5GY2

Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2 Family	FlgL-like	8097657	4007637	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	FlgL-like	8097658	3002287	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	FlgL-like	8097658	3002287	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)
A	LRR_8_1	e5gy2A1	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_1	ECOD (1.6)
C [auth B]	LRR_8_1	e5gy2B1	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_1	ECOD (1.6)
B [auth C]	Flagellin_N	e5gy2C1	A: alpha bundles	X: Four-helical up-and-down bundle	H: alpha-helical domain in phase 1 flagellin (From Topology)	T: alpha-helical domain in phase 1 flagellin	F: Flagellin_N	ECOD (1.6)
D	Flagellin_N	e5gy2D1	A: alpha bundles	X: Four-helical up-and-down bundle	H: alpha-helical domain in phase 1 flagellin (From Topology)	T: alpha-helical domain in phase 1 flagellin	F: Flagellin_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	1.20.1330.10	Mainly Alpha	Up-down Bundle	f41 fragment of flagellin, N-terminal domain	f41 fragment of flagellin, N-terminal domain	CATH (4.3.0)
D	1.20.1330.10	Mainly Alpha	Up-down Bundle	f41 fragment of flagellin, N-terminal domain	f41 fragment of flagellin, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF13855	Leucine rich repeat (LRR_8)	Leucine rich repeat	-	Repeat
A, C [auth B]	PF11921	Domain of unknown function (DUF3439) (DUF3439)	Domain of unknown function (DUF3439)	-	Repeat
B [auth C], D	PF00700	Bacterial flagellin C-terminal helical region (Flagellin_C)	Bacterial flagellin C-terminal helical region	Flagellins polymerise to form bacterial flagella. There is some similarity between this entry and Pfam:PF00669, particularly the motif NRFXSXIXXL. It has been suggested that these two regions associate [2] and this is shown to be correct as structur ...	Flagellins polymerise to form bacterial flagella. There is some similarity between this entry and Pfam:PF00669, particularly the motif NRFXSXIXXL. It has been suggested that these two regions associate [2] and this is shown to be correct as structurally this domain forms an extended helix that interacts with the N-terminal region (Pfam:PF00669) to form the D0 and D1 structural domains [3]. These domains are responsible for the activation of TLR5, with the C-terminal D0 region playing a key role [4-6].	Domain
B [auth C], D	PF00669	Bacterial flagellin N-terminal helical region (Flagellin_N)	Bacterial flagellin N-terminal helical region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	Tlr5b protein,Variable lymphocyte receptor B	molecular transducer activity signaling receptor activity transmembrane signaling receptor activity	cellular response to stimulus positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus pattern recognition receptor signaling pathway response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cell surface toll-like receptor signaling pathway cellular response to stimulus positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus pattern recognition receptor signaling pathway response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cell surface toll-like receptor signaling pathway innate immune response-activating signaling pathway regulation of biological process immune response response to other organism immune response-activating cell surface receptor signaling pathway regulation of innate immune response response to external stimulus regulation of response to stimulus defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response toll-like receptor 5 signaling pathway activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus signaling positive regulation of biological process innate immune response activating cell surface receptor signaling pathway positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response response to external biotic stimulus cell surface pattern recognition receptor signaling pathway positive regulation of innate immune response cell surface receptor signaling pathway defense response biological regulation defense response to symbiont immune system process cellular process inflammatory response toll-like receptor signaling pathway	cell periphery cellular anatomical structure plasma membrane membrane
B [auth C], D	Flagellin	structural molecule activity	-	cell projection cellular anatomical structure organelle membraneless organelle bacterial-type flagellum extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, C [auth B]	IPR000372	Leucine-rich repeat N-terminal domain	Domain
A, C [auth B]	IPR024592	Variable lymphocyte receptor, C-terminal	Domain
A, C [auth B]	IPR001611	Leucine-rich repeat	Repeat
A, C [auth B]	IPR050541	Leucine-rich repeat and transmembrane domain-containing protein	Family
A, C [auth B]	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A, C [auth B]	IPR000157	Toll/interleukin-1 receptor homology (TIR) domain	Domain
A, C [auth B]	IPR001611	Leucine-rich repeat	Repeat
A, C [auth B]	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A, C [auth B]	IPR017241	Toll-like receptor	Family
A, C [auth B]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, C [auth B]	IPR035897	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Homologous Superfamily
A, C [auth B]	IPR000483	Cysteine-rich flanking region, C-terminal	Domain
B [auth C], D	IPR046358	Flagellin, C-terminal domain	Domain
B [auth C], D	IPR001029	Flagellin, N-terminal domain	Domain
B [auth C], D	IPR042187	Flagellin, C-terminal domain, subdomain 2	Homologous Superfamily
B [auth C], D	IPR001492	Flagellin	Family

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.