8V7B

Human DNA polymerase eta-DNA-dT primer araCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion

• PDB DOI: https://doi.org/10.2210/pdb8V7B/pdb
• NAKB: 8V7B

• Classification: Transferase/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-04 Released: 2024-05-15 
• Deposition Author(s): Chang, C., Gao, Y.
• Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), Welch Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Human DNA polymerase eta-DNA-dT primer araCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion

Chang, C., Gao, Y.

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: 55.55 kDa 
• Atom Count: 4,268 
• Modelled Residue Count: 450 
• 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*GP*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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HF4 (Subject of Investigation/LOI)	G [auth A]	4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one C9 H16 N3 O14 P3 PCDQPRRSZKQHHS-CCXZUQQUSA-N
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K	I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.848	α = 90
b = 98.848	β = 90
c = 82.048	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Chang, C., Gao, Y.

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Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR190046
Welch Foundation	United States	C-2033-20200401
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM008280

Revision History  

• Version 1.0: 2024-05-15
  Type: Initial release