3H4D

Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP

• PDB DOI:  https://doi.org/10.2210/pdb3H4D/pdb
• NAKB: 3H4D

• Classification: REPLICATION/DNA
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2009-04-18 Released: 2009-07-21 
• Deposition Author(s): Jain, R., Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.254 
• R-Value Observed: 0.254 

Literature

Replication across template T/U by human DNA polymerase-iota.

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

(2009) Structure 17: 974-980

• PubMed: 19604477 
• DOI: https://doi.org/10.1016/j.str.2009.04.011
• Primary Citation of Related Structures:  
  3H40, 3H4B, 3H4D


• PubMed Abstract: 
  

Human DNA polymerase-iota (Poliota) incorporates correct nucleotides opposite template purines with a much higher efficiency and fidelity than opposite template pyrimidines. In fact, the fidelity opposite template T is so poor that Poliota inserts an incorrect dGTP approximately 10 times better than it inserts the correct dATP. We determine here how a template T/U is accommodated in the Poliota active site and why a G is incorporated more efficiently than an A. We show that in the absence of incoming dATP or dGTP (binary complex), template T/U exists in both syn and anti conformations, but in the presence of dATP or dGTP (ternary complexes), template T/U is predominantly in the anti conformation. We also show that dATP and dGTP insert differently opposite template T/U, and that the basis of selection of dGTP over dATP is a hydrogen bond between the N2 amino group of dGTP and Gln59 of Poliota.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 49.49 kDa 
• Atom Count: 3,489 
• Modelled Residue Count: 389 
• Deposited Residue Count: 406 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase iota	A	390	Homo sapiens	Mutation(s): 0  Gene Names: POLI, RAD30B EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNA4 (Homo sapiens) Explore Q9UNA4  Go to UniProtKB:  Q9UNA4
PHAROS:  Q9UNA4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*GP*GP*AP*CP*CP*(DOC))	B [auth P]	7	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T)	C [auth T]	9	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGT	F [auth T]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.254 
• R-Value Observed: 0.254 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.915	α = 90
b = 97.915	β = 90
c = 203.392	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Jain, R., Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description