6U2O | pdb_00006u2o

Structure of human DNA polymerase beta misinserting dAMPNPP opposite the 5'G of the cisplatin Pt-GG intrastrand crosslink

• PDB DOI: https://doi.org/10.2210/pdb6U2O/pdb
• NAKB: 6U2O

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-20 Released: 2020-08-26 
• Deposition Author(s): Ouzon-Shubeita, H., Vilas, C.K., Lee, S.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.248 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Structures of the Mutagenic Bypass of the Major Cisplatin-DNA Lesion by Human DNA Polymerase Beta Reveal Insights into Cisplatin-Induced Mutagenesis

Ouzon-Shubeita, H., Vilas, C.K., Lee, S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 48.57 kDa 
• Atom Count: 3,275 
• Modeled Residue Count: 357 
• Deposited Residue Count: 366 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	A	335	Homo sapiens	Mutation(s): 0  Gene Names: POLB EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens) Explore P06746  Go to UniProtKB:  P06746
PHAROS:  P06746 GTEx:  ENSG00000070501

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*CP*AP*CP*GP*GP*CP*CP*CP*AP*TP*CP*AP*CP*C)-3')	B [auth T]	16	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*TP*GP*AP*TP*GP*GP*GP*C)-3')	C [auth P]	10	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*GP*GP*G)-3')	D	5	Homo sapiens

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DZ4	G [auth A]	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine C10 H17 N6 O11 P3 WKIPJDSLGCBQCU-RRKCRQDMSA-N
CPT	H [auth T]	Cisplatin Cl2 H6 N2 Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	F [auth A], I [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.248 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.99	α = 90
b = 79.184	β = 107.6
c = 54.587	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Ouzon-Shubeita, H., Vilas, C.K., Lee, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES26676

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description