5JNX | pdb_00005jnx

The 6.6 A cryo-EM structure of the full-length human NPC1 in complex with the cleaved glycoprotein of Ebola virus

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: PDBTM
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	Frizzled domain-like	8090917	3001950	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)
G [auth H]	Ebola-like_HR1-HR2	e5jnxH1	A: a+b duplicates or obligate multimers	X: Envelope glycoprotein GP2-related (From Topology)	H: Envelope glycoprotein GP2-related (From Topology)	T: Envelope glycoprotein GP2-related	F: Ebola-like_HR1-HR2	ECOD (1.6)
E [auth F]	Ebola-like_HR1-HR2	e5jnxF1	A: a+b duplicates or obligate multimers	X: Envelope glycoprotein GP2-related (From Topology)	H: Envelope glycoprotein GP2-related (From Topology)	T: Envelope glycoprotein GP2-related	F: Ebola-like_HR1-HR2	ECOD (1.6)
C [auth D]	Ebola-like_HR1-HR2	e5jnxD1	A: a+b duplicates or obligate multimers	X: Envelope glycoprotein GP2-related (From Topology)	H: Envelope glycoprotein GP2-related (From Topology)	T: Envelope glycoprotein GP2-related	F: Ebola-like_HR1-HR2	ECOD (1.6)
F [auth G]	Filo_glycop	e5jnxG1	A: a+b complex topology	X: Envelope glycoprotein GP1 (From Topology)	H: Envelope glycoprotein GP1 (From Topology)	T: Envelope glycoprotein GP1	F: Filo_glycop	ECOD (1.6)
D [auth E]	Filo_glycop	e5jnxE1	A: a+b complex topology	X: Envelope glycoprotein GP1 (From Topology)	H: Envelope glycoprotein GP1 (From Topology)	T: Envelope glycoprotein GP1	F: Filo_glycop	ECOD (1.6)
B [auth C]	Filo_glycop	e5jnxC1	A: a+b complex topology	X: Envelope glycoprotein GP1 (From Topology)	H: Envelope glycoprotein GP1 (From Topology)	T: Envelope glycoprotein GP1	F: Filo_glycop	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth D], E [auth F], G [auth H]	PF22307	Envelope glycoprotein GP2-like, HR1-HR2 (Ebola-like_HR1-HR2)	Envelope glycoprotein GP2-like, HR1-HR2	This entry spans heptad repeats 1 and 2 of the glycoprotein (GP) from Ebola and Marburg viruses [1-5]. Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel ...	This entry spans heptad repeats 1 and 2 of the glycoprotein (GP) from Ebola and Marburg viruses [1-5]. Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). This domain may have been acquired via horizontal transfer from retroviruses.	Domain
B [auth C], D [auth E], F [auth G]	PF01611	Filovirus glycoprotein (Filo_glycop)	Filovirus glycoprotein	-	Family
A	PF02460	Patched SSD (Patched)	Patched SSD	The transmembrane protein Patched Swiss:P18502 is a receptor for the morphogenic Sonic Hedgehog. This protein associates with the smoothened protein (SMO) to transduce hedgehog signals. These proteins consist of twelve transmembrane segments and two ...	The transmembrane protein Patched Swiss:P18502 is a receptor for the morphogenic Sonic Hedgehog. This protein associates with the smoothened protein (SMO) to transduce hedgehog signals. These proteins consist of twelve transmembrane segments and two extracellular domains (ECDs) [1,2]. This entry represents the Sterol-sensing domain (SSD) formed by some of the TM segments. This domain may play a role in the transport and/or regulation of the SMO ligand [2].	Domain
A	PF22314	NPC1, middle luminal domain (NPC1_MLD)	NPC1, middle luminal domain	NPC intracellular cholesterol transporter 1 (NPC1) is a endosomal/lysosomal membrane protein that facilitates the trafficking of cholesterol and other cargo from lysosomes and is involved in cholesterol homeostasis. Mutations in the NPC1 gene cause t ...	NPC intracellular cholesterol transporter 1 (NPC1) is a endosomal/lysosomal membrane protein that facilitates the trafficking of cholesterol and other cargo from lysosomes and is involved in cholesterol homeostasis. Mutations in the NPC1 gene cause the rare neurodegenerative disease Niemann-Pick Type C (NPC). This entry represents the middle luminal domain (MLD) of NPC1, which contains the Ebola glycoprotein interacting site [5].	Domain
A	PF12349	Sterol-sensing domain of SREBP cleavage-activation (Sterol-sensing)	Sterol-sensing domain of SREBP cleavage-activation	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], E [auth F], G [auth H]	Envelope glycoprotein	binding lipid binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated-mediated suppression of host tetherin activity modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host viral life cycle import into cell viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated-mediated suppression of host tetherin activity modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host viral life cycle import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization clathrin-dependent endocytosis cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell adhesion of symbiont to host	cellular anatomical structure membrane virion component virion membrane extracellular region viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane other organism part
B [auth C], D [auth E], F [auth G]	Envelope glycoprotein	binding lipid binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated-mediated suppression of host tetherin activity modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host viral life cycle import into cell viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated-mediated suppression of host tetherin activity modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host viral life cycle import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization clathrin-dependent endocytosis cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell adhesion of symbiont to host	cellular anatomical structure membrane virion component virion membrane extracellular region viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane other organism part
