8KBL | pdb_00008kbl

Structure of AcrIIA7 complexed with 1',3'-cADPR and cGG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.234 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: in silico
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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

Single phage proteins sequester signals from TIR and cGAS-like enzymes.

Li, D.Xiao, Y.Fedorova, I.Xiong, W.Wang, Y.Liu, X.Huiting, E.Ren, J.Gao, Z.Zhao, X.Cao, X.Zhang, Y.Bondy-Denomy, J.Feng, Y.

(2024) Nature 635: 719-727

  • DOI: https://doi.org/10.1038/s41586-024-08122-4
  • Primary Citation Related Structures: 
    8KBB, 8KBC, 8KBD, 8KBE, 8KBF, 8KBG, 8KBH, 8KBI, 8KBJ, 8KBK, 8KBL, 8KBM, 8WJC, 8WJD, 8WJE

  • PubMed Abstract: 

    Prokaryotic anti-phage immune systems use TIR and cGAS-like enzymes to produce 1''-3'-glycocyclic ADP-ribose (1''-3'-gcADPR) and cyclic dinucleotide (CDN) and cyclic trinucleotide (CTN) signalling molecules, respectively, which limit phage replication 1-3 . However, how phages neutralize these distinct and common systems is largely unclear. Here we show that the Thoeris anti-defence proteins Tad1 4 and Tad2 5 both achieve anti-cyclic-oligonucleotide-based anti-phage signalling system (anti-CBASS) activity by simultaneously sequestering CBASS cyclic oligonucleotides. Apart from binding to the Thoeris signals 1''-3'-gcADPR and 1''-2'-gcADPR, Tad1 also binds to numerous CBASS CDNs and CTNs with high affinity, inhibiting CBASS systems that use these molecules in vivo and in vitro. The hexameric Tad1 has six binding sites for CDNs or gcADPR, which are independent of the two high-affinity binding sites for CTNs. Tad2 forms a tetramer that also sequesters various CDNs in addition to gcADPR molecules, using distinct binding sites to simultaneously bind to these signals. Thus, Tad1 and Tad2 are both two-pronged inhibitors that, alongside anti-CBASS protein 2 (Acb2 6-8 ), establish a paradigm of phage proteins that use distinct binding sites to flexibly sequester a considerable breadth of cyclic nucleotides.


  • Organizational Affiliation
    • State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 12.97 kDa 
  • Atom Count: 992 
  • Modeled Residue Count: 104 
  • Deposited Residue Count: 104 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inhibitor of Type II CRISPR-Cas system104metagenomeMutation(s): 0 
Gene Names: acrIIA7
UniProt
Find proteins for A0A447EB45 (metagenome)
Explore A0A447EB45 
Go to UniProtKB:  A0A447EB45
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A447EB45
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E
(Subject of Investigation/LOI)

Query on C2E



Download:Ideal Coordinates CCD File
C [auth A]9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
OJC
(Subject of Investigation/LOI)

Query on OJC



Download:Ideal Coordinates CCD File
B [auth A](2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione
C15 H21 N5 O13 P2
NDSLKXAJVDJCEG-ZQSHOCFMSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.234 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.729α = 90
b = 63.729β = 90
c = 63.153γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Database references, Structure summary
  • Version 1.2: 2024-11-13
    Changes: Database references
  • Version 1.3: 2024-12-04
    Changes: Data collection, Database references