8YLE | pdb_00008yle

Crystal structure of Werner syndrome helicase complexed with AMP-PCP

• PDB DOI: https://doi.org/10.2210/pdb8YLE/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-06 Released: 2024-04-10 
• Deposition Author(s): Yang, Y., Fu, L., Sun, X., Cheng, H., Chen, R.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.214 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Structure of werner syndrome helicase complexed with AMP-PCP at 1.86 Angstroms resolution.

Chen, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 49.76 kDa 
• Atom Count: 3,595 
• Modeled Residue Count: 416 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN	A	430	Homo sapiens	Mutation(s): 0  Gene Names: WRN, RECQ3, RECQL2 EC: 3.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14191 (Homo sapiens) Explore Q14191  Go to UniProtKB:  Q14191
PHAROS:  Q14191 GTEx:  ENSG00000165392

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP (Subject of Investigation/LOI)	B [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
ZN	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.214 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.663	α = 90
b = 89.561	β = 102.88
c = 54.359	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Yang, Y., Fu, L., Sun, X., Cheng, H., Chen, R.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release