5H8O | pdb_00005h8o

Crystal structure of an ASC-binding nanobody in complex with the CARD domain of ASC

• PDB DOI: https://doi.org/10.2210/pdb5H8O/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Lama glama, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-23 Released: 2016-04-06 
• Deposition Author(s): Lu, A., Schmidt, F.I., Ruan, J., Tang, C., Wu, H., Ploegh, H.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.21 Å
• R-Value Free: 
  0.356 (Depositor), 0.361 (DCC) 
• R-Value Work: 
  0.300 (Depositor), 0.309 (DCC) 
• R-Value Observed: 
  0.303 (Depositor) 

Literature

A single domain antibody fragment that recognizes the adaptor ASC defines the role of ASC domains in inflammasome assembly.

Schmidt, F.I., Lu, A., Chen, J.W., Ruan, J., Tang, C., Wu, H., Ploegh, H.L.

(2016) J Exp Medicine 213: 771-790

• PubMed: 27069117 
• DOI: https://doi.org/10.1084/jem.20151790
• Primary Citation Related Structures: 
  5H8D, 5H8O


• PubMed Abstract: 
  

  Myeloid cells assemble inflammasomes in response to infection or cell damage; cytosolic sensors activate pro-caspase-1, indirectly for the most part, via the adaptors ASC and NLRC4. This leads to secretion of proinflammatory cytokines and pyroptosis. To explore complex formation under physiological conditions, we generated an alpaca single domain antibody, VHHASC, which specifically recognizes the CARD of human ASC via its type II interface. VHHASC not only impairs ASC(CARD) interactions in vitro, but also inhibits inflammasome activation in response to NLRP3, AIM2, and NAIP triggers when expressed in living cells, highlighting a role of ASC in all three types of inflammasomes. VHHASC leaves the Pyrin domain of ASC functional and stabilizes a filamentous intermediate of inflammasome activation. Incorporation of VHHASC-EGFP into these structures allowed the visualization of endogenous ASC(PYD) filaments for the first time. These data revealed that cross-linking of ASC(PYD) filaments via ASC(CARD) mediates the assembly of ASC foci.

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Organizational Affiliation: 
• Whitehead Institute for Biomedical Research, Cambridge, MA 02142.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115 [e-mail] [e-mail].
Whitehead Institute for Biomedical Research, Cambridge, MA 02142 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.72 kDa 
• Atom Count: 1,051 
• Modeled Residue Count: 181 
• Deposited Residue Count: 195 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH nanobody	A	114	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis-associated speck-like protein containing a CARD	B	81	Homo sapiens	Mutation(s): 0  Gene Names: PYCARD, ASC, CARD5, TMS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULZ3 (Homo sapiens) Explore Q9ULZ3  Go to UniProtKB:  Q9ULZ3
PHAROS:  Q9ULZ3 GTEx:  ENSG00000103490

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.21 Å
• R-Value Free:  0.356 (Depositor), 0.361 (DCC) 
• R-Value Work:  0.300 (Depositor), 0.309 (DCC) 
• R-Value Observed: 0.303 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.625	α = 90
b = 30.996	β = 90
c = 79.244	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Lu, A., Schmidt, F.I., Ruan, J., Tang, C., Wu, H., Ploegh, H.L.

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2016-04-27
  Changes: Database references
• Version 1.2: 2016-05-18
  Changes: Derived calculations
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary