5TCT

The Structure of SV40 Large T Hexameric Helicase in Complex with AT-rich Origin DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.278 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of SV40 large T hexameric helicase in complex with AT-rich origin DNA.

Gai, D.Wang, D.Li, S.X.Chen, X.S.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.18129

  • PubMed Abstract: 
  • DNA replication is a fundamental biological process. The initial step in eukaryotic DNA replication is the assembly of the pre-initiation complex, including the formation of two head-to-head hexameric helicases around the replication origin. How thes ...

    DNA replication is a fundamental biological process. The initial step in eukaryotic DNA replication is the assembly of the pre-initiation complex, including the formation of two head-to-head hexameric helicases around the replication origin. How these hexameric helicases interact with their origin dsDNA remains unknown. Here, we report the co-crystal structure of the SV40 Large-T Antigen (LT) hexameric helicase bound to its origin dsDNA. The structure shows that the six subunits form a near-planar ring that interacts with the origin, so that each subunit makes unique contacts with the DNA. The origin dsDNA inside the narrower AAA+ domain channel shows partial melting due to the compression of the two phosphate backbones, forcing Watson-Crick base-pairs within the duplex to flip outward. This structure provides the first snapshot of a hexameric helicase binding to origin dsDNA, and suggests a possible mechanism of origin melting by LT during SV40 replication in eukaryotic cells.


    Organizational Affiliation

    Departments of Biological Sciences and Chemistry, Molecular and Computational Biology Program, University of Southern California, Los Angeles, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Large T antigen
A, B, E, F, C, D
362Simian virus 40Mutation(s): 2 
EC: 3.6.4.-
Find proteins for P03070 (Simian virus 40)
Go to UniProtKB:  P03070
Entity ID: 2
MoleculeChainsLengthOrganism
AT-rich Origin DNA (33-MER)W33Macaca mulatta polyomavirus 1
Entity ID: 3
MoleculeChainsLengthOrganism
AT-rich Origin DNA (33-MER)K33Macaca mulatta polyomavirus 1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
B, D, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.278 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 107.485α = 107.13
b = 107.587β = 106.95
c = 107.870γ = 106.86
Software Package:
Software NamePurpose
HKL-2000data collection
PDB_EXTRACTdata extraction
CNSrefinement
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI055926

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence