3JBL | pdb_00003jbl

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]		e3jblK1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
B [auth A]		e3jblA1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
C [auth B]		e3jblB1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
D [auth C]		e3jblC1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
E [auth D]		e3jblD1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
F [auth E]		e3jblE1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
G [auth F]		e3jblF1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
H [auth G]		e3jblG1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
I [auth H]		e3jblH1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
J [auth I]		e3jblI1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
K [auth J]		e3jblJ1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)

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 (WHD_Nlrc4)	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 anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein binding enzyme binding protease binding caspase binding identical protein binding protein homodimerization activity protein dimerization activity endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity endopeptidase regulator 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 positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular process detection of external biotic stimulus detection of biotic stimulus detection of bacterium detection of stimulus response to bacterium detection of other organism regulation of protein maturation positive regulation of protein maturation positive regulation of protein metabolic process positive regulation of macromolecule biosynthetic process positive regulation of protein processing protein maturation regulation of primary metabolic process positive regulation of metabolic process regulation of proteolysis positive regulation of biosynthetic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process regulation of biosynthetic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of proteolysis regulation of protein processing protein processing metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process defense response to bacterium multicellular organismal process interleukin-1 production regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production positive regulation of multicellular organismal process positive regulation of cytokine production inflammatory response 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol canonical inflammasome complex protein-containing complex IPAF inflammasome complex cell periphery plasma membrane membrane

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]	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]	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
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]	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

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.