6NK6 | pdb_00006nk6

Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse Mxra8 receptor

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth I]	SCOP2B Superfamily	Trypsin-like serine proteases	8071557	3000114	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Trypsin-like serine proteases	8071557	3000114	SCOP2B (2022-06-29)
M [auth K]	SCOP2B Superfamily	Trypsin-like serine proteases	8071557	3000114	SCOP2B (2022-06-29)
P [auth L]	SCOP2B Superfamily	Trypsin-like serine proteases	8071557	3000114	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 [auth M]	V-set_9	e6nk6M1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_9	ECOD (1.6)
A [auth M]	V-set_11	e6nk6M2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_11	ECOD (1.6)
B [auth N]	V-set_9	e6nk6N1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_9	ECOD (1.6)
B [auth N]	V-set_11	e6nk6N2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_11	ECOD (1.6)
C [auth O]	V-set_9	e6nk6O1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_9	ECOD (1.6)
C [auth O]	V-set_11	e6nk6O2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_11	ECOD (1.6)
D [auth P]	V-set_9	e6nk6P1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_9	ECOD (1.6)
D [auth P]	V-set_11	e6nk6P2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_11	ECOD (1.6)
E [auth A]	Alpha_E1_glycop_2nd	e6nk6A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E1_glycop_2nd	ECOD (1.6)
E [auth A]	Alpha_E1_glycop_1st	e6nk6A1	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: Alpha_E1_glycop_1st	ECOD (1.6)
E [auth A]	Alpha_E1_glycop_like	e6nk6A3	A: extended segments	X: Transmembrane helix of E1 envelope glycoprotein (From Topology)	H: Transmembrane helix of E1 envelope glycoprotein (From Topology)	T: Transmembrane helix of E1 envelope glycoprotein	F: Alpha_E1_glycop_like	ECOD (1.6)
H [auth B]	Alpha_E1_glycop_2nd	e6nk6B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E1_glycop_2nd	ECOD (1.6)
H [auth B]	Alpha_E1_glycop_1st	e6nk6B1	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: Alpha_E1_glycop_1st	ECOD (1.6)
H [auth B]	Alpha_E1_glycop_like	e6nk6B3	A: extended segments	X: Transmembrane helix of E1 envelope glycoprotein (From Topology)	H: Transmembrane helix of E1 envelope glycoprotein (From Topology)	T: Transmembrane helix of E1 envelope glycoprotein	F: Alpha_E1_glycop_like	ECOD (1.6)
K [auth C]	Alpha_E1_glycop_2nd	e6nk6C2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E1_glycop_2nd	ECOD (1.6)
K [auth C]	Alpha_E1_glycop_1st	e6nk6C1	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: Alpha_E1_glycop_1st	ECOD (1.6)
K [auth C]	Alpha_E1_glycop_like	e6nk6C3	A: extended segments	X: Transmembrane helix of E1 envelope glycoprotein (From Topology)	H: Transmembrane helix of E1 envelope glycoprotein (From Topology)	T: Transmembrane helix of E1 envelope glycoprotein	F: Alpha_E1_glycop_like	ECOD (1.6)
N [auth D]	Alpha_E1_glycop_2nd	e6nk6D2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Alpha_E1_glycop_2nd	ECOD (1.6)
N [auth D]	Alpha_E1_glycop_1st	e6nk6D1	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: Alpha_E1_glycop_1st	ECOD (1.6)
N [auth D]	Alpha_E1_glycop_like	e6nk6D3	A: extended segments	X: Transmembrane helix of E1 envelope glycoprotein (From Topology)	H: Transmembrane helix of E1 envelope glycoprotein (From Topology)	T: Transmembrane helix of E1 envelope glycoprotein	F: Alpha_E1_glycop_like	ECOD (1.6)
G [auth I]	Peptidase_S3	e6nk6I1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
J	Peptidase_S3	e6nk6J1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
M [auth K]	Peptidase_S3	e6nk6K1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)
P [auth L]	Peptidase_S3	e6nk6L1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Peptidase_S3	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth M], B [auth N], C [auth O], D [auth P]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
E [auth A], H [auth B], K [auth C], N [auth D]	PF01589	Alphavirus E1 glycoprotein (Alpha_E1_glycop)	Alphavirus E1 glycoprotein	-	Family
F [auth E], I [auth F], L [auth G], O [auth H]	PF00943	Alphavirus E2 glycoprotein (Alpha_E2_glycop)	Alphavirus E2 glycoprotein	-	Family
G [auth I], J, M [auth K], P [auth L]	PF00944	Alphavirus core protein (Peptidase_S3)	Alphavirus core protein	Also known as coat protein C and capsid protein C. This makes the literature very confusing. Alphaviruses consist of a nucleoprotein core, a lipid membrane which envelopes the core, and glycoprotein spikes protruding from the lipid membrane.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth M], B [auth N], C [auth O], D [auth P]	Matrix remodeling-associated protein 8	-	cell adhesion cellular process developmental process multicellular organismal process cellular developmental process establishment of blood-brain barrier cell development nervous system development glial cell development establishment of glial blood-brain barrier multicellular organism development neurogenesis central nervous system development gliogenesis cell adhesion cellular process developmental process multicellular organismal process cellular developmental process establishment of blood-brain barrier cell development nervous system development glial cell development establishment of glial blood-brain barrier multicellular organism development neurogenesis central nervous system development gliogenesis glial cell differentiation cell differentiation anatomical structure development system development	cell surface cellular anatomical structure cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus cell surface cellular anatomical structure cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle membrane plasma membrane cilium ciliary membrane plasma membrane bounded cell projection cell periphery cell projection bounding membrane of organelle plasma membrane region organelle membrane cell projection membrane
