4YIR

Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


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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

  • DOI: 10.1038/ncomms6849
  • Primary Citation of Related Structures:  
    6UBF, 4YIR

  • 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 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.


    Organizational Affiliation

    Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein RAD4A538Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: RAD4YER162C
UniProt
Find proteins for P14736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14736 
Go to UniProtKB:  P14736
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UV excision repair protein RAD23B [auth X]171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAD23YEL037CSYGP-ORF29
UniProt
Find proteins for P32628 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32628 
Go to UniProtKB:  P32628
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
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]24synthetic construct
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsLengthOrganismImage
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]24synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.405α = 90
b = 79.405β = 90
c = 404.366γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Searle Funds at The Chicago Community TrustUnited States--
The Chancellor's Discovery Fund, University of Illinois at ChicagoUnited States--
Startup funding, University of Illinois at ChicagoUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release