4BIK | pdb_00004bik

Structure of a disulfide locked mutant of Intermedilysin with human CD59

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
Membrane Protein Annotation: OPM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Snake toxin-like	8034633	3000545	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Snake toxin-like	8034633	3000545	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CDC membrane-sensing domain-like	8052023	3000285	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MAC/CDC-like	8052024	3002081	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MAC/CDC-like	8052024	3002081	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CDC membrane-sensing domain-like	8052023	3000285	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)
D	UPAR_LY6	e4bikD1	A: few secondary structure elements	X: Snake toxin-like (From Topology)	H: Snake toxin-like (From Topology)	T: Snake toxin-like	F: UPAR_LY6	ECOD (1.6)
B	UPAR_LY6	e4bikB1	A: few secondary structure elements	X: Snake toxin-like (From Topology)	H: Snake toxin-like (From Topology)	T: Snake toxin-like	F: UPAR_LY6	ECOD (1.6)
C	Thiol_cytolys_C	e4bikC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Perfringolysin O beta sandwich domain (From Topology)	T: Perfringolysin O beta sandwich domain	F: Thiol_cytolys_C	ECOD (1.6)
C	Thiol_cytolysin	e4bikC2	A: beta complex topology	X: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	H: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	T: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	F: Thiol_cytolysin	ECOD (1.6)
A	Thiol_cytolys_C	e4bikA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Perfringolysin O beta sandwich domain (From Topology)	T: Perfringolysin O beta sandwich domain	F: Thiol_cytolys_C	ECOD (1.6)
A	Thiol_cytolysin	e4bikA2	A: beta complex topology	X: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	H: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	T: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	F: Thiol_cytolysin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
B	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
C	3.90.840.10	Alpha Beta	Alpha-Beta Complex	HIV-1 Reverse Transcriptase	Chain A, domain 3	CATH (4.3.0)
C	3.30.1040.20	Alpha Beta	2-Layer Sandwich	Carboxypeptidase Inhibitor	Chain A	CATH (4.3.0)
C	3.40.30.40	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Perfringolysin	CATH (4.3.0)
C	2.60.40.1430	Mainly Beta	Sandwich	Immunoglobulin-like	Perfringolysin, domain 4	CATH (4.3.0)
A	3.90.840.10	Alpha Beta	Alpha-Beta Complex	HIV-1 Reverse Transcriptase	Chain A, domain 3	CATH (4.3.0)
A	3.30.1040.20	Alpha Beta	2-Layer Sandwich	Carboxypeptidase Inhibitor	Chain A	CATH (4.3.0)
A	3.40.30.40	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Perfringolysin	CATH (4.3.0)
A	2.60.40.1430	Mainly Beta	Sandwich	Immunoglobulin-like	Perfringolysin, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF25152	CD59 glycoprotein (CD59)	CD59 glycoprotein	This entry represents the human CD59 glycoprotein and related proteins. CD59 is a cell-surface glycoprotein that protects host cells from complement-mediated lysis. It binds to and prevents the normal functioning of the complement proteins C8 and C9 ...	This entry represents the human CD59 glycoprotein and related proteins. CD59 is a cell-surface glycoprotein that protects host cells from complement-mediated lysis. It binds to and prevents the normal functioning of the complement proteins C8 and C9 which form part of a membrane penetrating assembly called the membrane attack complex. CD59 folds into a compact domain with a central three-stranded antiparallel beta-sheet and a two-stranded antiparallel beta-sheet located on one side of it. This structure is stabilised by disulfide bonds and has a significant similarity to the snake venom neurotoxins and other members of the uPAR/Ly6/CD59/snake toxin-receptor superfamily [1]. CD59 binds the pore-forming beta-hairpins of C8 to form an intermolecular beta-sheet that prevents membrane perforation. While bound to C8, CD59 deflects the cascading C9 beta-hairpins, rerouting their trajectory into the membrane [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	CD59 GLYCOPROTEIN	protein binding binding complement binding molecular sequestering activity protein sequestering activity	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of humoral immune response regulation of immune effector process humoral immune response multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of humoral immune response regulation of immune effector process humoral immune response positive regulation of biological process negative regulation of biological process negative regulation of complement activation positive regulation of response to stimulus complement activation positive regulation of immune response regulation of immune system process positive regulation of immune system process regulation of biological process immune response negative regulation of response to stimulus negative regulation of immune response negative regulation of immune effector process negative regulation of humoral immune response immune effector process regulation of response to stimulus negative regulation of immune system process immune system process regulation of immune response regulation of complement activation activation of immune response regulation of cellular process regulation of complement-dependent cytotoxicity cellular process regulation of cell killing complement-dependent cytotoxicity cell killing negative regulation of cellular process negative regulation of complement-dependent cytotoxicity negative regulation of cell killing cellular response to stimulus cell surface receptor signaling pathway signaling signal transduction cell communication activation of membrane attack complex negative regulation of activation of membrane attack complex regulation of activation of membrane attack complex	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule 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 anchoring junction cell junction focal adhesion cell-substrate junction specific 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 transport vesicle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane Golgi membrane Golgi apparatus endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment transport vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane coated vesicle
A, C	INTERMEDILYSIN	sterol binding binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding cation binding ion binding metal ion binding toxin activity	biological process involved in interspecies interaction between organisms cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR045860	Snake toxin-like superfamily	Homologous Superfamily
B, D	IPR016054	Ly-6 antigen/uPA receptor-like	Domain
B, D	IPR018363	CD59 antigen, conserved site	Conserved Site
B, D	IPR056949	CD59 glycoprotein	Family
A, C	IPR038700	Thiol-activated cytolysin, C-terminal domain superfamily	Homologous Superfamily
A, C	IPR036359	Thiol-activated cytolysin superfamily	Homologous Superfamily
A, C	IPR035390	Thiol-activated cytolysin C-terminal	Domain
A, C	IPR001869	Thiol-activated cytolysin	Family
A, C	IPR036363	Thiol-activated cytolysin, alpha-beta domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: P13987	primary CD59 deficiency familial hemolytic anemia psoriasis acute myeloid leukemia congenital anemia esophageal adenocarcinoma hemolytic anemia malignant mesothelioma ovarian cancer spina bifida breast cancer Cytopenia large cell medulloblastoma medulloblastoma pilocytic astrocytoma primary CD59 deficiency familial hemolytic anemia psoriasis acute myeloid leukemia congenital anemia esophageal adenocarcinoma hemolytic anemia malignant mesothelioma ovarian cancer spina bifida breast cancer Cytopenia large cell medulloblastoma medulloblastoma pilocytic astrocytoma proteinuria breast carcinoma Down syndrome glioblastoma lung cancer osteosarcoma plasma cell myeloma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Monotopic/peripheral	All beta monotopic/peripheral	Cholesterol-dependent cytolysin	Thiol-activated cytolysin

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.