4LDB | pdb_00004ldb

Crystal Structure of Ebola Virus VP40 Dimer

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4ldba1	All beta proteins	EV matrix protein	EV matrix protein	EV matrix protein	automated matches	ZEBOV (Zaire ebolavirus ) [TaxId: 186538 ],	SCOPe (2.08)
B	d4ldbb1	All beta proteins	EV matrix protein	EV matrix protein	EV matrix protein	automated matches	ZEBOV (Zaire ebolavirus ) [TaxId: 186538 ],	SCOPe (2.08)
C	d4ldbc1	All beta proteins	EV matrix protein	EV matrix protein	EV matrix protein	automated matches	ZEBOV (Zaire ebolavirus ) [TaxId: 186538 ],	SCOPe (2.08)
D	d4ldbd1	All beta proteins	EV matrix protein	EV matrix protein	EV matrix protein	automated matches	ZEBOV (Zaire ebolavirus ) [TaxId: 186538 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	EV matrix protein-like	8044506	3000219	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EV matrix protein-like	8044506	3000219	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EV matrix protein-like	8044506	3000219	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EV matrix protein-like	8044506	3000219	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	VP40_C	e4ldbA2	A: beta barrels	X: EV matrix protein (From Homology)	H: EV matrix protein	T: EV matrix protein	F: VP40_C	ECOD (1.6)
A	VP40_N	e4ldbA1	A: beta barrels	X: EV matrix protein (From Homology)	H: EV matrix protein	T: EV matrix protein	F: VP40_N	ECOD (1.6)
B	VP40_C	e4ldbB2	A: beta barrels	X: EV matrix protein (From Homology)	H: EV matrix protein	T: EV matrix protein	F: VP40_C	ECOD (1.6)
B	VP40_N	e4ldbB1	A: beta barrels	X: EV matrix protein (From Homology)	H: EV matrix protein	T: EV matrix protein	F: VP40_N	ECOD (1.6)
C	VP40_C	e4ldbC2	A: beta barrels	X: EV matrix protein (From Homology)	H: EV matrix protein	T: EV matrix protein	F: VP40_C	ECOD (1.6)
C	VP40_N	e4ldbC1	A: beta barrels	X: EV matrix protein (From Homology)	H: EV matrix protein	T: EV matrix protein	F: VP40_N	ECOD (1.6)
D	VP40_C	e4ldbD1	A: beta barrels	X: EV matrix protein (From Homology)	H: EV matrix protein	T: EV matrix protein	F: VP40_C	ECOD (1.6)
D	VP40_N	e4ldbD2	A: beta barrels	X: EV matrix protein (From Homology)	H: EV matrix protein	T: EV matrix protein	F: VP40_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.70.20.20	Mainly Beta	Distorted Sandwich	Topoisomerase I	domain 3	CATH (4.3.0)
A	2.60.510.10	Mainly Beta	Sandwich	EV matrix protein fold	EV matrix protein	CATH (4.3.0)
B	2.70.20.20	Mainly Beta	Distorted Sandwich	Topoisomerase I	domain 3	CATH (4.3.0)
B	2.60.510.10	Mainly Beta	Sandwich	EV matrix protein fold	EV matrix protein	CATH (4.3.0)
C	2.70.20.20	Mainly Beta	Distorted Sandwich	Topoisomerase I	domain 3	CATH (4.3.0)
C	2.60.510.10	Mainly Beta	Sandwich	EV matrix protein fold	EV matrix protein	CATH (4.3.0)
D	2.70.20.20	Mainly Beta	Distorted Sandwich	Topoisomerase I	domain 3	CATH (4.3.0)
D	2.60.510.10	Mainly Beta	Sandwich	EV matrix protein fold	EV matrix protein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF07447	Matrix protein VP40 (Matrix_Filo)	Matrix protein VP40	This family contains viral VP40 matrix proteins that seem to be restricted to the Filoviridae. These play an important role in the assembly process of virus particles by interacting with cellular factors, cellular membranes, and the ribonuclearprotei ...	This family contains viral VP40 matrix proteins that seem to be restricted to the Filoviridae. These play an important role in the assembly process of virus particles by interacting with cellular factors, cellular membranes, and the ribonuclearprotein particle complex. It has been shown that the N-terminal region of VP40 folds into a mixture of hexameric and octameric states - these may have distinct roles [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Matrix protein VP40	structural constituent of virion structural molecule activity RNA binding binding nucleic acid binding identical protein binding protein binding	biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host defenses symbiont-mediated response to host defenses response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host defenses response to host response to external biotic stimulus non-lytic viral release viral budding biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host defenses symbiont-mediated response to host defenses response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host defenses response to host response to external biotic stimulus non-lytic viral release viral budding viral life cycle virion assembly exit from host cell viral process viral budding from plasma membrane viral release from host cell symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated perturbation of host cell cycle progression modulation of process of another organism symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host RNAi-mediated antiviral immune response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host innate immune response viral budding via host ESCRT complex intracellular transport of virus transport of virus	host cellular component cellular anatomical structure host cell other organism part host cell endomembrane system host cell part host cell membrane virion component virion membrane extracellular region host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part host cell late endosome membrane host cellular component cellular anatomical structure host cell other organism part host cell endomembrane system host cell part host cell membrane virion component virion membrane extracellular region host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part host cell late endosome membrane host intracellular organelle host cell cytoplasm host cell endosome membrane host cell late endosome host cell endosome host intracellular region membrane microdomain membrane raft membrane host cell plasma membrane protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR043079	EV matrix protein, N-terminal	Homologous Superfamily
A, B, C, D	IPR008986	EV matrix protein	Family
A, B, C, D	IPR038057	EV matrix domain superfamily	Homologous Superfamily
A, B, C, D	IPR035092	EV matrix protein, C-terminal	Homologous Superfamily

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.