4CG4 | pdb_00004cg4

Crystal structure of the CHS-B30.2 domains of TRIM20

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8060018	3000120	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8060018	3000120	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8060018	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8060018	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8060018	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8060018	3000120	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	SPRY	e4cg4F1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
E	SPRY	e4cg4E1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
D	SPRY	e4cg4D1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
C	SPRY	e4cg4C1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
B	SPRY	e4cg4B1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
A	SPRY	e4cg4A1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.60.120.920	Mainly Beta	Sandwich	Jelly Rolls	SPRY domain	CATH (4.3.0)
E	2.60.120.920	Mainly Beta	Sandwich	Jelly Rolls	SPRY domain	CATH (4.3.0)
D	2.60.120.920	Mainly Beta	Sandwich	Jelly Rolls	SPRY domain	CATH (4.3.0)
C	2.60.120.920	Mainly Beta	Sandwich	Jelly Rolls	SPRY domain	CATH (4.3.0)
B	2.60.120.920	Mainly Beta	Sandwich	Jelly Rolls	SPRY domain	CATH (4.3.0)
A	2.60.120.920	Mainly Beta	Sandwich	Jelly Rolls	SPRY domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00622	SPRY domain (SPRY)	SPRY domain	SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of ...	SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of histone H3 methylation, innate immunity or embryonic development [1,2,3,4]. It can be divided into 11 subfamilies based on amino acid sequence similarity or the presence of additional protein domains. The greater SPRY family is divided into the SPRY/B30.2 (which contains a PRY extension at the N-terminal) and SPRY-only sub-families which are preceded by a subdomain that is structurally similar to the PRY region [2]. SPRY/B30.2 structures revealed a bent beta-sandwich fold comprised of two beta-sheets. Distant homologues are domains in butyrophilin/ marenostrin/pyrin [1].	Domain
A, B, C, D, E A, B, C, D, E, F	PF13765	SPRY-associated domain (PRY)	SPRY-associated domain	PRY is a 50-60 amino acids domain associated with SPRY domains, adjacent to its N-terminal. PRY and SPRY domains are structurally very similar and consist of a beta sandwich fold [1,2,3]. Distant homologues are domains in butyrophilin/marenostrin/py ...	PRY is a 50-60 amino acids domain associated with SPRY domains, adjacent to its N-terminal. PRY and SPRY domains are structurally very similar and consist of a beta sandwich fold [1,2,3]. Distant homologues are domains in butyrophilin/marenostrin/pyrin, evolutionarily more ancient than SPRY/B30.2 counterpart.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	PYRIN	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity cytoskeletal protein binding actin binding protein binding binding cation binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity cytoskeletal protein binding actin binding protein binding binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization pyroptosome complex assembly protein-containing complex assembly cellular process cellular component organization or biogenesis regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization pyroptosome complex assembly protein-containing complex assembly cellular process cellular component organization or biogenesis regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway regulation of NLRP3 inflammasome complex assembly negative regulation of biological process regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway inflammasome-mediated signaling pathway positive regulation of immune response canonical inflammasome complex assembly regulation of immune system process signal transduction negative regulation of NLRP3 inflammasome complex assembly positive regulation of immune system process innate immune response-activating signaling pathway negative regulation of cellular component organization immune response response to other organism regulation of innate immune response regulation of inflammasome-mediated signaling pathway negative regulation of protein-containing complex assembly defense response to other organism regulation of pattern recognition receptor signaling pathway NLRP3 inflammasome complex assembly activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular component organization intracellular receptor signaling pathway signaling negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication regulation of protein-containing complex assembly immune response-regulating signaling pathway regulation of intracellular signal transduction innate immune response negative regulation of cellular process response to external biotic stimulus regulation of signaling positive regulation of innate immune response negative regulation of response to stimulus defense response to symbiont regulation of cellular component biogenesis negative regulation of signal transduction negative regulation of immune system process immune system process regulation of cell communication negative regulation of inflammasome-mediated signaling pathway regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of inflammatory response negative regulation of response to external stimulus negative regulation of defense response multicellular organismal process interleukin-1 production regulation of interleukin-1 beta production negative regulation of interleukin-1 beta production negative regulation of interleukin-1 production regulation of cytokine production cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of interleukin-1 production negative regulation of metabolic process negative regulation of cytokine production negative regulation of gene expression negative regulation of biosynthetic process interleukin-1 beta production negative regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of interleukin-1 beta production positive regulation of biosynthetic process positive regulation of interleukin-1 production positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production response to type II interferon response to cytokine response to peptide response to chemical regulation of interleukin-12 production negative regulation of interleukin-12 production interleukin-12 production pyroptotic inflammatory response positive regulation of autophagy catabolic process autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process process utilizing autophagic mechanism negative regulation of chemokine production negative regulation of macrophage inflammatory protein 1 alpha production macrophage inflammatory protein-1 alpha production regulation of macrophage inflammatory protein 1 alpha production regulation of chemokine production chemokine production regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytoplasmic vesicle intracellular vesicle vesicle vacuole autophagosome ruffle protein-containing complex cytoskeleton membraneless organelle microtubule associated complex intracellular membraneless organelle microtubule cytoskeleton polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex canonical inflammasome complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR006574	SPRY-associated	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR043136	B30.2/SPRY domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR004020	DAPIN domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003877	SPRY domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000315	B-box-type zinc finger	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001870	B30.2/SPRY domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003879	Butyrophylin-like, SPRY domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050143	Tripartite motif-containing	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: O15553	familial Mediterranean fever familial Mediterranean fever, autosomal dominant psoriatic arthritis amyloidosis autosomal recessive familial Mediterranean fever Behcet disease psoriasis acne ankylosing spondylitis autosomal dominant familial periodic fever brucellosis intermittent hydrarthrosis periodic fever syndrome acquired metabolic disease attention deficit hyperactivity disorder, inattentive type familial Mediterranean fever familial Mediterranean fever, autosomal dominant psoriatic arthritis amyloidosis autosomal recessive familial Mediterranean fever Behcet disease psoriasis acne ankylosing spondylitis autosomal dominant familial periodic fever brucellosis intermittent hydrarthrosis periodic fever syndrome acquired metabolic disease attention deficit hyperactivity disorder, inattentive type familial cold autoinflammatory syndrome hidradenitis suppurativa mevalonic aciduria Periodic syndrome pyoderma gangrenosum autoimmune disease Muckle-Wells syndrome

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

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.