4KXF | pdb_00004kxf

Crystal structure of NLRC4 reveals its autoinhibition mechanism

PDB DOI: https://doi.org/10.2210/pdb4KXF/pdb

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

Deposited: 2013-05-25 Released: 2013-07-24
Deposition Author(s): Chai, J., Hu, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.266 (Depositor), 0.271 (DCC)
R-Value Work:
0.226 (Depositor)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of NLRC4 reveals its autoinhibition mechanism

Hu, Z., Yan, C., Liu, P., Huang, Z., Ma, R., Zhang, C., Wang, R., Zhang, Y., Martinon, F., Miao, D., Deng, H., Wang, J., Chang, J., Chai, J.

(2013) Science 341: 172-175

PubMed: 23765277 Search on PubMed
DOI: https://doi.org/10.1126/science.1236381
Primary Citation Related Structures:
4KXF

PubMed Abstract:
Nucleotide-binding and oligomerization domain-like receptor (NLR) proteins oligomerize into multiprotein complexes termed inflammasomes when activated. Their autoinhibition mechanism remains poorly defined. Here, we report the crystal structure of mouse NLRC4 in a closed form. The adenosine diphosphate-mediated interaction between the central nucleotide-binding domain (NBD) and the winged-helix domain (WHD) was critical for stabilizing the closed conformation of NLRC4. The helical domain HD2 repressively contacted a conserved and functionally important α-helix of the NBD. The C-terminal leucine-rich repeat (LRR) domain is positioned to sterically occlude one side of the NBD domain and consequently sequester NLRC4 in a monomeric state. Disruption of ADP-mediated NBD-WHD or NBD-HD2/NBD-LRR interactions resulted in constitutive activation of NLRC4. Together, our data reveal the NBD-organized cooperative autoinhibition mechanism of NLRC4 and provide insight into its activation.

Organizational Affiliation

School of Life Sciences, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.

Macromolecule Content

Total Structure Weight: 939.34 kDa
Atom Count: 57,081
Modeled Residue Count: 7,145
Deposited Residue Count: 8,192
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NLR family CARD domain-containing protein 4	A [auth K] B C [auth D] D [auth F] E [auth H] A [auth K], B, C [auth D], D [auth F], E [auth H], F [auth L], G [auth N], H [auth P]	1,024	Mus musculus	Mutation(s): 0 Gene Names: Nlrc4, Card12, Ipaf
UniProt
Find proteins for Q3UP24 (Mus musculus) Explore Q3UP24 Go to UniProtKB: Q3UP24
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3UP24
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain I [auth K] SDF format, chain J [auth B] SDF format, chain L [auth D] SDF format, chain M [auth F] SDF format, chain O [auth L] SDF format, chain P [auth N] SDF format, chain R [auth P] SDF format, chain N [auth H] MOL2 format, chain I [auth K] MOL2 format, chain J [auth B] MOL2 format, chain L [auth D] MOL2 format, chain M [auth F] MOL2 format, chain O [auth L] MOL2 format, chain P [auth N] MOL2 format, chain R [auth P] MOL2 format, chain N [auth H] mmCIF format, chain I [auth K] mmCIF format, chain J [auth B] mmCIF format, chain L [auth D] mmCIF format, chain M [auth F] mmCIF format, chain O [auth L] mmCIF format, chain P [auth N] mmCIF format, chain R [auth P] mmCIF format, chain N [auth H]	I [auth K] J [auth B] L [auth D] M [auth F] N [auth H] I [auth K], J [auth B], L [auth D], M [auth F], N [auth H], O [auth L], P [auth N], R [auth P]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth K] Focus chain J [auth B] Focus chain L [auth D] Focus chain M [auth F] Focus chain N [auth H] Focus chain O [auth L] Focus chain P [auth N] Focus chain R [auth P] Interactions & Density Focus chain I [auth K] Focus chain J [auth B] Focus chain L [auth D] Focus chain M [auth F] Focus chain N [auth H] Focus chain O [auth L] Focus chain P [auth N] Focus chain R [auth P]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth N] SDF format, chain K [auth B] MOL2 format, chain Q [auth N] MOL2 format, chain K [auth B] mmCIF format, chain Q [auth N] mmCIF format, chain K [auth B]	K [auth B], Q [auth N]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Focus chain Q [auth N] Interactions & Density Focus chain K [auth B] Focus chain Q [auth N]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.266 (Depositor), 0.271 (DCC)
R-Value Work: 0.226 (Depositor)
R-Value Observed: 0.228 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 334.052	α = 90
b = 334.052	β = 90
c = 177.567	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Chai, J.

Hu, Z.

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary