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 [ DOI: doi:10.1038/s41467-023-40106-2 Pubmed: 37474605 ]
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Complex of t4 bacteriophage helicase gp41 with ssdna/rna hybrid (Complex from Escherichia phage T4)
- 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)
- Dnab-like replicative helicase (53 kDa, Protein from Escherichia phage T4)
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 [ DOI: doi:10.1038/s41467-023-40106-2 Pubmed: 37474605 ]
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (2 kDa, DNA from Escherichia phage T4)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dnab-like replicative helicase (48 kDa, Protein from Escherichia phage T4)
- Complex of t4 bacteriophage helicase gp41 with ssdna/rna hybrid (Complex from Escherichia phage T4)
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 [ DOI: doi:10.1038/s41467-023-40106-2 Pubmed: 37474605 ]
- Dnab-like replicative helicase (53 kDa, Protein from Escherichia phage T4)
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Complex of bacteriophage t4 helicase gp41 hexamer with nucleotide bound (Complex from Escherichia phage T4)
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 [ DOI: doi:10.1038/s41467-023-40106-2 Pubmed: 37474605 ]
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna (5'-d(p*gp*gp*cp*tp*g)-3') (1 kDa, DNA 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)
- Complex of t4 bacteriophage primosome including helicase gp41, primase gp61 and ssdna/rna hybrid (Complex from Escherichia phage T4)
- Dnab-like replicative helicase (53 kDa, Protein from Escherichia phage T4)
- Dna primase (39 kDa, Protein 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 [ DOI: doi:10.1038/s41467-023-40106-2 Pubmed: 37474605 ]
- Magnesium ion (24 Da, Ligand)
- 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)
- Complex of t4 bacteriophage primosome including helicase gp41, primase gp61 and ssdna/rna hybrid (Complex 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)
- Dna primase (39 kDa, Protein from Escherichia phage T4)
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 [ DOI: doi:10.1038/s41467-023-40106-2 Pubmed: 37474605 ]
- Magnesium ion (24 Da, Ligand)
- 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)
- Complex of t4 bacteriophage primosome including helicase gp41, primase gp61 and ssdna/rna hybrid (Complex from Escherichia phage T4)
- Zinc ion (65 Da, Ligand)
- Dna (70-mer) (1 kDa, DNA from Escherichia phage T4)
- Dnab-like replicative helicase (53 kDa, Protein from Escherichia phage T4)
- Dna primase (39 kDa, Protein from Escherichia phage T4)
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 [ DOI: doi:10.1038/s41467-023-40106-2 Pubmed: 37474605 ]
- Complex of t4 bacteriophage primosome including helicase gp41, primase gp61 and ssdna/rna hybrid (Complex from Escherichia phage T4)
- Zinc ion (65 Da, Ligand)
- Dna (70-mer) (21 kDa, DNA from Escherichia phage T4)
- Dna primase (39 kDa, Protein from Escherichia phage T4)
- Rna(5'-ppp-gccga-3') (1 kDa, RNA 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 [ DOI: doi:10.1038/s41467-023-40106-2 Pubmed: 37474605 ]
- Complex of mutated t4 bacteriophage helicase gp41 with ssdna/rna hybrid (Complex from Escherichia phage T4)
- Magnesium ion (24 Da, Ligand)
- 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)
- Dnab-like replicative helicase (48 kDa, Protein from Escherichia phage T4)
bacteriophage T4 stalled primosome with mutant gp41-E227Q
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8gao
Q-score: 0.323
Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H
Nat Commun (2023) 14 pp. 4396-4396 [ DOI: doi:10.1038/s41467-023-40106-2 Pubmed: 37474605 ]
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Complex of t4 primosome with mutant helicase gp41 (Complex from Escherichia phage T4)
- Dna (70-mer) (21 kDa, DNA from synthetic construct)
- Dnab-like replicative helicase (48 kDa, Protein from Escherichia phage T4)
- Zinc ion (65 Da, Ligand)
- Dna (70-mer) (3 kDa, DNA from synthetic construct)
- Rna (5'-d(*(gtp))-r(p*cp*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- Dna primase (39 kDa, Protein from Escherichia phage T4)