6N9V

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1126/science.aav7003
  • Primary Citation of Related Structures:  
    6N9V, 6N9U, 6N9X, 6N9W, 6N7W, 6N7T, 6N7S, 6N7V, 6N7I, 6N7N

  • 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 ...

    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. wei.yang@nih.gov.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA primase/helicaseA, B, C, D, E, F566Escherichia phage T7Mutation(s): 1 
Gene Names: 4
EC: 2.7.7 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
UniProt
Find proteins for P03692 (Escherichia phage T7)
Explore P03692 
Go to UniProtKB:  P03692
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed DNA polymeraseG [auth H]704Escherichia phage T7Mutation(s): 2 
Gene Names: 5
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
UniProt
Find proteins for P00581 (Escherichia phage T7)
Explore P00581 
Go to UniProtKB:  P00581
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    PrimerH [auth P]6Escherichia phage T7
    Protein Feature View
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    • Reference Sequence
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 4
    MoleculeChainsLengthOrganismImage
    TemplateI [auth T]44Escherichia phage T7
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    TTP (Subject of Investigation/LOI)
    Query on TTP

    Download Ideal Coordinates CCD File 
    J [auth B], L [auth C], N [auth D], Q [auth E], S [auth F], U [auth H]THYMIDINE-5'-TRIPHOSPHATE
    C10 H17 N2 O14 P3
    NHVNXKFIZYSCEB-XLPZGREQSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    P [auth E]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    K [auth B], M [auth C], O [auth D], R [auth E], T [auth F], V [auth H], W [auth H]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 4.00 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    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