Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52881.62 
• Atom Count: 3203 
• Residue Count: 438 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

3G6X

Ternary complex of DNA Polymerase iota:DNA:dGTP with an abasic site at the templating position

• DOI: 10.2210/pdb3G6X/pdb
• NDB: PD1248

• Classification: REPLICATION/DNA
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae


• Deposited: 2009-02-09 Released: 2009-05-12 
• Deposition Author(s): Nair, D.T., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.265 
• R-Value Work: 0.222 

Literature

DNA Synthesis across an Abasic Lesion by Human DNA Polymerase iota.

Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2009) Structure 17: 530-537

• PubMed: 19368886 
• DOI: 10.1016/j.str.2009.02.015
• Primary Citation of Related Structures:  
  3G6Y, 3G6V


• PubMed Abstract: 
  

Abasic sites are among the most abundant DNA lesions formed in human cells, and they present a strong block to replication. DNA polymerase iota (Poliota) is one of the few DNA Pols that does not follow the A-rule opposite an abasic site. We present here three structures of human Poliota in complex with DNAs containing an abasic lesion and dGTP, dTTP, or dATP as the incoming nucleotide. The structures reveal a mechanism of translesion synthesis across an abasic lesion that differs from that in other Pols. Both the abasic lesion and the incoming dNTPs are intrahelical and are closely apposed across a constricted active site cleft. The dNTPs partake in distinct networks of hydrogen bonds in the "void" opposite the lesion. These different patterns of hydrogen bonds, as well as stacking interactions, may underlie Poliota's small preference for insertion of dGTP over other nucleotides opposite this common lesion.

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Organizational Affiliation: 

Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase iota	A	420	Homo sapiens	Mutation(s): 0  Gene Names: POLI (RAD30B) EC: 2.7.7.7
Find proteins for Q9UNA4 (Homo sapiens) Go to Gene View: POLI Go to UniProtKB:  Q9UNA4

Entity ID: 2
Molecule	Chains	Length	Organism
Primer DNA strand	P	7	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
Template DNA strand	T	11	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
DGT	A	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3DR	T	DNA LINKING	C5 H11 O6 P		--
DOC	P	DNA LINKING	C9 H14 N3 O6 P		DC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.265 
• R-Value Work: 0.222 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 98.114	α = 90.00
b = 98.114	β = 90.00
c = 202.823	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
JDirector	data collection
HKL-2000	data reduction
CNS	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-09 
• Released Date: 2009-05-12 
• Deposition Author(s): Nair, D.T., Aggarwal, A.K.

Revision History 

• Version 1.0: 2009-05-12
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Type: Refinement description
• Version 1.3: 2019-07-24
  Type: Data collection, Derived calculations, Refinement description