3JBL

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

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth K]	LRR_8_4	e3jblK1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
A [auth K]	EUF07890	e3jblK5	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EUF07890	ECOD (1.6)
A [auth K]	EUF07948	e3jblK4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07948	ECOD (1.6)
A [auth K]	EUF08241	e3jblK2	A: alpha superhelices	X: NLRC4 helical domain HD2 (From Topology)	H: NLRC4 helical domain HD2 (From Topology)	T: NLRC4 helical domain HD2	F: EUF08241	ECOD (1.6)
A [auth K]	NACHT	e3jblK3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NACHT	ECOD (1.6)
B [auth A]	LRR_8_4	e3jblA2	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
B [auth A]	EUF07890	e3jblA4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EUF07890	ECOD (1.6)
B [auth A]	EUF07948	e3jblA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07948	ECOD (1.6)
B [auth A]	EUF08241	e3jblA5	A: alpha superhelices	X: NLRC4 helical domain HD2 (From Topology)	H: NLRC4 helical domain HD2 (From Topology)	T: NLRC4 helical domain HD2	F: EUF08241	ECOD (1.6)
B [auth A]	NACHT	e3jblA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NACHT	ECOD (1.6)
C [auth B]	LRR_8_4	e3jblB5	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
C [auth B]	EUF07890	e3jblB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EUF07890	ECOD (1.6)
C [auth B]	EUF07948	e3jblB3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07948	ECOD (1.6)
C [auth B]	EUF08241	e3jblB4	A: alpha superhelices	X: NLRC4 helical domain HD2 (From Topology)	H: NLRC4 helical domain HD2 (From Topology)	T: NLRC4 helical domain HD2	F: EUF08241	ECOD (1.6)
C [auth B]	NACHT	e3jblB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NACHT	ECOD (1.6)
D [auth C]	LRR_8_4	e3jblC5	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
D [auth C]	EUF07890	e3jblC2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EUF07890	ECOD (1.6)
D [auth C]	EUF07948	e3jblC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07948	ECOD (1.6)
D [auth C]	EUF08241	e3jblC3	A: alpha superhelices	X: NLRC4 helical domain HD2 (From Topology)	H: NLRC4 helical domain HD2 (From Topology)	T: NLRC4 helical domain HD2	F: EUF08241	ECOD (1.6)
D [auth C]	NACHT	e3jblC4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NACHT	ECOD (1.6)
E [auth D]	LRR_8_4	e3jblD2	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
E [auth D]	EUF07890	e3jblD5	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EUF07890	ECOD (1.6)
E [auth D]	EUF07948	e3jblD3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07948	ECOD (1.6)
E [auth D]	EUF08241	e3jblD1	A: alpha superhelices	X: NLRC4 helical domain HD2 (From Topology)	H: NLRC4 helical domain HD2 (From Topology)	T: NLRC4 helical domain HD2	F: EUF08241	ECOD (1.6)
E [auth D]	NACHT	e3jblD4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NACHT	ECOD (1.6)
F [auth E]	LRR_8_4	e3jblE3	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
F [auth E]	EUF07890	e3jblE2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EUF07890	ECOD (1.6)
F [auth E]	EUF07948	e3jblE4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07948	ECOD (1.6)
F [auth E]	EUF08241	e3jblE1	A: alpha superhelices	X: NLRC4 helical domain HD2 (From Topology)	H: NLRC4 helical domain HD2 (From Topology)	T: NLRC4 helical domain HD2	F: EUF08241	ECOD (1.6)
F [auth E]	NACHT	e3jblE5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NACHT	ECOD (1.6)
G [auth F]	LRR_8_4	e3jblF2	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
G [auth F]	EUF07890	e3jblF4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EUF07890	ECOD (1.6)
G [auth F]	EUF07948	e3jblF3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07948	ECOD (1.6)
G [auth F]	EUF08241	e3jblF1	A: alpha superhelices	X: NLRC4 helical domain HD2 (From Topology)	H: NLRC4 helical domain HD2 (From Topology)	T: NLRC4 helical domain HD2	F: EUF08241	ECOD (1.6)
G [auth F]	NACHT	e3jblF5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NACHT	ECOD (1.6)
H [auth G]	LRR_8_4	e3jblG4	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
H [auth G]	EUF07890	e3jblG2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EUF07890	ECOD (1.6)
H [auth G]	EUF07948	e3jblG3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07948	ECOD (1.6)
H [auth G]	EUF08241	e3jblG1	A: alpha superhelices	X: NLRC4 helical domain HD2 (From Topology)	H: NLRC4 helical domain HD2 (From Topology)	T: NLRC4 helical domain HD2	F: EUF08241	ECOD (1.6)
H [auth G]	NACHT	e3jblG5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NACHT	ECOD (1.6)
I [auth H]	LRR_8_4	e3jblH5	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
I [auth H]	EUF07890	e3jblH3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EUF07890	ECOD (1.6)
I [auth H]	EUF07948	e3jblH2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07948	ECOD (1.6)
I [auth H]	EUF08241	e3jblH4	A: alpha superhelices	X: NLRC4 helical domain HD2 (From Topology)	H: NLRC4 helical domain HD2 (From Topology)	T: NLRC4 helical domain HD2	F: EUF08241	ECOD (1.6)
I [auth H]	NACHT	e3jblH1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NACHT	ECOD (1.6)
J [auth I]	LRR_8_4	e3jblI1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
J [auth I]	EUF07890	e3jblI5	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EUF07890	ECOD (1.6)
