6N7T | pdb_00006n7t

Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (form III)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6N7T

This is version 1.2 of the entry. See complete history

Literature

Structures and operating principles of the replisome.

Gao, Y.Cui, Y.Fox, T.Lin, S.Wang, H.de Val, N.Zhou, Z.H.Yang, W.

(2019) Science 363

  • DOI: https://doi.org/10.1126/science.aav7003
  • Primary Citation Related Structures: 
    6N7I, 6N7N, 6N7S, 6N7T, 6N7V, 6N7W, 6N9U, 6N9V, 6N9W, 6N9X

  • PubMed Abstract: 

    Visualization in atomic detail of the replisome that performs concerted leading- and lagging-DNA strand synthesis at a replication fork has not been reported. Using bacteriophage T7 as a model system, we determined cryo-electron microscopy structures up to 3.2-angstroms resolution of helicase translocating along DNA and of helicase-polymerase-primase complexes engaging in synthesis of both DNA strands. Each domain of the spiral-shaped hexameric helicase translocates sequentially hand-over-hand along a single-stranded DNA coil, akin to the way AAA+ ATPases (adenosine triphosphatases) unfold peptides. Two lagging-strand polymerases are attached to the primase, ready for Okazaki fragment synthesis in tandem. A β hairpin from the leading-strand polymerase separates two parental DNA strands into a T-shaped fork, thus enabling the closely coupled helicase to advance perpendicular to the downstream DNA duplex. These structures reveal the molecular organization and operating principles of a replisome.


  • Organizational Affiliation
    • Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 386.53 kDa 
  • Atom Count: 12,890 
  • Modeled Residue Count: 1,626 
  • Deposited Residue Count: 3,421 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA primase/helicase
A, B, C, D, E
A, B, C, D, E, F
566Escherichia phage T7Mutation(s): 1 
EC: 2.7.7 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
Find proteins for P03692 (Escherichia phage T7)
Explore P03692 
Go to UniProtKB:  P03692
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03692
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (25-MER)G [auth T]25Escherichia phage T7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TTP

Query on TTP



Download:Ideal Coordinates CCD File
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E]
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States1S10RR23057

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description