6C8C | pdb_00006c8c

Chimeric Pol kappa RIR Rev1 C-terminal domain in complex with JHRE06

• PDB DOI: https://doi.org/10.2210/pdb6C8C/pdb

• Classification: REPLICATION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-24 Released: 2019-06-12 
• Deposition Author(s): Najeeb, J., Zhou, P.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

A Small Molecule Targeting Mutagenic Translesion Synthesis Improves Chemotherapy.

Wojtaszek, J.L., Chatterjee, N., Najeeb, J., Ramos, A., Lee, M., Bian, K., Xue, J.Y., Fenton, B.A., Park, H., Li, D., Hemann, M.T., Hong, J., Walker, G.C., Zhou, P.

(2019) Cell 178: 152

• PubMed: 31178121 
• DOI: https://doi.org/10.1016/j.cell.2019.05.028
• Primary Citation Related Structures: 
  6C59, 6C8C


• PubMed Abstract: 
  

  Intrinsic and acquired drug resistance and induction of secondary malignancies limit successful chemotherapy. Because mutagenic translesion synthesis (TLS) contributes to chemoresistance as well as treatment-induced mutations, targeting TLS is an attractive avenue for improving chemotherapeutics. However, development of small molecules with high specificity and in vivo efficacy for mutagenic TLS has been challenging. Here, we report the discovery of a small-molecule inhibitor, JH-RE-06, that disrupts mutagenic TLS by preventing recruitment of mutagenic POL ζ. Remarkably, JH-RE-06 targets a nearly featureless surface of REV1 that interacts with the REV7 subunit of POL ζ. Binding of JH-RE-06 induces REV1 dimerization, which blocks the REV1-REV7 interaction and POL ζ recruitment. JH-RE-06 inhibits mutagenic TLS and enhances cisplatin-induced toxicity in cultured human and mouse cell lines. Co-administration of JH-RE-06 with cisplatin suppresses the growth of xenograft human melanomas in mice, establishing a framework for developing TLS inhibitors as a novel class of chemotherapy adjuvants.

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Organizational Affiliation: 
• Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Department of Chemistry, Duke University, Durham, NC 27708, USA.
Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA.
Trinity College of Arts & Sciences, Duke University, Durham, NC 27708, USA.
The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: [e-mail].
Department of Chemistry, Duke University, Durham, NC 27708, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA. Electronic address: [e-mail].
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: [e-mail].
Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 28 kDa 
• Atom Count: 2,396 
• Modeled Residue Count: 233 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric protein of the Pol Kappa RIR helix and the Rev1 C-terminal domain	A, B	119	Mus musculus	Mutation(s): 0  Gene Names: Polk, Dinb1, Rev1, Rev1l EC: 2.7.7.7 (PDB Primary Data), 2.7.7 (PDB Primary Data)
UniProt
Find proteins for Q920Q2 (Mus musculus) Explore Q920Q2  Go to UniProtKB:  Q920Q2
Find proteins for Q9QUG2 (Mus musculus) Explore Q9QUG2  Go to UniProtKB:  Q9QUG2
UniProt Groups	Q920Q2Q9QUG2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EQ7 (Subject of Investigation/LOI)	C [auth B]	8-chloro-2-(2,4-dichloroanilino)-3-(3-methylbutanoyl)-5-nitroquinolin-4(1H)-one C20 H16 Cl3 N3 O4 LRTXIQCBQIKIOH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.55	α = 90
b = 51.02	β = 90
c = 98.92	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Najeeb, J., Zhou, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA191448

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2019-06-26
  Changes: Data collection, Database references
• Version 1.2: 2019-07-10
  Changes: Data collection, Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2026-04-15
  Changes: Data collection, Derived calculations, Structure summary