E [auth A], H [auth B], K [auth C], N [auth D]	E1 glycoprotein	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle
F [auth E], I [auth F], L [auth G], O [auth H]	E2 glycoprotein	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle
G [auth I], J, M [auth K], P [auth L]	Capsid protein	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth M], B [auth N], C [auth O], D [auth P]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth M], B [auth N], C [auth O], D [auth P]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth M], B [auth N], C [auth O], D [auth P]	IPR042472	Matrix remodeling-associated protein 8	Family
A [auth M], B [auth N], C [auth O], D [auth P]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth M], B [auth N], C [auth O], D [auth P]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth M], B [auth N], C [auth O], D [auth P]	IPR007110	Immunoglobulin-like domain	Domain
E [auth A], H [auth B], K [auth C], N [auth D]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
E [auth A], H [auth B], K [auth C], N [auth D]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
E [auth A], H [auth B], K [auth C], N [auth D]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
E [auth A], H [auth B], K [auth C], N [auth D]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
E [auth A], H [auth B], K [auth C], N [auth D]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
E [auth A], H [auth B], K [auth C], N [auth D]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
E [auth A], H [auth B], K [auth C], N [auth D]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
E [auth A], H [auth B], K [auth C], N [auth D]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
E [auth A], H [auth B], K [auth C], N [auth D]	IPR000936	Alphavirus E2 glycoprotein	Family
E [auth A], H [auth B], K [auth C], N [auth D]	IPR000930	Peptidase S3, togavirin	Domain
E [auth A], H [auth B], K [auth C], N [auth D]	IPR002548	Alphavirus E1 glycoprotein	Domain
E [auth A], H [auth B], K [auth C], N [auth D]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
E [auth A], H [auth B], K [auth C], N [auth D]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
F [auth E], I [auth F], L [auth G], O [auth H]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
F [auth E], I [auth F], L [auth G], O [auth H]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
F [auth E], I [auth F], L [auth G], O [auth H]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
F [auth E], I [auth F], L [auth G], O [auth H]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
F [auth E], I [auth F], L [auth G], O [auth H]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
F [auth E], I [auth F], L [auth G], O [auth H]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
F [auth E], I [auth F], L [auth G], O [auth H]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
F [auth E], I [auth F], L [auth G], O [auth H]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
F [auth E], I [auth F], L [auth G], O [auth H]	IPR000936	Alphavirus E2 glycoprotein	Family
F [auth E], I [auth F], L [auth G], O [auth H]	IPR000930	Peptidase S3, togavirin	Domain
F [auth E], I [auth F], L [auth G], O [auth H]	IPR002548	Alphavirus E1 glycoprotein	Domain
F [auth E], I [auth F], L [auth G], O [auth H]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
F [auth E], I [auth F], L [auth G], O [auth H]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
G [auth I], J, M [auth K], P [auth L]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
G [auth I], J, M [auth K], P [auth L]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
G [auth I], J, M [auth K], P [auth L]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
G [auth I], J, M [auth K], P [auth L]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
G [auth I], J, M [auth K], P [auth L]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
G [auth I], J, M [auth K], P [auth L]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
G [auth I], J, M [auth K], P [auth L]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
G [auth I], J, M [auth K], P [auth L]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
G [auth I], J, M [auth K], P [auth L]	IPR000936	Alphavirus E2 glycoprotein	Family
G [auth I], J, M [auth K], P [auth L]	IPR000930	Peptidase S3, togavirin	Domain
G [auth I], J, M [auth K], P [auth L]	IPR002548	Alphavirus E1 glycoprotein	Domain
G [auth I], J, M [auth K], P [auth L]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
G [auth I], J, M [auth K], P [auth L]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth M], B [auth N], C [auth O], D [auth P], E [auth A] A [auth M], B [auth N], C [auth O], D [auth P], E [auth A], F [auth E], G [auth I], H [auth B], I [auth F], J, K [auth C], L [auth G], M [auth K], N [auth D], O [auth H], P [auth L]	OPM	Transmembrane	Bitopic proteins	Viral membrane fusion glycoprotein	Alphavirus E1 glycoprotein

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth M], B [auth N], C [auth O], D [auth P], E [auth A] A [auth M], B [auth N], C [auth O], D [auth P], E [auth A], F [auth E], G [auth I], H [auth B], I [auth F], J, K [auth C], L [auth G], M [auth K], N [auth D], O [auth H], P [auth L]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth M], B [auth N], C [auth O], D [auth P], E [auth A] A [auth M], B [auth N], C [auth O], D [auth P], E [auth A], F [auth E], G [auth I], H [auth B], I [auth F], J, K [auth C], L [auth G], M [auth K], N [auth D], O [auth H], P [auth L]	MemProtMD	Annotated as membrane protein by MemProtMD