Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 67.41 kDa 
• Atom Count: 4519 
• Modelled Residue Count: 541 
• Deposited Residue Count: 585 
• Unique protein chains: 1

6YHR

Crystal structure of Werner syndrome helicase

• PDB DOI: 10.2210/pdb6YHR/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-03-30 Released: 2020-04-29 
• Deposition Author(s): Newman, J.A., Gavard, A.E., Savitsky, P., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Structure of the helicase core of Werner helicase, a key target in microsatellite instability cancers.

Newman, J.A., Gavard, A.E., Lieb, S., Ravichandran, M.C., Hauer, K., Werni, P., Geist, L., Bottcher, J., Engen, J.R., Rumpel, K., Samwer, M., Petronczki, M., Gileadi, O.

(2021) Life Sci Alliance 4

• PubMed: 33199508 
• DOI: 10.26508/lsa.202000795
• Primary Citation of Related Structures:  
  6YHR


• PubMed Abstract: 
  

Loss of WRN, a DNA repair helicase, was identified as a strong vulnerability of microsatellite instable (MSI) cancers, making WRN a promising drug target. We show that ATP binding and hydrolysis are required for genome integrity and viability of MSI cancer cells. We report a 2.2-Å crystal structure of the WRN helicase core (517-1,093), comprising the two helicase subdomains and winged helix domain but not the HRDC domain or nuclease domains. The structure highlights unusual features. First, an atypical mode of nucleotide binding that results in unusual relative positioning of the two helicase subdomains. Second, an additional β-hairpin in the second helicase subdomain and an unusual helical hairpin in the Zn ²⁺ binding domain. Modelling of the WRN helicase in complex with DNA suggests roles for these features in the binding of alternative DNA structures. NMR analysis shows a weak interaction between the HRDC domain and the helicase core, indicating a possible biological role for this association. Together, this study will facilitate the structure-based development of inhibitors against WRN helicase.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Oxford, Oxford, UK [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Werner syndrome ATP-dependent helicase	A	585	Homo sapiens	Mutation(s): 1  Gene Names: WRN, RECQ3, RECQL2 EC: 3.6.4.12 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14191 (Homo sapiens) Explore Q14191  Go to UniProtKB:  Q14191
PHAROS:  Q14191

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.595	α = 90
b = 90.627	β = 90
c = 138.233	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-03-30 
• Released Date: 2020-04-29 
Deposition Author(s): Newman, J.A., Gavard, A.E., Savitsky, P., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-12-09
  Changes: Database references, Derived calculations