6RHV | pdb_00006rhv

Crystal structure of mouse CD11b I-domain (CD11b-I) in complex with Staphylococcus aureus octameric bi-component leukocidin LukGH (LukH K319A mutant)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d6rhvc_	Alpha and beta proteins (a/b)	vWA-like	vWA-like	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d6rhvh_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A [auth G]	d6rhvg_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Integrin A (or I) domain	8098285	4000639	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	vWA-like	8098286	3000832	SCOP2 (2022-06-29)
B [auth H]	SCOP2 Family	Leukocidin (pore-forming toxin)	8099269	4003101	SCOP2 (2022-06-29)
B [auth H]	SCOP2 Superfamily	Leukocidin-like	8099270	3000256	SCOP2 (2022-06-29)
A [auth G]	SCOP2 Family	Leukocidin (pore-forming toxin)	8099271	4003101	SCOP2 (2022-06-29)
A [auth G]	SCOP2 Superfamily	Leukocidin-like	8099272	3000256	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	VWA	e6rhvC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: VWA	ECOD (1.6)
B [auth H]	Leukocidin	e6rhvH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Leukocidin-like (From Topology)	T: Leukocidin-like	F: Leukocidin	ECOD (1.6)
A [auth G]	Leukocidin	e6rhvG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Leukocidin-like (From Topology)	T: Leukocidin-like	F: Leukocidin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (utative)
B [auth H]	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (utative)
A [auth G]	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00092	von Willebrand factor type A domain (VWA)	von Willebrand factor type A domain		Domain
B [auth H]	PF07968	Leukocidin/Hemolysin toxin family (Leukocidin)	Leukocidin/Hemolysin toxin family		Domain
A [auth G]	PF07968	Leukocidin/Hemolysin toxin family (Leukocidin)	Leukocidin/Hemolysin toxin family		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Integrin alpha-M	opsonin binding protein binding binding complement component C3b binding complement binding cation binding ion binding metal ion binding small molecule binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding cargo receptor activity heparin binding opsonin binding protein binding binding complement component C3b binding complement binding cation binding ion binding metal ion binding small molecule binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding cargo receptor activity heparin binding glycosaminoglycan binding sulfur compound binding	regulation of biological process regulation of cellular process reactive oxygen species metabolic process biological regulation positive regulation of biological process regulation of superoxide metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process positive regulation of metabolic process superoxide anion generation metabolic process cellular process positive regulation of superoxide anion generation regulation of superoxide anion generation regulation of biological process regulation of cellular process reactive oxygen species metabolic process biological regulation positive regulation of biological process regulation of superoxide metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process positive regulation of metabolic process superoxide anion generation metabolic process cellular process positive regulation of superoxide anion generation regulation of superoxide anion generation regulation of metabolic process regulation of reactive oxygen species metabolic process positive regulation of cellular process membrane organization import into cell transport establishment of localization vesicle-mediated transport cellular component organization localization phagocytosis, engulfment membrane invagination phagocytosis cellular component organization or biogenesis endocytosis plasma membrane invagination cell adhesion cell-cell adhesion leukocyte adhesion to vascular endothelial cell leukocyte cell-cell adhesion myeloid cell apoptotic process multicellular organismal process homeostatic process leukocyte apoptotic process cell death neutrophil homeostasis neutrophil apoptotic process multicellular organismal-level homeostasis leukocyte homeostasis immune system process inflammatory cell apoptotic process homeostasis of number of cells apoptotic process myeloid cell homeostasis programmed cell death cell chemotaxis cellular response to stimulus chemotaxis response to stimulus neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis granulocyte chemotaxis response to chemical myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion cellular extravasation defense response response to stress inflammatory response leukocyte migration involved in inflammatory response developmental process visual system development pattern specification process nervous system development regionalization multicellular organism development central nervous system development anatomical structure development sensory system development vertebrate eye-specific patterning system development negative regulation of dopamine metabolic process regulation of amine metabolic process negative regulation of metabolic process negative regulation of biological process dopamine metabolic process primary metabolic process catechol-containing compound metabolic process regulation of primary metabolic process amine metabolic process catecholamine metabolic process phenol-containing compound metabolic process negative regulation of cellular process negative regulation of amine metabolic process regulation of catecholamine metabolic process biogenic amine metabolic process regulation of dopamine metabolic process myeloid leukocyte differentiation regulation of leukocyte differentiation cellular developmental process regulation of developmental process positive regulation of mast cell differentiation cell development regulation of cell differentiation regulation of cell development positive regulation of developmental process positive regulation of cell differentiation positive regulation of hemopoiesis cell