J [auth I]	EUF07948	e3jblI3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07948	ECOD (1.6)
J [auth I]	EUF08241	e3jblI4	A: alpha superhelices	X: NLRC4 helical domain HD2 (From Topology)	H: NLRC4 helical domain HD2 (From Topology)	T: NLRC4 helical domain HD2	F: EUF08241	ECOD (1.6)
J [auth I]	NACHT	e3jblI2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NACHT	ECOD (1.6)
K [auth J]	LRR_8_4	e3jblJ1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
K [auth J]	EUF07890	e3jblJ4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EUF07890	ECOD (1.6)
K [auth J]	EUF07948	e3jblJ5	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07948	ECOD (1.6)
K [auth J]	EUF08241	e3jblJ2	A: alpha superhelices	X: NLRC4 helical domain HD2 (From Topology)	H: NLRC4 helical domain HD2 (From Topology)	T: NLRC4 helical domain HD2	F: EUF08241	ECOD (1.6)
K [auth J]	NACHT	e3jblJ3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NACHT	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	PF05729	NACHT domain (NACHT)	NACHT domain	This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation [1]. This family is closely related to Pfam:PF00931.	Domain
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	PF22524	Nlrc4-like, winged helix domain (Nlrc4-like_WHD)	Nlrc4-like, winged helix domain	This entry represents the winged helix domain (WHD) of NLR family CARD domain-containing protein 4 from mouse (Nlrc4) and similar sequences from vertebrates. Nlrc4 is a component of the inflammasome activated as part of the innate immune response [1] ...	This entry represents the winged helix domain (WHD) of NLR family CARD domain-containing protein 4 from mouse (Nlrc4) and similar sequences from vertebrates. Nlrc4 is a component of the inflammasome activated as part of the innate immune response [1].	Domain
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	PF17889	NLRC4 helical domain (NLRC4_HD)	NLRC4 helical domain	This is a helical domain found in NLRC4 , Nucleotide-binding and oligomerization domain-like receptor (NLR) proteins. Structural and functional studies indicate that the helical domain HD2 repressively contacted a conserved and functionally important ...	This is a helical domain found in NLRC4 , Nucleotide-binding and oligomerization domain-like receptor (NLR) proteins. Structural and functional studies indicate that the helical domain HD2 repressively contacted a conserved and functionally important alpha-helix of the NBD (nucleotide binding domain) in Swiss:Q3UP24. Furthermore, the HD2 domain was shown to cap the N-terminal side of the LRR (leucine-rich repeat) domain via extensive interactions [1]. Other family members carrying this domain include baculoviral IAP repeat-containing protein 1 (Birc1) also known as neuronal apoptosis inhibitory protein (Naip).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	NLR family CARD domain-containing protein 4	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity	regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus positive regulation of biological process response to biotic stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus positive regulation of biological process response to biotic stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus positive regulation of immune system process regulation of biological process positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response biological regulation defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cellular process apoptotic process cell death programmed cell death inflammatory response detection of external biotic stimulus detection of biotic stimulus detection of bacterium detection of stimulus response to bacterium detection of other organism regulation of cellular process regulation of apoptotic process regulation of programmed cell death cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis pyroptotic inflammatory response defense response to bacterium multicellular organismal process interleukin-1 production regulation of interleukin-1 beta production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of interleukin-1 beta production positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of interleukin-1 production positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of interleukin-1 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process interleukin-1 beta production positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol canonical inflammasome complex protein-containing complex IPAF inflammasome complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	IPR011029	Death-like domain superfamily	Homologous Superfamily
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	IPR040535	NLRC4, helical domain	Domain
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	IPR053882	Nlrc4-like, winged helix domain	Domain
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	IPR001315	CARD domain	Domain
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	IPR042220	NLR family CARD domain-containing protein 4	Family
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	IPR007111	NACHT nucleoside triphosphatase	Domain
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth K], B [auth A], C [auth B], D [auth C], E [auth D], 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]	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046