4YIR

Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0501 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  

  • 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 crys ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA repair protein RAD4
A
538Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
Gene Names: RAD4
Find proteins for P14736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P14736
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UV excision repair protein RAD23
X
171Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RAD23
Find proteins for P32628 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32628
Entity ID: 3
MoleculeChainsLengthOrganism
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')W24synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
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')Y24synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
G47
Query on G47
W
DNA LINKINGC12 H18 N5 O7 P SDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0501 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.405α = 90.00
b = 79.405β = 90.00
c = 404.366γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXphasing
PHENIXrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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