1IG9

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

• PDB DOI: https://doi.org/10.2210/pdb1IG9/pdb
• NAKB: 1IG9

• Classification: TRANSFERASE/DNA
• Organism(s): Escherichia phage RB69
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-04-17 Released: 2001-06-11 
• Deposition Author(s): Franklin, M.C., Wang, J., Steitz, T.A.

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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 

Starting Model: experimental

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

• PubMed: 11389835 
• 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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 115.09 kDa 
• Atom Count: 8,394 
• Modelled Residue Count: 933 
• Deposited Residue Count: 935 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE	C [auth A]	903	Escherichia phage RB69	Mutation(s): 2  Gene Names: gp43 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 ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'	A [auth T]	18	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*(DOC))-3'	B [auth P]	14	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP	H [auth A]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
CA	D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 80.787	α = 90
b = 118.602	β = 90
c = 127.997	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-06-11 
Deposition Author(s): Franklin, M.C., Wang, J., Steitz, T.A.

Revision History  

• 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