1G5I | pdb_00001g5i

CRYSTAL STRUCTURE OF THE ACCESSORY SUBUNIT OF MURINE MITOCHONDRIAL POLYMERASE GAMMA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.233 (Depositor) 
  • R-Value Work: 
    0.189 (Depositor) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1G5I

This is version 1.3 of the entry. See complete history

Literature

Crystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase gamma, Pol gamma B, functions as a homodimer.

Carrodeguas, J.A.Theis, K.Bogenhagen, D.F.Kisker, C.

(2001) Mol Cell 7: 43-54

  • DOI: https://doi.org/10.1016/s1097-2765(01)00153-8
  • Primary Citation Related Structures: 
    1G5H, 1G5I

  • PubMed Abstract: 

    Polymerase gamma, which replicates and repairs mitochondrial DNA, requires the Pol gamma B subunit for processivity. We determined the crystal structure of mouse Pol gamma B, a core component of the mitochondrial replication machinery. Pol gamma B shows high similarity to glycyl-tRNA synthetase and dimerizes through an unusual intermolecular four-helix bundle. A human Pol gamma B mutant lacking the four-helix bundle failed to dimerize in solution or to stimulate the catalytic subunit Pol gamma A, but retained the ability to bind with Pol gamma A to a primer-template construct, indicating that the functional holoenzyme contains two Pol gamma B molecules. Other mutants retained stimulatory activity but lost the ability to bind folded ssDNA. These results suggest that the Pol gamma B dimer contains distinct sites for Pol gamma A binding, dimerization, and DNA binding.


  • Organizational Affiliation
    • Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA.

Macromolecule Content 

  • Total Structure Weight: 204.5 kDa 
  • Atom Count: 13,774 
  • Modeled Residue Count: 1,622 
  • Deposited Residue Count: 1,816 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
A, B, C, D
454Mus musculusMutation(s): 0 
Gene Names: DNA POLYMERASE GAMMA SUBUNIT B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QZM2 (Mus musculus)
Explore Q9QZM2 
Go to UniProtKB:  Q9QZM2
IMPC:  MGI:1354947
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QZM2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.233 (Depositor) 
  • R-Value Work:  0.189 (Depositor) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.743α = 90
b = 134.01β = 90
c = 135.144γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
MARMADdata reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description