differentiation regulation of immune system process regulation of multicellular organismal process positive regulation of immune system process regulation of mast cell differentiation regulation of multicellular organismal development hemopoiesis regulation of myeloid cell differentiation positive regulation of cell development regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation myeloid cell differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of multicellular organismal process positive regulation of leukocyte differentiation mast cell differentiation leukocyte differentiation cell activation myeloid leukocyte activation leukocyte activation macrophage activation leukocyte activation involved in inflammatory response microglial cell activation glial cell activation neuroinflammatory response regulation of localization cellular localization establishment of protein localization regulation of protein localization protein targeting positive regulation of establishment of protein localization regulation of protein targeting to membrane intracellular protein localization establishment of protein localization to membrane regulation of establishment of protein localization localization within membrane protein targeting to membrane regulation of cellular localization regulation of protein targeting macromolecule localization positive regulation of protein targeting to membrane receptor-mediated endocytosis mononuclear cell differentiation glial cell development neurogenesis gliogenesis microglia differentiation macrophage differentiation microglia development glial cell differentiation myeloid cell development cellular component disassembly complement-mediated synapse pruning cell junction organization cell junction disassembly synapse pruning synapse organization immune response-regulating cell surface receptor signaling pathway complement receptor mediated signaling pathway signaling cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response signal transduction cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response regulation of response to stimulus regulation of immune response activation of immune response amyloid-beta clearance integrin-mediated signaling pathway microglial cell mediated cytotoxicity regulation of immune effector process regulation of myeloid leukocyte mediated immunity positive regulation of leukocyte mediated immunity myeloid leukocyte mediated immunity positive regulation of leukocyte mediated cytotoxicity leukocyte mediated immunity positive regulation of immune effector process regulation of leukocyte mediated cytotoxicity positive regulation of microglial cell mediated cytotoxicity leukocyte mediated cytotoxicity immune effector process regulation of leukocyte mediated immunity positive regulation of myeloid leukocyte mediated immunity regulation of cell killing positive regulation of cell killing regulation of microglial cell mediated cytotoxicity cell killing head development forebrain development animal organ development brain development cell population proliferation lymphocyte activation leukocyte proliferation activated T cell proliferation mononuclear cell proliferation T cell activation lymphocyte proliferation T cell proliferation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane microdomain membrane raft protein-containing complex plasma membrane protein complex membrane protein complex receptor complex integrin alphaM-beta2 complex cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane microdomain membrane raft protein-containing complex plasma membrane protein complex membrane protein complex receptor complex integrin alphaM-beta2 complex integrin complex plasma membrane signaling receptor complex protein complex involved in cell adhesion membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
B [auth H]	Beta-channel forming cytolysin	-	biological process involved in interspecies interaction between organisms cytolysis in another organism cellular process disruption of cell in another organism disruption of anatomical structure in another organism cytolysis killing of cells of another organism cell killing	cellular anatomical structure extracellular region
A [auth G]	Beta-channel forming cytolysin	-	biological process involved in interspecies interaction between organisms cytolysis in another organism cellular process disruption of cell in another organism disruption of anatomical structure in another organism cytolysis killing of cells of another organism cell killing	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR013517	FG-GAP repeat	Repeat
C	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
C	IPR013649	Integrin alpha, first immunoglubulin-like domain	Domain
C	IPR002035	von Willebrand factor, type A	Domain
C	IPR048285	Integrin alpha, second immunoglobulin-like domain	Domain
C	IPR032695	Integrin domain superfamily	Homologous Superfamily
C	IPR013519	Integrin alpha beta-propellor	Repeat
C	IPR000413	Integrin alpha chain	Family
C	IPR048633	Integrin alpha-X-like, third Ig-like domain	Domain
C	IPR028994	Integrin alpha, N-terminal	Homologous Superfamily
C	IPR018184	Integrin alpha chain, C-terminal cytoplasmic region, conserved site	Conserved Site
B [auth H]	IPR016183	Leukocidin/Hemolysin toxin	Domain
B [auth H]	IPR036435	Leukocidin/porin MspA superfamily	Homologous Superfamily
B [auth H]	IPR003963	Bi-component toxin, staphylococci	Family
A [auth G]	IPR016183	Leukocidin/Hemolysin toxin	Domain
A [auth G]	IPR036435	Leukocidin/porin MspA superfamily	Homologous Superfamily
A [auth G]	IPR003963	Bi-component toxin, staphylococci	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth G], B [auth H], C	OPM	Transmembrane	Beta-barrel transmembrane	Pore-forming beta-sheet toxins	Aerolysin (n=14,S=14 or n=16,S=16)

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth G], B [auth H], C	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes	Leukocidin (LukFG) in complex with mouse CD11b I-domain (CD11b-I)

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.