1SL0

Ternary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.282 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    1SKR, 1SKS, 1SKW, 1SL0, 1SL1, 1SL2

  • 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 template containing a cis-syn cyclobutane pyrimidine dimer (CPD) ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseE [auth A],
G [auth C]
698Escherichia phage T7Mutation(s): 0 
Gene Names: 5
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for P00581 (Escherichia phage T7)
Explore P00581 
Go to UniProtKB:  P00581
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00581
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Thioredoxin 1F [auth B],
H [auth D]
108Escherichia coliMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P0AA25 (Escherichia coli (strain K12))
Explore P0AA25 
Go to UniProtKB:  P0AA25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AA25
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*(2DT))-3'A [auth P],
C [auth Q]
21N/A
Protein Feature View
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Entity ID: 2
MoleculeChainsLengthOrganismImage
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'B [auth T],
D [auth U]
25N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAD
Query on DAD

Download Ideal Coordinates CCD File 
J [auth A],
L [auth C]
2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O11 P3
OAKPWEUQDVLTCN-RQJHMYQMSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
K [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.282 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.266α = 90
b = 105.466β = 91.57
c = 213.931γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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