7AUD | pdb_00007aud

Structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 
    0.269 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein.

Chen, X., Ali, Y.I., Fisher, C.E., Arribas-Bosacoma, R., Rajasekaran, M.B., Williams, G., Walker, S., Booth, J.R., Hudson, J.J., Roe, S.M., Pearl, L.H., Ward, S.E., Pearl, F.M., Oliver, A.W.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.65339
  • Primary Citation Related Structures: 
    7AUC, 7AUD

  • PubMed Abstract: 

    BLM (Bloom syndrome protein) is a RECQ-family helicase involved in the dissolution of complex DNA structures and repair intermediates. Synthetic lethality analysis implicates BLM as a promising target in a range of cancers with defects in the DNA damage response; however, selective small molecule inhibitors of defined mechanism are currently lacking. Here, we identify and characterise a specific inhibitor of BLM's ATPase-coupled DNA helicase activity, by allosteric trapping of a DNA-bound translocation intermediate. Crystallographic structures of BLM-DNA-ADP-inhibitor complexes identify a hitherto unknown interdomain interface, whose opening and closing are integral to translocation of ssDNA, and which provides a highly selective pocket for drug discovery. Comparison with structures of other RECQ helicases provides a model for branch migration of Holliday junctions by BLM.

    • Organizational Affiliation: 
    • Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 417.98 kDa 
  • Atom Count: 25,271 
  • Modeled Residue Count: 3,165 
  • Deposited Residue Count: 3,468 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bloom syndrome protein,Bloom syndrome protein
A, B, C, D, E
A, B, C, D, E, F
563Homo sapiensMutation(s): 0 
Gene Names: BLM, RECQ2, RECQL3
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
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*AP*CP*CP*CP*GP*AP*TP*GP*TP*GP*T)-3')15synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP


Download:Ideal Coordinates CCD File
BA [auth D]
FA [auth E]
JA [auth F]
N [auth A]
S [auth B]
BA [auth D],
FA [auth E],
JA [auth F],
N [auth A],
S [auth B],
W [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
RY8
(Subject of Investigation/LOI)

Query on RY8


Download:Ideal Coordinates CCD File
CA [auth D]
GA [auth E]
KA [auth F]
O [auth A]
T [auth B]
CA [auth D],
GA [auth E],
KA [auth F],
O [auth A],
T [auth B],
X [auth C]
N-(2,3-dimethyl-5-sulfamoylphenyl)-4-(2-methylthiazol-4-yl)benzamide
C19 H19 N3 O3 S2
GGIKQVGRVUTAKR-UHFFFAOYSA-N
PG4

Query on PG4


Download:Ideal Coordinates CCD File
DA [auth D]
HA [auth E]
P [auth A]
Q [auth A]
U [auth B]
DA [auth D],
HA [auth E],
P [auth A],
Q [auth A],
U [auth B],
Y [auth C],
Z [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
AA [auth D]
EA [auth E]
IA [auth F]
M [auth A]
R [auth B]
AA [auth D],
EA [auth E],
IA [auth F],
M [auth A],
R [auth B],
V [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
LA [auth F]
MA [auth M]
NA [auth N]
OA [auth P]
PA [auth Q]
LA [auth F],
MA [auth M],
NA [auth N],
OA [auth P],
PA [auth Q],
QA [auth Q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free:  0.269 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.916α = 72.64
b = 111.709β = 80.18
c = 132.344γ = 79.22
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC302/A24386
Wellcome TrustUnited Kingdom110578/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.3: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary