1IH7

High-Resolution Structure of Apo RB69 DNA Polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • Primary Citation of Related Structures:  
  • Also Cited By: 3CFR, 3CFP

  • 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 r ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE
A
903Enterobacteria phage RB69Mutation(s): 0 
Gene Names: 43
EC: 2.7.7.7, 3.1.11.-
Find proteins for Q38087 (Enterobacteria phage RB69)
Go to UniProtKB:  Q38087
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
GMP
Query on GMP

Download SDF File 
Download CCD File 
A
GUANOSINE
C10 H13 N5 O5
NYHBQMYGNKIUIF-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.196α = 90.00
b = 116.309β = 90.00
c = 194.391γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance