Close state of T4 bacteriophage gp41 hexamer bound with single strand DNA
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8dtp
Q-score: 0.535
Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H
Nat Commun (2023) 14 pp. 4396-4396 [ Pubmed: 37474605 DOI: doi:10.1038/s41467-023-40106-2 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Complex of t4 bacteriophage helicase gp41 with ssdna/rna hybrid (Complex from Escherichia phage T4)
- Dnab-like replicative helicase (53 kDa, Protein from Escherichia phage T4)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (5 kDa, DNA from Escherichia phage T4)
Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H
Nat Commun (2023) 14 pp. 4396-4396 [ Pubmed: 37474605 DOI: doi:10.1038/s41467-023-40106-2 ]
Open state of T4 bacteriophage gp41 hexamer bound with single strand DNA
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8due
Q-score: 0.39
Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H
Nat Commun (2023) 14 pp. 4396-4396 [ Pubmed: 37474605 DOI: doi:10.1038/s41467-023-40106-2 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Complex of t4 bacteriophage helicase gp41 with ssdna/rna hybrid (Complex from Escherichia phage T4)
- Dnab-like replicative helicase (48 kDa, Protein from Escherichia phage T4)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (2 kDa, DNA from Escherichia phage T4)
- Magnesium ion (24 Da, Ligand)
Open coformation of bacteriophage T4 helicase hexamer around single strand DNA without primase added
Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H
Nat Commun (2023) 14 pp. 4396-4396 [ Pubmed: 37474605 DOI: doi:10.1038/s41467-023-40106-2 ]
DNA-free T4 Bacteriophage gp41 hexamer
Resolution: 5.7 Å
EM Method: Single-particle
Fitted PDBs: 8duo
Q-score: 0.18
Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H
Nat Commun (2023) 14 pp. 4396-4396 [ Pubmed: 37474605 DOI: doi:10.1038/s41467-023-40106-2 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dnab-like replicative helicase (53 kDa, Protein from Escherichia phage T4)
- Complex of bacteriophage t4 helicase gp41 hexamer with nucleotide bound (Complex from Escherichia phage T4)
- Magnesium ion (24 Da, Ligand)
T4 Bacteriophage primosome with single strand DNA, state 1
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8dvf
Q-score: 0.413
Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H
Nat Commun (2023) 14 pp. 4396-4396 [ Pubmed: 37474605 DOI: doi:10.1038/s41467-023-40106-2 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Complex of t4 bacteriophage primosome including helicase gp41, primase gp61 and ssdna/rna hybrid (Complex from Escherichia phage T4)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (3 kDa, DNA from Escherichia phage T4)
- Dna primase (39 kDa, Protein from Escherichia phage T4)
- Dnab-like replicative helicase (53 kDa, Protein from Escherichia phage T4)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*gp*gp*cp*tp*g)-3') (1 kDa, DNA from Escherichia phage T4)
T4 bacteriophage primosome with single strand DNA, State 2
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8dvi
Q-score: 0.433
Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H
Nat Commun (2023) 14 pp. 4396-4396 [ Pubmed: 37474605 DOI: doi:10.1038/s41467-023-40106-2 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Complex of t4 bacteriophage primosome including helicase gp41, primase gp61 and ssdna/rna hybrid (Complex from Escherichia phage T4)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (3 kDa, DNA from Escherichia phage T4)
- Dna primase (39 kDa, Protein from Escherichia phage T4)
- Dna (70-mer) (1 kDa, DNA from Escherichia phage T4)
- Dnab-like replicative helicase (53 kDa, Protein from Escherichia phage T4)
- Magnesium ion (24 Da, Ligand)
T4 bacteriophage primosome with single-strand DNA, State 3
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8dw6
Q-score: 0.326
Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H
Nat Commun (2023) 14 pp. 4396-4396 [ Pubmed: 37474605 DOI: doi:10.1038/s41467-023-40106-2 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Complex of t4 bacteriophage primosome including helicase gp41, primase gp61 and ssdna/rna hybrid (Complex from Escherichia phage T4)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (3 kDa, DNA from Escherichia phage T4)
- Dna primase (39 kDa, Protein from Escherichia phage T4)
- Dna (70-mer) (1 kDa, DNA from Escherichia phage T4)
- Dnab-like replicative helicase (53 kDa, Protein from Escherichia phage T4)
- Magnesium ion (24 Da, Ligand)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8dwj
Q-score: 0.183
Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H
Nat Commun (2023) 14 pp. 4396-4396 [ Pubmed: 37474605 DOI: doi:10.1038/s41467-023-40106-2 ]
- Zinc ion (65 Da, Ligand)
- Complex of t4 bacteriophage primosome including helicase gp41, primase gp61 and ssdna/rna hybrid (Complex from Escherichia phage T4)
- Rna(5'-ppp-gccga-3') (1 kDa, RNA from Escherichia phage T4)
- Dna (70-mer) (21 kDa, DNA from Escherichia phage T4)
- Dna primase (39 kDa, Protein from Escherichia phage T4)
Resolution: 3.61 Å
EM Method: Single-particle
Fitted PDBs: 8g0z
Q-score: 0.321
Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H
Nat Commun (2023) 14 pp. 4396-4396 [ Pubmed: 37474605 DOI: doi:10.1038/s41467-023-40106-2 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (3 kDa, DNA from Escherichia phage T4)
- Magnesium ion (24 Da, Ligand)
- Complex of mutated t4 bacteriophage helicase gp41 with ssdna/rna hybrid (Complex from Escherichia phage T4)
- Dnab-like replicative helicase (48 kDa, Protein from Escherichia phage T4)