8GBF | pdb_00008gbf

Crystal structure of human DNA polymerase eta incorporating syn-ITP across dT

• PDB DOI: https://doi.org/10.2210/pdb8GBF/pdb
• NAKB: 8GBF

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


• Deposited: 2023-02-25 Released: 2024-02-28 
• Deposition Author(s): Jung, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human DNA polymerase eta incorporating syn-ITP across dT

Jung, H.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.94 kDa 
• Atom Count: 3,912 
• Modeled Residue Count: 445 
• Deposited Residue Count: 452 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase eta	A	432	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(P*AP*TP*TP*CP*TP*CP*AP*CP*AP*CP*T)-3')	B [auth T]	12	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3')	C [auth P]	8	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CZU (Subject of Investigation/LOI)	D [auth A]	[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate C10 H15 N4 O14 P3 HAEJPQIATWHALX-KQYNXXCUSA-N
CA (Subject of Investigation/LOI)	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.297	α = 90
b = 99.297	β = 90
c = 81.609	γ = 120

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Jung, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release