3KWV

Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers

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
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FIP-like	8054214	3002056	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Anthrax PA domain 3-like	8054212	3000301	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GLEYA/PA14-like	8054210	3002282	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GLEYA/PA14-like	8054210	3002282	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FIP-like	8054214	3002056	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Anthrax PA domain 3-like	8054212	3000301	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	FIP-like	8054214	3002056	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Anthrax PA domain 3-like	8054212	3000301	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GLEYA/PA14-like	8054210	3002282	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	FIP-like	8054214	3002056	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GLEYA/PA14-like	8054210	3002282	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Anthrax PA domain 3-like	8054212	3000301	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8036789	3001975	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8036789	3001975	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	Binary_toxB_2	e3kwvA1	A: beta sandwiches	X: Middle beta-sandwich domain in anthrax protective antigen (From Topology)	H: Middle beta-sandwich domain in anthrax protective antigen (From Topology)	T: Middle beta-sandwich domain in anthrax protective antigen	F: Binary_toxB_2	ECOD (1.6)
A	EUF07840	e3kwvA2	A: beta sandwiches	X: Ig-like domain in anthrax protective antigen (From Topology)	H: Ig-like domain in anthrax protective antigen (From Topology)	T: Ig-like domain in anthrax protective antigen	F: EUF07840	ECOD (1.6)
A	Binary_toxB_3	e3kwvA3	A: a+b two layers	X: beta-grasp domain in anthrax protective antigen (From Topology)	H: beta-grasp domain in anthrax protective antigen (From Topology)	T: beta-grasp domain in anthrax protective antigen	F: Binary_toxB_3	ECOD (1.6)
A	Binary_toxB	e3kwvA4	A: few secondary structure elements	X: Ca-binding domain in anthrax protective antigen (From Topology)	H: Ca-binding domain in anthrax protective antigen (From Topology)	T: Ca-binding domain in anthrax protective antigen	F: Binary_toxB	ECOD (1.6)
B	Binary_toxB_2	e3kwvB1	A: beta sandwiches	X: Middle beta-sandwich domain in anthrax protective antigen (From Topology)	H: Middle beta-sandwich domain in anthrax protective antigen (From Topology)	T: Middle beta-sandwich domain in anthrax protective antigen	F: Binary_toxB_2	ECOD (1.6)
B	EUF07840	e3kwvB2	A: beta sandwiches	X: Ig-like domain in anthrax protective antigen (From Topology)	H: Ig-like domain in anthrax protective antigen (From Topology)	T: Ig-like domain in anthrax protective antigen	F: EUF07840	ECOD (1.6)
B	Binary_toxB_3	e3kwvB3	A: a+b two layers	X: beta-grasp domain in anthrax protective antigen (From Topology)	H: beta-grasp domain in anthrax protective antigen (From Topology)	T: beta-grasp domain in anthrax protective antigen	F: Binary_toxB_3	ECOD (1.6)
B	Binary_toxB	e3kwvB4	A: few secondary structure elements	X: Ca-binding domain in anthrax protective antigen (From Topology)	H: Ca-binding domain in anthrax protective antigen (From Topology)	T: Ca-binding domain in anthrax protective antigen	F: Binary_toxB	ECOD (1.6)
D	Binary_toxB_2	e3kwvD1	A: beta sandwiches	X: Middle beta-sandwich domain in anthrax protective antigen (From Topology)	H: Middle beta-sandwich domain in anthrax protective antigen (From Topology)	T: Middle beta-sandwich domain in anthrax protective antigen	F: Binary_toxB_2	ECOD (1.6)
D	EUF07840	e3kwvD2	A: beta sandwiches	X: Ig-like domain in anthrax protective antigen (From Topology)	H: Ig-like domain in anthrax protective antigen (From Topology)	T: Ig-like domain in anthrax protective antigen	F: EUF07840	ECOD (1.6)
D	Binary_toxB_3	e3kwvD3	A: a+b two layers	X: beta-grasp domain in anthrax protective antigen (From Topology)	H: beta-grasp domain in anthrax protective antigen (From Topology)	T: beta-grasp domain in anthrax protective antigen	F: Binary_toxB_3	ECOD (1.6)
D	Binary_toxB	e3kwvD4	A: few secondary structure elements	X: Ca-binding domain in anthrax protective antigen (From Topology)	H: Ca-binding domain in anthrax protective antigen (From Topology)	T: Ca-binding domain in anthrax protective antigen	F: Binary_toxB	ECOD (1.6)
E	Binary_toxB_2	e3kwvE1	A: beta sandwiches	X: Middle beta-sandwich domain in anthrax protective antigen (From Topology)	H: Middle beta-sandwich domain in anthrax protective antigen (From Topology)	T: Middle beta-sandwich domain in anthrax protective antigen	F: Binary_toxB_2	ECOD (1.6)
E	EUF07840	e3kwvE2	A: beta sandwiches	X: Ig-like domain in anthrax protective antigen (From Topology)	H: Ig-like domain in anthrax protective antigen (From Topology)	T: Ig-like domain in anthrax protective antigen	F: EUF07840	ECOD (1.6)
E	Binary_toxB_3	e3kwvE3	A: a+b two layers	X: beta-grasp domain in anthrax protective antigen (From Topology)	H: beta-grasp domain in anthrax protective antigen (From Topology)	T: beta-grasp domain in anthrax protective antigen	F: Binary_toxB_3	ECOD (1.6)
E	Binary_toxB	e3kwvE4	A: few secondary structure elements	X: Ca-binding domain in anthrax protective antigen (From Topology)	H: Ca-binding domain in anthrax protective antigen (From Topology)	T: Ca-binding domain in anthrax protective antigen	F: Binary_toxB	ECOD (1.6)
C	ATLF	e3kwvC1	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: ATLF	ECOD (1.6)
F	ATLF	e3kwvF1	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: ATLF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.240	Mainly Beta	Sandwich	Jelly Rolls	Protective antigen, heptamerisation domain	CATH (4.3.0)
A	3.10.20.110	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
