4CDG

Crystal structure of the Bloom's syndrome helicase BLM in complex with Nanobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Crystal Structure of the Bloom'S Syndrome Helicase Indicates a Role for the Hrdc Domain in Conformational Changes.

Newman, J.A.Savitsky, P.Allerston, C.K.Bizard, A.H.Ozer, O.Sarlos, K.Liu, Y.Pardon, E.Steyaert, J.Hickson, I.D.Gileadi, O.

(2015) Nucleic Acids Res 43: 5221

  • DOI: https://doi.org/10.1093/nar/gkv373
  • Primary Citation of Related Structures:  
    4CDG, 4CGZ

  • PubMed Abstract: 

    Bloom's syndrome helicase (BLM) is a member of the RecQ family of DNA helicases, which play key roles in the maintenance of genome integrity in all organism groups. We describe crystal structures of the BLM helicase domain in complex with DNA and with an antibody fragment, as well as SAXS and domain association studies in solution. We show an unexpected nucleotide-dependent interaction of the core helicase domain with the conserved, poorly characterized HRDC domain. The BLM-DNA complex shows an unusual base-flipping mechanism with unique positioning of the DNA duplex relative to the helicase core domains. Comparison with other crystal structures of RecQ helicases permits the definition of structural transitions underlying ATP-driven helicase action, and the identification of a nucleotide-regulated tunnel that may play a role in interactions with complex DNA substrates.


  • Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BLOOM SYNDROME PROTEIN
A, B
673Homo sapiensMutation(s): 0 
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P54132 (Homo sapiens)
Explore P54132 
Go to UniProtKB:  P54132
PHAROS:  P54132
GTEx:  ENSG00000197299 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54132
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NANOBODY
C, D
147Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.666α = 69.39
b = 88.425β = 89.84
c = 95.12γ = 77.07
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2014-01-08
    Changes: Source and taxonomy
  • Version 1.2: 2015-05-06
    Changes: Database references
  • Version 1.3: 2015-06-10
    Changes: Database references
  • Version 1.4: 2018-01-24
    Changes: Structure summary
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description