11CQ | pdb_000011cq

KpSwz in complex with bacteriophage Bas14 Portal


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 11CQ

This is version 1.1 of the entry. See complete history

Literature

TIR-like NADases act in bacterial immunity and the RNA vault.

Osinski, A.Mayro, B.Lopez, V.A.Schrad, J.Choi, H.Tomchick, D.R.Pawlowski, K.Forsberg, K.Shahmoradian, S.H.Tagliabracci, V.S.

(2026) bioRxiv 

  • DOI: https://doi.org/10.64898/2026.05.01.722283
  • Primary Citation Related Structures: 
    10WC, 11CQ, 11CV, 11DR, 11DV, 11EE, 11EQ, 11FH, 11GZ, 11JB, 11JC, 11JD, 11JF

  • PubMed Abstract: 

    Across all domains of life, organisms exploit NAD + metabolism as a central line of defense against invading pathogens. Here, we show that domain of unknown function 4062 (DUF4062) is a widespread family of TIR-like NADases that hydrolyze NAD + to ADP-ribose and nicotinamide. In bacteria, DUF4062 homologs form a previously unrecognized antiphage defense system, which we name Swarożyc, that assembles with the phage portal into a supramolecular NADase complex to induce abortive infection. In eukaryotes, DUF4062 is found in TEP1, which we demonstrate functions as an active NADase within the RNA vault, an enigmatic organelle-like structure. Single-particle cryo-electron microscopy reveals ADP-ribose bound within the shoulder of both reconstituted and human brain vaults, while cryo-electron tomography positions TEP1 along the central axis at the shoulder. Thus, TEP1, like bacterial Swarożyc, functions by depleting NAD + , providing new insight into the long-standing mystery of vault function.

Macromolecule Content 

  • Total Structure Weight: 1,164.94 kDa 
  • Atom Count: 46,563 
  • Modeled Residue Count: 5,944 
  • Deposited Residue Count: 10,406 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Portal protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
514Escherichia phage TheodorHerzlMutation(s): 0 
Gene Names: bas14_0003
UniProt
Find proteins for A0AAE7VZF8 (Escherichia phage TheodorHerzl)
Explore A0AAE7VZF8 
Go to UniProtKB:  A0AAE7VZF8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAE7VZF8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
KpSwz326Klebsiella pneumoniaeMutation(s): 0 
Gene Names: MS5452_35130
UniProt
Find proteins for A0A0H3ET69 (Escherichia coli O83:H1 (strain NRG 857C / AIEC))
Explore A0A0H3ET69 
Go to UniProtKB:  A0A0H3ET69
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3ET69
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth C]
CA [auth D]
DA [auth E]
EA [auth F]
AA [auth B],
BA [auth C],
CA [auth D],
DA [auth E],
EA [auth F],
FA [auth G],
GA [auth H],
HA [auth I],
IA [auth J],
JA [auth K],
KA [auth L],
Z [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21.2_5419
MODEL REFINEMENTISOLDE

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
Welch FoundationUnited StatesI-1911
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2GM137419
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM158265
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR150033

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-20
    Type: Initial release
  • Version 1.1: 2026-06-03
    Changes: Data collection, Database references