6UG1 | pdb_00006ug1

Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex

• PDB DOI: https://doi.org/10.2210/pdb6UG1/pdb
• NAKB: 6UG1

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2019-09-25 Released: 2021-03-31 
• Deposition Author(s): Paul, D., Min, J.-H.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.272 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex.

Paul, D., Mu, H., Tavakoli, A., Dai, Q., Chakraborty, S., He, C., Ansari, A., Broyde, S., Min, J.H.

(2021) DNA Repair (Amst) 107: 103194-103194

• PubMed: 34428697 
• DOI: https://doi.org/10.1016/j.dnarep.2021.103194
• Primary Citation Related Structures: 
  6UG1


• PubMed Abstract: 
  

  Rad4/XPC recognizes diverse DNA lesions to initiate nucleotide excision repair (NER). However, NER propensities among lesions vary widely and repair-resistant lesions are persistent and thus highly mutagenic. Rad4 recognizes repair-proficient lesions by unwinding ('opening') the damaged DNA site. Such 'opening' is also observed on a normal DNA sequence containing consecutive C/G's (CCC/GGG) when tethered to Rad4 to prevent protein diffusion. However, it was unknown if such tethering-facilitated DNA 'opening' could occur on any DNA or if certain structures/sequences would resist being 'opened'. Here, we report that DNA containing alternating C/G's (CGC/GCG) failed to be opened even when tethered; instead, Rad4 bound in a 180°-reversed manner, capping the DNA end. Fluorescence lifetime studies of DNA conformations in solution showed that CCC/GGG exhibits local pre-melting that is absent in CGC/GCG. In MD simulations, CGC/GCG failed to engage Rad4 to promote 'opening' contrary to CCC/GGG. Altogether, our study illustrates how local sequences can impact DNA recognition by Rad4/XPC and how certain DNA sites resist being 'opened' even with Rad4 held at that site indefinitely. The contrast between CCC/GGG and CGC/GCG sequences in Rad4-DNA recognition may help decipher a lesion's mutagenicity in various genomic sequence contexts to explain lesion-determined mutational hot and cold spots.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA.
Department of Biology, New York University, New York, NY, 10003, USA.
Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA.
Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA; Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA.
Department of Biology, New York University, New York, NY, 10003, USA. Electronic address: [e-mail].
Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 78.12 kDa 
• Atom Count: 5,231 
• Modeled Residue Count: 576 
• Deposited Residue Count: 603 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD4	A	504	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RAD4, YER162C
UniProt
Find proteins for P14736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14736  Go to UniProtKB:  P14736

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UV excision repair protein RAD23	B [auth X]	57	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RAD23, YEL037C, SYGP-ORF29
UniProt
Find proteins for P32628 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32628  Go to UniProtKB:  P32628

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3')	C [auth Y]	21	Saccharomyces cerevisiae

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*CP*CP*TP*AP*CP*AP*A)-3')	D [auth W]	21	Saccharomyces cerevisiae

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.272 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.244	α = 105.51
b = 59.571	β = 97.88
c = 78.24	γ = 107.14

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Paul, D., Min, J.-H.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2021-09-08
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Structure summary