9DBJ | pdb_00009dbj

Structure of Hailong HalB R164A mutant with non-hydrolyzable dATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.239 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

A DNA-gated molecular guard controls bacterial Hailong anti-phage defence.

Tan, J.M.J.Melamed, S.Cofsky, J.C.Syangtan, D.Hobbs, S.J.Del Marmol, J.Jost, M.Kruse, A.C.Sorek, R.Kranzusch, P.J.

(2025) Nature 643: 794-800

  • DOI: https://doi.org/10.1038/s41586-025-09058-z
  • Primary Citation Related Structures: 
    9DBH, 9DBI, 9DBJ, 9NYI

  • PubMed Abstract: 

    Animal and bacterial cells use nucleotidyltransferase (NTase) enzymes to respond to viral infection and control major forms of immune signaling including cGAS-STING innate immunity and CBASS anti-phage defence 1-4 . Here we discover a family of bacterial defence systems, which we name Hailong, that use NTase enzymes to constitutively synthesize DNA signals and guard against phage infection. Hailong protein B (HalB) is an NTase that converts deoxy-ATP into single-stranded DNA oligomers. A series of X-ray crystal structures define a stepwise mechanism of HalB DNA synthesis initiated by a C-terminal tyrosine residue that enables de novo enzymatic priming. We show that HalB DNA signals bind to and repress activation of a partnering Hailong protein A (HalA) effector complex. A 2.0 Å cryo-EM structure of the HalA-DNA complex reveals a membrane protein with a conserved ion channel domain and a unique crown domain that binds the DNA signal and gates activation. Analyzing Hailong defence in vivo, we demonstrate that viral DNA exonucleases required for phage replication trigger release of the primed HalA complex and induce protective host cell growth arrest. Our results explain how inhibitory nucleotide immune signals can serve as molecular guards against phage infection and expand the mechanisms NTase enzymes use to control antiviral immunity.


  • Organizational Affiliation
    • Department of Microbiology, Harvard Medical School, Boston, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 160.14 kDa 
  • Atom Count: 11,025 
  • Modeled Residue Count: 1,298 
  • Deposited Residue Count: 1,374 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HalB
A, B, C, D, E
A, B, C, D, E, F
229Rhodobacteraceae bacterium QY30Mutation(s): 0 

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A3G
(Subject of Investigation/LOI)

Query on A1A3G



Download:Ideal Coordinates CCD File
G [auth A](2R)-3-(4-{[(S)-{[(2R,3R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}phenyl)-2-{[(2R)-pyrrolidine-2-carbonyl]amino}propanoic acid (non-preferred name)
C24 H30 N7 O9 P
FVPBNOZKHKXLRZ-UHFFFAOYSA-N
A1A3H
(Subject of Investigation/LOI)

Query on A1A3H



Download:Ideal Coordinates CCD File
N [auth C](2R)-2-amino-3-(4-{[(R)-{[(2R,3R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}phenyl)propanoic acid (non-preferred name)
C19 H23 N6 O8 P
FVTPNOGUOYZKIO-UHFFFAOYSA-N
F2A
(Subject of Investigation/LOI)

Query on F2A



Download:Ideal Coordinates CCD File
H [auth A]
K [auth B]
O [auth C]
S [auth D]
V [auth E]
H [auth A],
K [auth B],
O [auth C],
S [auth D],
V [auth E],
Y [auth F]
2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine
C11 H18 N5 O11 P3
XETARULVTCYJAN-XLPZGREQSA-N
D5M
(Subject of Investigation/LOI)

Query on D5M



Download:Ideal Coordinates CCD File
R [auth D]2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
MN
(Subject of Investigation/LOI)

Query on MN



Download:Ideal Coordinates CCD File
AA [auth F]
I [auth A]
J [auth A]
L [auth B]
M [auth B]
AA [auth F],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
T [auth D],
U [auth D],
W [auth E],
X [auth E],
Z [auth F]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.239 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.05α = 90
b = 169.05β = 90
c = 139.384γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1DP2GM146250

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Database references
  • Version 1.2: 2025-07-30
    Changes: Database references