Biological Assembly 1  

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

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 176.20 kDa 
• Atom Count: 9733 
• Modelled Residue Count: 1131 
• Deposited Residue Count: 1316 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2WWY

Structure of human RECQ-like helicase in complex with a DNA substrate

• PDB DOI: 10.2210/pdb2WWY/pdb
• NDB: NA0414

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-30 Released: 2009-12-29 
• Deposition Author(s): Pike, A.C.W., Zhang, Y., Schnecke, C., Chaikuad, A., Krojer, T., Cooper, C.D.O., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., Gileadi, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Recq1 Helicase-Driven DNA Unwinding, Annealing, and Branch Migration: Insights from DNA Complex Structures

Pike, A.C.W., Zhang, Y., Schnecke, C., Chaikuad, A., Krojer, T., Cooper, C.D.O., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., Gileadi, O.

(2015) Proc Natl Acad Sci U S A 112: 4286

• PubMed: 25831490 
• DOI: 10.1073/pnas.1417594112
• Primary Citation of Related Structures:  
  2WWY, 4U7D


• PubMed Abstract: 
  

RecQ helicases are a widely conserved family of ATP-dependent motors with diverse roles in nearly every aspect of bacterial and eukaryotic genome maintenance. However, the physical mechanisms by which RecQ helicases recognize and process specific DNA replication and repair intermediates are largely unknown. Here, we solved crystal structures of the human RECQ1 helicase in complexes with tailed-duplex DNA and ssDNA. The structures map the interactions of the ssDNA tail and the branch point along the helicase and Zn-binding domains, which, together with reported structures of other helicases, define the catalytic stages of helicase action. We also identify a strand-separating pin, which (uniquely in RECQ1) is buttressed by the protein dimer interface. A duplex DNA-binding surface on the C-terminal domain is shown to play a role in DNA unwinding, strand annealing, and Holliday junction (HJ) branch migration. We have combined EM and analytical ultracentrifugation approaches to show that RECQ1 can form what appears to be a flat, homotetrameric complex and propose that RECQ1 tetramers are involved in HJ recognition. This tetrameric arrangement suggests a platform for coordinated activity at the advancing and receding duplexes of an HJ during branch migration.

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Related Citations: 

• Structure of the Human Recq1 Helicase Reveals a Putative Strand-Separation Pin.
  Pike, A.C.W., Shrestha, B., Popuri, V., Burgess-Brown, N., Muzzolini, L., Costantini, S., Vindigni, A., Gileadi, O.
  (2009) Proc Natl Acad Sci U S A 106: 1039

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Organizational Affiliation: 

Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-DEPENDENT DNA HELICASE Q1	A, B	591	Homo sapiens	Mutation(s): 0  Gene Names: RECQL, RECQ1, RECQL1 EC: 3.6.1 (PDB Primary Data), 3.6.4.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P46063 (Homo sapiens) Explore P46063  Go to UniProtKB:  P46063
PHAROS:  P46063 GTEx:  ENSG00000004700

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA OLIGO (27BP)	C [auth O], E [auth Q], F [auth R], H [auth T]	27	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*DA DG DC DG DT DC DG DA DG DA DT DC DCP)-3'	D [auth P], G [auth S]	13	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	J [auth A], K [auth A], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	I [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	L [auth A], P [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.333	α = 90
b = 174.218	β = 93.31
c = 100.229	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-30 
• Released Date: 2009-12-29 
Deposition Author(s): Pike, A.C.W., Zhang, Y., Schnecke, C., Chaikuad, A., Krojer, T., Cooper, C.D.O., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., Gileadi, O.

Revision History  

• Version 1.0: 2009-12-29
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Database references, Derived calculations, Version format compliance
• Version 1.2: 2015-04-15
  Changes: Database references
• Version 1.3: 2015-04-22
  Changes: Database references
• Version 1.4: 2015-09-16
  Changes: Derived calculations, Source and taxonomy
• Version 1.5: 2018-01-24
  Changes: Database references