Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 55318.82 
• Atom Count: 3776 
• Residue Count: 454 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

6M7T

Human DNA polymerase eta in a non-productive ternary complex with Ca2+ and dTTP oppositing cdA

• DOI: 10.2210/pdb6M7T/pdb
• NDB: 6M7T

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2018-08-21 Released: 2018-09-12 
• Deposition Author(s): Weng, P., Gao, Y., Yang, W.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.261 
• R-Value Work: 0.220 

Literature

Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution.

Weng, P.J., Gao, Y., Gregory, M.T., Wang, P., Wang, Y., Yang, W.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 10660-10665

• PubMed: 30275308 
• Primary Citation of Related Structures:  
  6M7V, 6M7U, 6M7P, 6M7O

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase eta	A	435	Homo sapiens	Mutation(s): 0  Gene Names: POLH (RAD30, RAD30A, XPV) EC: 2.7.7.7
Find proteins for Q9Y253 (Homo sapiens) Go to Gene View: POLH Go to UniProtKB:  Q9Y253

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3')	P	8	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-D(*AP*TP*(02I)P*CP*TP*CP*AP*CP*AP*CP*T)-3')	T	11	Homo sapiens

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
TTP	A	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	A	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
02I	T	DNA LINKING	C10 H12 N5 O6 P		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.261 
• R-Value Work: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 65.650	α = 90.00
b = 80.930	β = 90.00
c = 140.380	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-08-21 
• Released Date: 2018-09-12 
• Deposition Author(s): Weng, P., Gao, Y., Yang, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease	United States	DK036146

Revision History 

• Version 1.0: 2018-09-12
  Type: Initial release
• Version 1.1: 2018-10-17
  Type: Data collection, Database references
• Version 1.2: 2018-10-31
  Type: Data collection, Database references