1SL2

Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.

Li, Y.Dutta, S.Doublie, S.Bdour, H.M.Taylor, J.S.Ellenberger, T.

(2004) Nat Struct Mol Biol 11: 784-790

  • DOI: 10.1038/nsmb792
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ultraviolet-induced DNA damage poses a lethal block to replication. To understand the structural basis for this, we determined crystal structures of a replicative DNA polymerase from bacteriophage T7 in complex with nucleotide substrates and a DNA te ...

    Ultraviolet-induced DNA damage poses a lethal block to replication. To understand the structural basis for this, we determined crystal structures of a replicative DNA polymerase from bacteriophage T7 in complex with nucleotide substrates and a DNA template containing a cis-syn cyclobutane pyrimidine dimer (CPD). When the 3' thymine is the templating base, the CPD is rotated out of the polymerase active site and the fingers subdomain adopts an open orientation. When the 5' thymine is the templating base, the CPD lies within the polymerase active site where it base-pairs with the incoming nucleotide and the 3' base of the primer, while the fingers are in a closed conformation. These structures reveal the basis for the strong block of DNA replication that is caused by this photolesion.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase
A
698Escherichia phage T7Mutation(s): 0 
Gene Names: 5
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for P00581 (Escherichia phage T7)
Go to UniProtKB:  P00581

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Thioredoxin 1
B
108Escherichia coliMutation(s): 0 
Gene Names: 
Find proteins for P0AA25 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA25

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*TP*(2DA))-3'P22N/A

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3'T25N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAD
Query on DAD

Download CCD File 
A
2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O11 P3
OAKPWEUQDVLTCN-RQJHMYQMSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.983α = 90
b = 212.599β = 90
c = 51.945γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance