3JBL | pdb_00003jbl

Cryo-EM Structure of the Activated NAIP2/NLRC4 Inflammasome Reveals Nucleated Polymerization

• PDB DOI: https://doi.org/10.2210/pdb3JBL/pdb
• EM Map EMD-6458: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-09-05 Released: 2015-10-21 
• Deposition Author(s): Zhang, L., Chen, S., Ruan, J., Wu, J., Tong, A.B., Yin, Q., Li, Y., David, L., Lu, A., Wang, W.L., Marks, C., Ouyang, Q., Zhang, X., Mao, Y., Wu, H.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization.

Zhang, L., Chen, S., Ruan, J., Wu, J., Tong, A.B., Yin, Q., Li, Y., David, L., Lu, A., Wang, W.L., Marks, C., Ouyang, Q., Zhang, X., Mao, Y., Wu, H.

(2015) Science 350: 404-409

• PubMed: 26449474 
• DOI: https://doi.org/10.1126/science.aac5789
• Primary Citation Related Structures: 
  3JBL


• PubMed Abstract: 
  

  The NLR family apoptosis inhibitory proteins (NAIPs) bind conserved bacterial ligands, such as the bacterial rod protein PrgJ, and recruit NLR family CARD-containing protein 4 (NLRC4) as the inflammasome adapter to activate innate immunity. We found that the PrgJ-NAIP2-NLRC4 inflammasome is assembled into multisubunit disk-like structures through a unidirectional adenosine triphosphatase polymerization, primed with a single PrgJ-activated NAIP2 per disk. Cryo-electron microscopy (cryo-EM) reconstruction at subnanometer resolution revealed a ~90° hinge rotation accompanying NLRC4 activation. Unlike in the related heptameric Apaf-1 apoptosome, in which each subunit needs to be conformationally activated by its ligand before assembly, a single PrgJ-activated NAIP2 initiates NLRC4 polymerization in a domino-like reaction to promote the disk assembly. These insights reveal the mechanism of signal amplification in NAIP-NLRC4 inflammasomes.

---

Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
Center for Quantitative Biology, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China. Department of Cancer Immunology and Virology, Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Department of Cancer Immunology and Virology, Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
Center for Nanoscale Systems, Harvard University, Cambridge, MA 02138, USA.
Center for Quantitative Biology, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China.
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
Center for Quantitative Biology, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China. Department of Cancer Immunology and Virology, Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. [e-mail] [e-mail].
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C11  (Explore in 3D)
Global Stoichiometry: Homo 11-mer - A11 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 1,168.64 kDa 
• Atom Count: 80,124 
• Modeled Residue Count: 9,999 
• Deposited Residue Count: 10,252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NLR family CARD domain-containing protein 4	A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J]	932	Mus musculus	Mutation(s): 0  Gene Names: Nlrc4, Card12, Ipaf
UniProt
Find proteins for Q3UP24 (Mus musculus) Explore Q3UP24  Go to UniProtKB:  Q3UP24

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN	2
RECONSTRUCTION	RELION
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Zhang, L., Chen, S., Ruan, J., Wu, J., Tong, A.B., Yin, Q., Li, Y., David, L., Lu, A., Wang, W.L., Marks, C., Ouyang, Q., Zhang, X., Mao, Y., Wu, H.

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2015-11-04
  Changes: Database references, Other
• Version 1.2: 2018-07-18
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary