6UIN

Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex

• PDB DOI: https://doi.org/10.2210/pdb6UIN/pdb
• NAKB: 6UIN

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


• Deposited: 2019-10-01 Released: 2020-10-14 
• 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: 3.35 Å
• R-Value Free: 0.262 
• R-Value Work: 0.209 
• R-Value Observed: 0.214 

Literature

Tethering-facilitated DNA 'opening' and complementary roles of beta-hairpin motifs in the Rad4/XPC DNA damage sensor protein

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

(2021) Nucleic Acids Res 48: 12348-12364

• DOI: https://doi.org/10.1093/nar/gkaa909

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: 94.61 kDa 
• Atom Count: 5,178 
• Modelled Residue Count: 573 
• 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	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]	171	Saccharomyces cerevisiae	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*CP*CP*TP*AP*CP*AP*A)-3')	C [auth W]	24	Saccharomyces cerevisiae

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 0.262 
• R-Value Work: 0.209 
• R-Value Observed: 0.214 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.665	α = 90
b = 77.665	β = 90
c = 264.054	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-14 
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: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2021-04-28
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description