2WWY | pdb_00002wwy

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.236 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2WWY

This is version 1.6 of the entry. See complete history

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

  • DOI: https://doi.org/10.1073/pnas.1417594112
  • Primary Citation 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.


  • Organizational Affiliation
    • Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom;

Macromolecule Content 

  • Total Structure Weight: 176.2 kDa 
  • Atom Count: 9,733 
  • Modeled Residue Count: 1,131 
  • Deposited Residue Count: 1,316 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-DEPENDENT DNA HELICASE Q1
A, B
591Homo sapiensMutation(s): 0 
EC: 3.6.1 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P46063 (Homo sapiens)
Explore P46063 
Go to UniProtKB:  P46063
PHAROS:  P46063
GTEx:  ENSG00000004700 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46063
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA OLIGO (27BP)C [auth O],
E [auth Q],
F [auth R],
H [auth T]
27synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*DA DG DC DG DT DC DG DA DG DA DT DC DCP)-3'D [auth P],
G [auth S]
13synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A],
M [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
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 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.333α = 90
b = 174.218β = 93.31
c = 100.229γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.6: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description