Resolution: 3.42 Å
EM Method: Single-particle
Fitted PDBs: 9j1j
Q-score: 0.441
Nat Commun (2025) 16 pp. 1695- [ DOI: doi:10.1038/s41467-025-57075-3 ]
- Duf5072 domain-containing protein (14 kDa, Protein from Listeria monocytogenes)
- Aa protein (18 kDa, Protein from Listeria monocytogenes)
- Monocin (Complex from Listeria monocytogenes)
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 9j1k
Q-score: 0.515
Nat Commun (2025) 16 pp. 1695- [ DOI: doi:10.1038/s41467-025-57075-3 ]
- Ftbj (65 kDa, Protein from Listeria monocytogenes)
- Aa protein (18 kDa, Protein from Listeria monocytogenes)
- Monocin (Complex from Listeria monocytogenes)
- Ftbk (31 kDa, Protein from Listeria monocytogenes)
- Ftbl (43 kDa, Protein from Listeria monocytogenes)
- Cca-adding enzyme (10 kDa, Protein from Listeria monocytogenes)
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 9j1l
Q-score: 0.347
Nat Commun (2025) 16 pp. 1695- [ DOI: doi:10.1038/s41467-025-57075-3 ]
- Ftbp (19 kDa, Protein from Listeria monocytogenes)
- Ftbo (17 kDa, Protein from Listeria monocytogenes)
- Monocin (Complex from Listeria monocytogenes)
- Ftbo (15 kDa, Protein from Listeria monocytogenes)
- Fe (iii) ion (55 Da, Ligand)
- Alpha-amylase (21 kDa, Protein from Listeria monocytogenes)
Tail tip complex of bacteriophage lambda in the open state
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 8xcg
Q-score: 0.5
Nat Commun (2024) 15 pp. 4185-4185 [ DOI: doi:10.1038/s41467-024-48686-3 Pubmed: 38760367 ]
- Tail tip protein m (12 kDa, Protein from Escherichia phage Lambda)
- Bacteriophage lambda tail with lamb (Complex from Escherichia phage Lambda)
- Tip attachment protein j (124 kDa, Protein from Escherichia phage Lambda)
- Tail tip protein l (25 kDa, Protein from Escherichia phage Lambda)
- Iron/sulfur cluster (351 Da, Ligand)
- Tail tip assembly protein i (23 kDa, Protein from Escherichia phage Lambda)
Open state of central tail fiber of bacteriophage lambda upon binding to LamB
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 8xci
Q-score: 0.424
Nat Commun (2024) 15 pp. 4185-4185 [ DOI: doi:10.1038/s41467-024-48686-3 Pubmed: 38760367 ]
Open State of central tail fiber of bacteriophage lambda upon binding to LamB (gpJ713-LamB complex)
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8xcj
Q-score: 0.568
Nat Commun (2024) 15 pp. 4185-4185 [ DOI: doi:10.1038/s41467-024-48686-3 Pubmed: 38760367 ]
- Lamb (Complex from Shigella sonnei)
- Tip attachment protein j (Complex from Escherichia phage Lambda)
- Bacteriophage lambda tail with lamb (Complex)
- Tip attachment protein j (46 kDa, Protein from Escherichia phage Lambda)
- Maltoporin (47 kDa, Protein from Shigella sonnei)
Closed state of central tail fiber of bacteriophage lambda
Resolution: 2.75 Å
EM Method: Single-particle
Fitted PDBs: 8xck
Q-score: 0.573
Nat Commun (2024) 15 pp. 4185-4185 [ DOI: doi:10.1038/s41467-024-48686-3 Pubmed: 38760367 ]
- Peptidyl-prolyl cis-trans isomerase a (20 kDa, Protein from Escherichia coli)
- Ppia (Complex from Escherichia coli)
- Bacteriophage lambda tail with lamb (Complex)
- Tip attachment protein j (46 kDa, Protein from Escherichia phage Lambda)
- Tip attachment protein j (Complex from Escherichia phage Lambda)
SARS-CoV-2 RNA E-RTC complex with RMP-nsp9 and GMPPNP
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 8gwk
Q-score: 0.423
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_rmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- [(2~{r},3~{s},4~{r},5~{r})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate (371 Da, Ligand)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 E-RTC bound with MMP-nsp9 and GMPPNP
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8gwm
Q-score: 0.41
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- E-rtc_mmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate) (420 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (26-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (25-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.31 Å
EM Method: Single-particle
Fitted PDBs: 8gw1
Q-score: 0.332
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- E-rtc_ump-nsp9 (350 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Uridine-5'-monophosphate (324 Da, Ligand)
- Replicase polyprotein 1ab (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Manganese (ii) ion (54 Da, Ligand)
- Rna (25-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)