9TMK | pdb_00009tmk

Structure of CYLD CAP-Gly2 bound to Listeria effector protein InlC

• PDB DOI: https://doi.org/10.2210/pdb9TMK/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Listeria monocytogenes, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-12-14 Released: 2026-09-30 
• Deposition Author(s): Ellison, C.J., Elliott, P.R.
• Funding Organization(s): Cancer Research UK, UK Research and Innovation (UKRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Models: experimental

Literature

Listeria promotes systemic infection by targeting the host deubiquitinase CYLD.

Ammendolia, D.A., Ellison, C.J., Zheng, Y., Coyaud, E., Laurent, E.M.N., Yan, B.R., Manning, B., Waldmann, A.K., Tan, J.M.J., Frendo-Cumbo, S., Lyons, C., Youn, J.Y., Raught, B., Ireton, K., Higgins, D.E., Elliott, P.R., Brumell, J.H.

(2026) Nat Commun 17

• PubMed: 42811002 
• DOI: https://doi.org/10.1038/s41467-026-77063-5
• Primary Citation Related Structures: 
  9TMK


• PubMed Abstract: 
  

  Listeria monocytogenes (Lm) is an intracellular pathogen that can cause life-threatening systemic infections. Internalin C (InlC) is a secreted factor required for full Lm virulence in systemic models of infection by mechanisms that remain unclear. Here, we show that InlC binds to CYLD, a host deubiquitinase and regulator of innate immunity. Structurally, we reveal the LRR domain of InlC binds the CAP-Gly2 domain of CYLD, independently of InlC's binding site for other host target proteins. Lm strains harboring amino acid substitutions in InlC that selectively disrupt binding to CYLD were examined. We demonstrate that after Lm accesses the host cytosol, InlC recruits CYLD to ubiquitin-positive bacteria. Recruitment of CYLD was dependent on the host E3 ligase RNF213, a major initiator of ubiquitin-mediated defenses. Furthermore, InlC-CYLD binding contributed to Lm virulence in mice. Together, these findings reveal how a secreted bacterial factor promotes the recruitment of a host deubiquitinase to cytosolic bacteria in response to ubiquitin-mediated defenses.

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Organizational Affiliation: 
• Cell & Systems Biology Program, Hospital for Sick Children, Toronto, ON, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Department of Biochemistry, University of Oxford, Oxford, UK.
Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
Department of Physiology, University of Toronto, Toronto, ON, Canada.
Molecular Medicine Program, Hospital for Sick Children, Toronto, ON, Canada.
Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
Cell & Systems Biology Program, Hospital for Sick Children, Toronto, ON, Canada. [e-mail].
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. [e-mail].
Institute of Medical Science, University of Toronto, Toronto, ON, Canada. [e-mail].
SickKids IBD Centre, Hospital for Sick Children, Toronto, ON, Canada. [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: 39.57 kDa 
• Atom Count: 3,017 
• Modeled Residue Count: 343 
• Deposited Residue Count: 355 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Internalin C	A	265	Listeria monocytogenes	Mutation(s): 0  Gene Names: inlC, irpA
UniProt
Find proteins for P71451 (Listeria monocytogenes serotype 1/2a (strain EGD / Mackaness)) Explore P71451  Go to UniProtKB:  P71451

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase CYLD	B	90	Homo sapiens	Mutation(s): 0  Gene Names: CYLD, CYLD1, KIAA0849, HSPC057 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQC7 (Homo sapiens) Explore Q9NQC7  Go to UniProtKB:  Q9NQC7
PHAROS:  Q9NQC7 GTEx:  ENSG00000083799

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.833	α = 90
b = 70.01	β = 90
c = 97.723	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-30 
Deposition Author(s): Ellison, C.J., Elliott, P.R.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	DRCPFA-Jun24/100003
UK Research and Innovation (UKRI)	United Kingdom	MR/Z506217/1

Revision History  

• Version 1.0: 2026-09-30
  Type: Initial release
  
• Version 1.1: 2026-10-14
  Changes: Database references