5F9L | pdb_00005f9l

CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING dAMPNPP ACROSS A DNA TEMPLATE CONTAINING 1,N2-ETHENODEOXYGUANOSINE LESION

• PDB DOI: https://doi.org/10.2210/pdb5F9L/pdb
• NAKB: 5F9L

• Classification: Transferase/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-09 Released: 2016-12-21 
• Deposition Author(s): Patra, A., Egli, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Bypass of the 1, N2-Ethenodeoxyguanosine Lesion by Human DNA Polymerase Eta

Patra, A., Egli, M.

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)

Macromolecule Content 

• Total Structure Weight: 55.36 kDa 
• Atom Count: 4,018 
• Modeled Residue Count: 451 
• Deposited Residue Count: 455 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase eta	A	435	Homo sapiens	Mutation(s): 0  Gene Names: POLH, RAD30, RAD30A, XPV EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y253 (Homo sapiens) Explore Q9Y253  Go to UniProtKB:  Q9Y253
PHAROS:  Q9Y253 GTEx:  ENSG00000170734

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*TP*(GNE)P*AP*TP*GP*AP*CP*GP*CP*T)-3')	B [auth T]	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')	C [auth P]	8	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DZ4	D [auth A]	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine C10 H17 N6 O11 P3 WKIPJDSLGCBQCU-RRKCRQDMSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.111	α = 90
b = 99.111	β = 90
c = 81.856	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Patra, A., Egli, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-01-16
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description