A	Niemann-Pick C1 protein	sterol transfer activity lipid transporter activity lipid transfer activity transporter activity cholesterol transfer activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity protein binding binding virus receptor activity exogenous protein binding sterol binding alcohol binding sterol transfer activity lipid transporter activity lipid transfer activity transporter activity cholesterol transfer activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity protein binding binding virus receptor activity exogenous protein binding sterol binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding	response to stimulus response to chemical response to xenobiotic stimulus cellular localization intracellular lipid transport transport lipid localization lipid transport intracellular transport establishment of localization localization macromolecule localization establishment of localization in cell cellular process response to stimulus response to chemical response to xenobiotic stimulus cellular localization intracellular lipid transport transport lipid localization lipid transport intracellular transport establishment of localization localization macromolecule localization establishment of localization in cell cellular process biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction catabolic process autophagy metabolic process process utilizing autophagic mechanism cholesterol transport sterol transport organic hydroxy compound transport cell death programmed cell death cellular response to stimulus response to lipid response to endogenous stimulus cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to steroid hormone cellular response to lipid cellular response to steroid hormone stimulus cellular response to hormone stimulus intracellular cholesterol transport intracellular sterol transport intestinal lipid absorption multicellular organismal process digestion system process intestinal absorption digestive system process intestinal cholesterol absorption lipid digestion cellular response to low-density lipoprotein particle stimulus response to lipoprotein particle response to nitrogen compound cellular response to lipoprotein particle stimulus cholesterol efflux carbohydrate metabolic process glucan metabolic process polysaccharide metabolic process oligosaccharide metabolic process primary metabolic process macromolecule metabolic process cyclodextrin metabolic process adult walking behavior adult locomotory behavior behavior adult behavior locomotory behavior walking behavior regulation of biological process regulation of cellular process regulation of epithelial cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death epithelial cell apoptotic process negative regulation of apoptotic process negative regulation of epithelial cell apoptotic process negative regulation of cellular process apoptotic process developmental process multicellular organism development hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development neurogenesis cellular developmental process cell differentiation nervous system development oxoacid metabolic process steroid metabolic process carboxylic acid metabolic process organic acid metabolic process bile acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process lipid metabolic process membrane organization cellular component organization membrane raft organization cellular component organization or biogenesis import into cell endocytosis vesicle-mediated transport negative regulation of catabolic process macroautophagy negative regulation of metabolic process regulation of catabolic process regulation of autophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy regulation of metabolic process sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis secondary alcohol metabolic process sterol metabolic process cholesterol metabolic process alcohol metabolic process cholesterol storage lipid storage nutrient storage biosynthetic process gene expression macromolecule biosynthetic process vacuolar transport lysosomal transport signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication negative regulation of TORC1 signaling regulation of intracellular signal transduction negative regulation of TOR signaling signal transduction regulation of TORC1 signaling TOR signaling regulation of signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication TORC1 signaling establishment of protein localization establishment of protein localization to membrane localization within membrane response to metal ion response to cadmium ion	cellular anatomical structure membrane membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system extracellular exosome extracellular vesicle extracellular organelle cellular anatomical structure membrane membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle endosome membrane endosome intracellular vesicle late endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome cytoplasm organelle membrane vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi apparatus perinuclear region of cytoplasm cell periphery plasma membrane membrane microdomain membrane raft endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D], E [auth F], G [auth H]	IPR014625	Filoviruses glycoprotein	Family
C [auth D], E [auth F], G [auth H]	IPR002561	Filoviruses glycoprotein, extracellular domain	Domain
C [auth D], E [auth F], G [auth H]	IPR054584	Envelope glycoprotein GP2-like, HR1-HR2	Domain
B [auth C], D [auth E], F [auth G]	IPR014625	Filoviruses glycoprotein	Family
B [auth C], D [auth E], F [auth G]	IPR002561	Filoviruses glycoprotein, extracellular domain	Domain
B [auth C], D [auth E], F [auth G]	IPR054584	Envelope glycoprotein GP2-like, HR1-HR2	Domain
A	IPR032190	Niemann-Pick C1, N-terminal	Domain
A	IPR004765	NPC1-like	Family
A	IPR000731	Sterol-sensing domain	Domain
A	IPR053958	HMGCR/SNAP/NPC1-like, sterol-sensing domain	Domain
A	IPR053956	NPC1, middle luminal domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O15118	Niemann-Pick disease ophthalmoplegia Niemann-Pick disease, type C1 obesity disorder gastrointestinal stromal tumor Ataxia atherosclerosis cirrhosis of liver liver disease brucellosis osteosarcoma sphingolipidosis histiocytosis inborn errors of metabolism large cell medulloblastoma Niemann-Pick disease ophthalmoplegia Niemann-Pick disease, type C1 obesity disorder gastrointestinal stromal tumor Ataxia atherosclerosis cirrhosis of liver liver disease brucellosis osteosarcoma sphingolipidosis histiocytosis inborn errors of metabolism large cell medulloblastoma lysosomal storage disease metabolic syndrome X ovarian cancer Gaucher disease hydrops fetalis adrenal cortex carcinoma intellectual disability leukodystrophy lung cancer malignant pancreatic neoplasm C syndrome non-Langerhans cell histiocytosis psoriasis heart disease tuberculosis arteriosclerosis disorder lung carcinoma medulloblastoma cholestasis Niemann-Pick disease type C Down syndrome

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B [auth C], C [auth D], D [auth E], E [auth F] A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B [auth C], C [auth D], D [auth E], E [auth F] A, B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sterol-Sensing Domain (SSD) Proteins	Niemann-Pick C1 protein, full-length

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.