1IH7

High-Resolution Structure of Apo RB69 DNA Polymerase

• PDB DOI:  https://doi.org/10.2210/pdb1IH7/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia phage RB69
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-04-18 Released: 2001-06-13 
• Deposition Author(s): Franklin, M.C., Wang, J., Steitz, T.A.

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Experimental Data Snapshot

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

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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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

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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: 105.1 kDa 
• Atom Count: 7,703 
• Modelled Residue Count: 897 
• Deposited Residue Count: 903 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE	A	903	Escherichia phage RB69	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GMP	D [auth A]	GUANOSINE C10 H13 N5 O5 NYHBQMYGNKIUIF-UUOKFMHZSA-N
K	B [auth A], C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.258 
• R-Value Work: 0.215 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.196	α = 90
b = 116.309	β = 90
c = 194.391	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-06-13 
Deposition Author(s): Franklin, M.C., Wang, J., Steitz, T.A.

Revision History  

• Version 1.0: 2001-06-13
  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: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description