4A15 | pdb_00004a15

Crystal structure of an XPD DNA complex

• PDB DOI: https://doi.org/10.2210/pdb4A15/pdb
• NAKB: 4A15

• Classification: HYDROLASE
• Organism(s): Thermoplasma acidophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-14 Released: 2012-02-01 
• Deposition Author(s): Kuper, J., Wolski, S.C., Michels, G., Kisker, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.250 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Functional and Structural Studies of the Nucleotide Excision Repair Helicase Xpd Suggest a Polarity for DNA Translocation.

Kuper, J., Wolski, S.C., Michels, G., Kisker, C.

(2011) EMBO J 31: 494

• PubMed: 22081108 
• DOI: https://doi.org/10.1038/emboj.2011.374
• Primary Citation Related Structures: 
  4A15


• PubMed Abstract: 
  

  The XPD protein is a vital subunit of the general transcription factor TFIIH which is not only involved in transcription but is also an essential component of the eukaryotic nucleotide excision DNA repair (NER) pathway. XPD is a superfamily-2 5'-3' helicase containing an iron-sulphur cluster. Its helicase activity is indispensable for NER and it plays a role in the damage verification process. Here, we report the first structure of XPD from Thermoplasma acidophilum (taXPD) in complex with a short DNA fragment, thus revealing the polarity of the translocated strand and providing insights into how the enzyme achieves its 5'-3' directionality. Accompanied by a detailed mutational and biochemical analysis of taXPD, we define the path of the translocated DNA strand through the protein and identify amino acids that are critical for protein function.

---

Organizational Affiliation: 
• Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Würzburg, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 73.35 kDa 
• Atom Count: 5,067 
• Modeled Residue Count: 600 
• Deposited Residue Count: 624 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-DEPENDENT DNA HELICASE TA0057	A	620	Thermoplasma acidophilum	Mutation(s): 0  EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
Find proteins for Q9HM14 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HM14  Go to UniProtKB:  Q9HM14

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*DTP*AP*CP*GP)-3'	B [auth E]	4	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.250 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.06	α = 90
b = 79.06	β = 90
c = 175.69	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Kuper, J., Wolski, S.C., Michels, G., Kisker, C.

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description