5G35 | pdb_00005g35

Structure of Rad14 in complex with acetylaminopyren-C8-guanine containing DNA

• PDB DOI: https://doi.org/10.2210/pdb5G35/pdb
• NAKB: 5G35

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-04-18 Released: 2016-06-01 
• Deposition Author(s): Simon, N., Ebert, C., Schneider, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for Bulky Adduct DNA Lesion Recognition by the Nucleotide Excision Repair Protein Rad14.

Schneider, S., Simon, N., Ebert, C.

(2016) Chemistry 22: 10782

• PubMed: 27223336 
• DOI: https://doi.org/10.1002/chem.201602438
• Primary Citation Related Structures: 
  5G32, 5G33, 5G34, 5G35


• PubMed Abstract: 
  

  Heterocyclic aromatic amines react with purine bases and result in bulky DNA adducts that cause mutations. Such structurally diverse lesions are substrates for the nucleotide excision repair (NER). It is thought that the NER machinery recognises and verifies distorted DNA conformations, also involving the xeroderma pigmentosum group A and C proteins (XPA, XPC) that act as a scaffold between the DNA substrate and several other NER proteins. Here we present the synthesis of DNA molecules containing the polycyclic, aromatic amine C8-guanine lesions acetylaminophenyl, acetylaminonaphthyl, acetylaminoanthryl, and acetylaminopyrenyl, as well as their crystal structures in complex with the yeast XPA homologue Rad14. This work further substantiates the indirect lesion-detection mechanism employed by the NER system that recognises destabilised and deformable DNA structures.

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Organizational Affiliation: 
• Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstrasse 13, 81377, München, Germany.
Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.65 kDa 
• Atom Count: 3,093 
• Modeled Residue Count: 285 
• Deposited Residue Count: 320 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAD14	A, B	131	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: RAD14, YMR201C, YM8325.02C
UniProt
Find proteins for P28519 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P28519  Go to UniProtKB:  P28519

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*TP*CP*TP*AP*8PYP*TP*CP*AP*TP*CP*AP*CP)-3'	C, E	15	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'	D, F	14	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.17	α = 90
b = 53.17	β = 90
c = 131.307	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-01 
Deposition Author(s): Simon, N., Ebert, C., Schneider, S.

Revision History  

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Database references
• Version 1.2: 2016-08-03
  Changes: Database references
• Version 2.0: 2019-05-15
  Changes: Data collection, Derived calculations, Other, Polymer sequence
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description