escherichia coli)
- Rna (8 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna dc->du-editing enzyme apobec-3g (45 kDa, Protein from Macaca mulatta)
Cryo-EM structure of Cytochrome bo3 from Escherichia coli, apo structure with DMSO
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7xmc
Q-score: 0.526
Nishida Y, Yanagisawa S, Morita R, Shigematsu H, Shinzawa-Itoh K, Yuki H, Ogasawara S, Shimuta K, Iwamoto T, Nakabayashi C, Matsumura W, Kato H, Gopalasingam C, Nagao T, Qaqorh T, Takahashi Y, Yamazaki S, Kamiya K, Harada R, Mizuno N, Takahashi H, Akeda Y, Ohnishi M, Ishii Y, Kumasaka T, Murata T, Muramoto K, Tosha T, Shiro Y, Honma T, Shigeta Y, Kubo M, Takashima S, Shintani Y
Nat Commun (2022) 13 pp. 7591-7591 [ Pubmed: 36481732 DOI: doi:10.1038/s41467-022-34771-y ]
- Cytochrome bo3 ubiquinol oxidase (144 kDa, Complex from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Unknown atom or ion (744 Da, Ligand)
- Heme o (838 Da, Ligand)
- Ubiquinol oxidase subunit 2 (36 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 7xmd
Q-score: 0.535
Nishida Y, Yanagisawa S, Morita R, Shigematsu H, Shinzawa-Itoh K, Yuki H, Ogasawara S, Shimuta K, Iwamoto T, Nakabayashi C, Matsumura W, Kato H, Gopalasingam C, Nagao T, Qaqorh T, Takahashi Y, Yamazaki S, Kamiya K, Harada R, Mizuno N, Takahashi H, Akeda Y, Ohnishi M, Ishii Y, Kumasaka T, Murata T, Muramoto K, Tosha T, Shiro Y, Honma T, Shigeta Y, Kubo M, Takashima S, Shintani Y
Nat Commun (2022) 13 pp. 7591-7591 [ DOI: doi:10.1038/s41467-022-34771-y Pubmed: 36481732 ]
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Methyl 3-oxidanyl-5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-1-benzothiophene-2-carboxylate (253 Da, Ligand)
- Cytochrome bo3 ubiquinol oxidase (144 kDa, Complex from Escherichia coli)
- Ubiquinol oxidase subunit 2 (36 kDa, Protein from Escherichia coli)
- Heme o (838 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Unknown atom or ion (Ligand)