4YIR | pdb_00004yir

Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA

• PDB DOI: https://doi.org/10.2210/pdb4YIR/pdb
• Entry: 4YIR supersedes: 4U29
• NAKB: 4YIR

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Saccharomyces cerevisiae S288C, synthetic construct
• Expression System: Trichoplusia ni, synthetic construct
• Mutation(s): Yes 


• Deposited: 2015-03-02 Released: 2015-03-11 
• Deposition Author(s): Min, J.-H., Chen, X., Kim, Y.
• Funding Organization(s): The Searle Funds at The Chicago Community Trust, The Chancellor's Discovery Fund, University of Illinois at Chicago, Startup funding, University of Illinois at Chicago

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Kinetic gating mechanism of DNA damage recognition by Rad4/XPC.

Chen, X., Velmurugu, Y., Zheng, G., Park, B., Shim, Y., Kim, Y., Liu, L., Van Houten, B., He, C., Ansari, A., Min, J.H.

(2015) Nat Commun 6: 5849

• PubMed: 25562780 
• DOI: https://doi.org/10.1038/ncomms6849
• Primary Citation Related Structures: 
  4YIR, 6UBF


• PubMed Abstract: 
  

  The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.

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Organizational Affiliation: 
• Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA.
Department of Physics, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA.
Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA.
Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, Illinois 60439, USA.
Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, USA.
1] Department of Physics, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA [2] Department of Bioengineering, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 95.17 kDa 
• Atom Count: 5,459 
• Modeled Residue Count: 599 
• Deposited Residue Count: 757 
• 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	538	Saccharomyces cerevisiae S288C	Mutation(s): 2  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]	171	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(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*CP*CP*CP*GP*CP*TP*AP*CP*AP*A)-3')	C [auth W]	24	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*G*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3')	D [auth Y]	24	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.405	α = 90
b = 79.405	β = 90
c = 404.366	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-03-11 
Deposition Author(s): Min, J.-H., Chen, X., Kim, Y.
• This entry supersedes: 4U29

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Funding Organization	Location	Grant Number
The Searle Funds at The Chicago Community Trust	United States	--
The Chancellor's Discovery Fund, University of Illinois at Chicago	United States	--
Startup funding, University of Illinois at Chicago	United States	--

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2024-10-23
  Changes: Structure summary