A	2.60.40.810	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B	2.60.120.240	Mainly Beta	Sandwich	Jelly Rolls	Protective antigen, heptamerisation domain	CATH (4.3.0)
B	3.10.20.110	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
B	2.60.40.810	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
D	2.60.120.240	Mainly Beta	Sandwich	Jelly Rolls	Protective antigen, heptamerisation domain	CATH (4.3.0)
D	3.10.20.110	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
D	2.60.40.810	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
E	2.60.120.240	Mainly Beta	Sandwich	Jelly Rolls	Protective antigen, heptamerisation domain	CATH (4.3.0)
E	3.10.20.110	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
E	2.60.40.810	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
C	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
F	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, D, E	PF17475	Clostridial binary toxin B/anthrax toxin PA domain 2 (Binary_toxB_2)	Clostridial binary toxin B/anthrax toxin PA domain 2	This domain forms the middle beta sandwish domain in anthrax toxin.	Domain
A, B, D, E	PF03495	Clostridial binary toxin B/anthrax toxin PA Ca-binding domain (Binary_toxB)	Clostridial binary toxin B/anthrax toxin PA Ca-binding domain	This domain is a calcium binding domain in the anthrax toxin protective antigen.	Domain
A, B, D, E	PF17476	Clostridial binary toxin B/anthrax toxin PA domain 3 (Binary_toxB_3)	Clostridial binary toxin B/anthrax toxin PA domain 3	This entry represents the beta-grasp domain in anthrax protective antigen.	Domain
A, B, D, E	PF20835	Anthrax protective antigen, immunoglobulin-like domain (PA_Ig-like)	Anthrax protective antigen, immunoglobulin-like domain	Anthrax protective antigen (PA) is one of the three proteins forming the anthrax toxin. It is involved in the first step of toxin entry into host cells, enabling lethal factor (LF) and oedema factor (EF) to cross to the cytosol. PA undergoes cleavage ...	Anthrax protective antigen (PA) is one of the three proteins forming the anthrax toxin. It is involved in the first step of toxin entry into host cells, enabling lethal factor (LF) and oedema factor (EF) to cross to the cytosol. PA undergoes cleavage by Furin to generate PA20 and PA63. The latter, which adopts a ring-shaped heptameric assembly, shows four distinct domains. The fourth domain, a carboxy- terminal receptor-binding domain, shows an initial hairpin and helix, followed by a beta-sandwich with an immunoglobulin-like fold (this entry) [1-5].	Domain
C, F	PF07737	Anthrax toxin lethal factor, N- and C-terminal domain (ATLF)	Anthrax toxin lethal factor, N- and C-terminal domain	The C-terminal domain is the catalytically active domain whereas the N-terminal domain is likely to be inactive.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, D, E	Protective antigen PA-63	toxin activity cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of biological process regulation of signaling negative regulation of response to stimulus biological regulation regulation of MAPK cascade negative regulation of signal transduction regulation of response to stimulus MAPK cascade regulation of cell communication cellular process negative regulation of MAPK cascade positive regulation of apoptotic process in another organism modulation of apoptotic process in another organism biological process involved in interspecies interaction between organisms positive regulation of biological process regulation of programmed cell death regulation of killing of cells of another organism disruption of cell in another organism modulation of process of another organism positive regulation of cellular process killing of cells of another organism positive regulation of programmed cell death regulation of apoptotic process cell death positive regulation of apoptotic process regulation of cell killing apoptotic process disruption of anatomical structure in another organism programmed cell death cell killing cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis	cellular anatomical structure membrane extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region cellular anatomical structure membrane extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region host cell plasma membrane host cell cytosol
C, F	Lethal factor	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding metalloendopeptidase activity endopeptidase activity peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding metalloendopeptidase activity endopeptidase activity toxin activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region host cell cytosol host cell cytoplasm part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, D, E	IPR035331	Clostridial binary toxin B/anthrax toxin PA, domain 3	Domain
A, B, D, E	IPR048853	Anthrax protective antigen, immunoglobulin-like domain	Domain
A, B, D, E	IPR011658	PA14 domain	Domain
A, B, D, E	IPR027439	Protective antigen, heptamerisation domain	Domain
A, B, D, E	IPR035088	Protective antigen, Ca-binding domain	Domain
A, B, D, E	IPR037524	PA14/GLEYA domain	Domain
A, B, D, E	IPR037149	Protective antigen, heptamerisation domain superfamily	Homologous Superfamily
A, B, D, E	IPR003896	Bacterial exotoxin B	Family
A, B, D, E	IPR027441	Protective antigen, domain 4	Homologous Superfamily
C, F	IPR024079	Metallopeptidase, catalytic domain superfamily	Homologous Superfamily
C, F	IPR047568	Anthrax toxin lethal factor-like domain	Domain
C, F	IPR003541	Anthrax toxin, lethal/endema factor	Family
C, F	IPR014781	Anthrax toxin, lethal/endema factor, N-/C-terminal	Domain
C, F	IPR015239	Anthrax toxin lethal factor, central domain	Domain

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes	Anthrax Protective Antigen (PA) and Lethal Factor (LF) Prechannel Complex

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.