6RHW | pdb_00006rhw

Crystal structure of human CD11b I-domain (CD11b-I) in complex with Staphylococcus aureus octameric bi-component leukocidin LukGH

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
Pharos: Disease Associations
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	d6rhwc_	Alpha and beta proteins (a/b)	vWA-like	vWA-like	Integrin A (or I) domain	Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha subunit)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d6rhwh_	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]	d6rhwg_	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	SCOP2B Superfamily	vWA-like	8033178	3000832	SCOP2B (2022-06-29)
B [auth H]	SCOP2B Superfamily	Leukocidin-like	8099270	3000256	SCOP2B (2022-06-29)
A [auth G]	SCOP2B Superfamily	Leukocidin-like	8099272	3000256	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)
C	VWA	e6rhwC1	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	e6rhwH1	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	e6rhwG1	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	amide binding amyloid-beta binding binding peptide binding protein binding heat shock protein binding opsonin binding complement component C3b binding complement binding cation binding ion binding metal ion binding small molecule binding cargo receptor activity amide binding amyloid-beta binding binding peptide binding protein binding heat shock protein binding opsonin binding complement component C3b binding complement binding cation binding ion binding metal ion binding small molecule binding cargo receptor activity cell adhesion molecule binding protein-containing complex binding integrin binding signaling receptor 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 response to stimulus response to stress response to ischemia response to ketone response to curcumin response to ether response to chemical response to oxygen-containing compound biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus developmental process multicellular organismal 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 cell adhesion 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 heterotypic cell-cell adhesion cell-cell adhesion regulation of immune effector process neutrophil activation regulation of localization regulation of myeloid leukocyte mediated immunity positive regulation of leukocyte mediated immunity regulated exocytosis cell activation involved in immune response leukocyte degranulation myeloid leukocyte mediated immunity myeloid leukocyte activation neutrophil activation involved in immune response positive regulation of leukocyte degranulation positive regulation of regulated secretory pathway positive regulation of immune response establishment of localization in cell leukocyte mediated immunity regulation of immune system process positive regulation of immune system process immune effector process regulation of secretion regulation of leukocyte mediated immunity exocytosis regulation of response to stimulus positive regulation of myeloid leukocyte mediated immunity regulation of immune response cellular localization positive regulation of secretion by cell positive regulation of exocytosis leukocyte activation regulation of regulated secretory pathway positive regulation of response to stimulus neutrophil mediated immunity secretion by cell regulation of secretion by cell positive regulation of secretion regulation of neutrophil degranulation leukocyte activation involved in immune response neutrophil degranulation positive regulation of immune effector process regulation of leukocyte degranulation secretion regulation of transport cell activation export from cell regulation of vesicle-mediated transport myeloid cell activation involved in immune response positive regulation of transport regulation of exocytosis positive regulation of neutrophil degranulation granulocyte activation macrophage activation leukocyte activation involved in inflammatory response microglial cell activation inflammatory response glial cell activation neuroinflammatory response 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 cell-matrix adhesion cell-substrate adhesion cellular developmental process ectoderm development cell differentiation ectodermal cell differentiation tissue development cellular component disassembly complement-mediated synapse pruning cell junction organization cell junction disassembly synapse pruning synapse organization cellular response to stimulus immune response-regulating cell surface receptor signaling pathway complement receptor mediated signaling pathway signaling cell communication immune response-activating signaling pathway immune response-regulating signaling pathway signal transduction cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway activation of immune response amyloid-beta clearance integrin-mediated signaling pathway microglial cell mediated cytotoxicity positive regulation of leukocyte mediated cytotoxicity regulation of leukocyte mediated cytotoxicity positive regulation of microglial cell mediated cytotoxicity leukocyte mediated cytotoxicity regulation of cell killing positive regulation of cell killing regulation of microglial cell mediated cytotoxicity cell killing cell adhesion mediated by integrin head development forebrain development animal organ development brain development response to mechanical stimulus response to abiotic stimulus response to bacterium response to Gram-positive bacterium response to lipid response to estradiol	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule cell periphery cell surface plasma membrane external side of plasma membrane side of membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle tertiary granule membrane tertiary granule protein-containing complex plasma membrane protein complex membrane protein complex receptor complex integrin complex plasma membrane signaling receptor complex protein complex involved in cell adhesion integrin alphaM-beta2 complex membrane microdomain membrane raft plasma membrane raft plasma membrane region
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: P11215	systemic lupus erythematosus acute promyelocytic leukemia systemic lupus erythematosus, susceptibility to, 6 IgA glomerulonephritis allergic contact dermatitis systemic sclerosis Crohn ileitis interstitial cystitis Libman-Sacks Disease lung disease MALT lymphoma non-small cell lung carcinoma arthritic joint disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia bipolar disorder systemic lupus erythematosus acute promyelocytic leukemia systemic lupus erythematosus, susceptibility to, 6 IgA glomerulonephritis allergic contact dermatitis systemic sclerosis Crohn ileitis interstitial cystitis Libman-Sacks Disease lung disease MALT lymphoma non-small cell lung carcinoma arthritic joint disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia bipolar disorder chronic obstructive pulmonary disease tuberculosis cutaneous lupus erythematosus Graves disease hematologic disease invasive ductal breast carcinoma lung cancer lupus erythematosus medulloblastoma adrenal cortex carcinoma osteosarcoma astrocytic tumor schizophrenia cancer colitis ulcerative colitis diffuse scleroderma Hashimoto thyroiditis large cell medulloblastoma lung carcinoma malignant mesothelioma ovarian cancer autoimmune disease subependymal giant cell astrocytoma central nervous system lupus Duchenne muscular dystrophy head and neck cancer

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.