7S9W | pdb_00007s9w

Structure of DrmAB:ADP:DNA complex

• PDB DOI: https://doi.org/10.2210/pdb7S9W/pdb
• NAKB: 7S9W
• EM Map EMD-24939: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Serratia, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-09-21 Released: 2022-06-15 
• Deposition Author(s): Bravo, J.P.K., Taylor, D.W., Brounds, S.J.J., Aparicio-Maldonado, C.
• Funding Organization(s): Welch Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for broad anti-phage immunity by DISARM.

Bravo, J.P.K., Aparicio-Maldonado, C., Nobrega, F.L., Brouns, S.J.J., Taylor, D.W.

(2022) Nat Commun 13: 2987-2987

• PubMed: 35624106 
• DOI: https://doi.org/10.1038/s41467-022-30673-1
• Primary Citation Related Structures: 
  7S9V, 7S9W


• PubMed Abstract: 
  

  In the evolutionary arms race against phage, bacteria have assembled a diverse arsenal of antiviral immune strategies. While the recently discovered DISARM (Defense Island System Associated with Restriction-Modification) systems can provide protection against a wide range of phage, the molecular mechanisms that underpin broad antiviral targeting but avoiding autoimmunity remain enigmatic. Here, we report cryo-EM structures of the core DISARM complex, DrmAB, both alone and in complex with an unmethylated phage DNA mimetic. These structures reveal that DrmAB core complex is autoinhibited by a trigger loop (TL) within DrmA and binding to DNA substrates containing a 5' overhang dislodges the TL, initiating a long-range structural rearrangement for DrmAB activation. Together with structure-guided in vivo studies, our work provides insights into the mechanism of phage DNA recognition and specific activation of this widespread antiviral defense system.

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Organizational Affiliation: 
• Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands.
Kavli Institute of Nanoscience, Delft, The Netherlands.
School of Biological Sciences, University of Southampton, SO17 1BJ, Southampton, UK.
Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands. [e-mail].
Kavli Institute of Nanoscience, Delft, The Netherlands. [e-mail].
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA. [e-mail].
Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX, 78712, USA. [e-mail].
Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA. [e-mail].
LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX, 78712, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 219.16 kDa 
• Atom Count: 14,052 
• Modeled Residue Count: 1,774 
• Deposited Residue Count: 1,951 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DrmA	A	1,325	Serratia	Mutation(s): 0
UniProt
Find proteins for A0A979HMQ0 (Serratia) Explore A0A979HMQ0  Go to UniProtKB:  A0A979HMQ0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DrmB	B	619	Serratia	Mutation(s): 0
UniProt
Find proteins for A0A979HMQ1 (Serratia) Explore A0A979HMQ1  Go to UniProtKB:  A0A979HMQ1

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')	C	7	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): Bravo, J.P.K., Taylor, D.W., Brounds, S.J.J., Aparicio-Maldonado, C.

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Funding Organization	Location	Grant Number
Welch Foundation	United States	F-1938

Revision History  

• Version 1.0: 2022-06-15
  Type: Initial release
  
• Version 1.1: 2024-06-05
  Changes: Data collection
• Version 1.2: 2025-05-14
  Changes: Data collection, Structure summary