1IG9

Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase

Franklin, M.C., Wang, J., Steitz, T.A.

(2001) Cell 105: 657-667

  • DOI: https://doi.org/10.1016/s0092-8674(01)00367-1
  • Primary Citation of Related Structures:  
    1IG9, 1IH7

  • PubMed Abstract: 

    • We describe the 2.6 A resolution crystal structure of RB69 DNA polymerase with primer-template DNA and dTTP, capturing the step just before primer extension. This ternary complex structure in the human DNA polymerase alpha family shows a 60 degrees rotation of the fingers domain relative to the apo-protein structure, similar to the fingers movement in pol I family polymerases ...

    We describe the 2.6 A resolution crystal structure of RB69 DNA polymerase with primer-template DNA and dTTP, capturing the step just before primer extension. This ternary complex structure in the human DNA polymerase alpha family shows a 60 degrees rotation of the fingers domain relative to the apo-protein structure, similar to the fingers movement in pol I family polymerases. Minor groove interactions near the primer 3' terminus suggest a common fidelity mechanism for pol I and pol alpha family polymerases. The duplex product DNA orientation differs by 40 degrees between the polymerizing mode and editing mode structures. The role of the thumb in this DNA motion provides a model for editing in the pol alpha family.

    Related Citations: 
    • Crystal Structure of a Pol Alpha Family Replication DNA Polymerase from Bacteriophage RB69
      Wang, J., Sattar, A.K., Wang, C.C., Karam, J.D., Konigsberg, W.H., Steitz, T.A.
      (1997) Cell 89: 1087
    • Building a Replisome from Interacting Pieces: Sliding Clamp Complexed to a Peptide from DNA Polymerase and a Polymerase Editing Complex
      Shamoo, Y., Steitz, T.A.
      (1999) Cell 99: 155
    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASEC [auth A]903Escherichia phage RB69Mutation(s): 2 
Gene Names: gp43, 43
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for Q38087 (Escherichia phage RB69)
Explore Q38087 
Go to UniProtKB:  Q38087
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38087
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'A [auth T]18N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*(DOC))-3'B [auth P]14N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP
Download Ideal Coordinates CCD File 
H [auth A]THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.787α = 90
b = 118.602β = 90
c = 127.997γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description