Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of the T4 bacteriophage primosome assembly and primer synthesis.
Journal, issue, pages	Nat Commun, Vol. 14, Issue 1, Page 4396, Year 2023
Publish date	Jul 20, 2023
Authors	Xiang Feng / Michelle M Spiering / Ruda de Luna Almeida Santos / Stephen J Benkovic / Huilin Li /
PubMed Abstract	The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome to couple DNA unwinding with RNA primer synthesis for DNA replication. How the primosome is assembled and how the primer ...The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome to couple DNA unwinding with RNA primer synthesis for DNA replication. How the primosome is assembled and how the primer length is defined are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates. We show that gp41 alone is an open spiral, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the ring closure and activates the helicase. Helicase activation exposes a cryptic hydrophobic surface to recruit the gp61 primase. The primase binds the helicase in a bipartite mode in which the N-terminal Zn-binding domain and the C-terminal RNA polymerase domain each contain a helicase-interacting motif that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Our study reveals the T4 primosome assembly process and sheds light on the RNA primer synthesis mechanism.
External links	Nat Commun / PubMed:37474605 / PubMed Central
Methods	EM (single particle)
Resolution	2.7 - 5.7 Å
Structure data	27707 8dtp EMDB-27707, PDB-8dtp: Close state of T4 bacteriophage gp41 hexamer bound with single strand DNA Method: EM (single particle) / Resolution: 2.7 Å EMDB-27708: Closed conformation of bacteriophage T4 helicase hexamer with single strand DNA but no primase added. Method: EM (single particle) / Resolution: 3.4 Å 27719 8due EMDB-27719, PDB-8due: Open state of T4 bacteriophage gp41 hexamer bound with single strand DNA Method: EM (single particle) / Resolution: 2.9 Å EMDB-27720: Open coformation of bacteriophage T4 helicase hexamer around single strand DNA without primase added Method: EM (single particle) / Resolution: 3.5 Å 27724 8duo EMDB-27724, PDB-8duo: DNA-free T4 Bacteriophage gp41 hexamer Method: EM (single particle) / Resolution: 5.7 Å 27737 8dvf EMDB-27737, PDB-8dvf: T4 Bacteriophage primosome with single strand DNA, state 1 Method: EM (single particle) / Resolution: 3.3 Å 27739 8dvi EMDB-27739, PDB-8dvi: T4 bacteriophage primosome with single strand DNA, State 2 Method: EM (single particle) / Resolution: 3.2 Å 27751 8dw6 EMDB-27751, PDB-8dw6: T4 bacteriophage primosome with single-strand DNA, State 3 Method: EM (single particle) / Resolution: 3.5 Å 27756 8dwj EMDB-27756, PDB-8dwj: Primase of mutant bacteriophage T4 primosome with single strand DNA/RNA primer hybrid in primer exiting state Method: EM (single particle) / Resolution: 3.9 Å 29658 8g0z EMDB-29658, PDB-8g0z: Mutant bacteriophage T4 gp41 helicase hexamer bound with single strand DNA and ATPgammaS in the stalled primosome Method: EM (single particle) / Resolution: 3.61 Å EMDB-29744: local refinement of the primase/DNA/primer region in mutant T4 primosome Method: EM (single particle) / Resolution: 4.1 Å 29902 8gao EMDB-29902, PDB-8gao: bacteriophage T4 stalled primosome with mutant gp41-E227Q Method: EM (single particle) / Resolution: 4.1 Å
Chemicals	ChemComp-AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogueYM ChemComp-MG: Unknown entry ChemComp-ZN*: Unknown entry
Source	escherichia phage t4 (virus) synthetic construct (others)
Keywords	REPLICATION/DNA/RNA / phage / complex / helicase / REPLICATION-DNA-RNA complex / REPLICATION