4KML

Probing the N-terminal beta-sheet conversion in the crystal structure of the full-length human prion protein bound to a Nanobody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4kmlb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
B	d4kmlb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Prion-like	8036527	3001941	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	Prion	e4kmlA1	A: a+b two layers	X: Prion-like (From Topology)	H: Prion-like (From Topology)	T: Prion-like	F: Prion	ECOD (1.6)
B	V-set_12	e4kmlB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B	NANOBODY	VH	Lama glama (llama)	IGHV3S101, IGHV3S201, IGHJ4*01	V-DOMAIN VH	IG	(VH)	IMGT (202508-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV3	-	major prion protein	SAbDab (2025-03-07)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00377	Prion/Doppel alpha-helical domain (Prion)	Prion/Doppel alpha-helical domain	The prion protein is thought to be the infectious agent that causes transmissible spongiform encephalopathies, such as scrapie and BSE. It is thought that the prion protein can exist in two different forms: one is the normal cellular protein, and the ...	The prion protein is thought to be the infectious agent that causes transmissible spongiform encephalopathies, such as scrapie and BSE. It is thought that the prion protein can exist in two different forms: one is the normal cellular protein, and the other is the infectious form which can change the normal prion protein into the infectious form. It has been found that the prion alpha-helical domain is also found in the Doppel protein.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Major prion protein	cation binding cuprous ion binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding amide binding amyloid-beta binding peptide binding cupric ion binding protein binding protein-folding chaperone binding cation binding cuprous ion binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding amide binding amyloid-beta binding peptide binding cupric ion binding protein binding protein-folding chaperone binding cytoskeletal protein binding microtubule binding tubulin binding protein-containing complex binding molecular adaptor activity identical protein binding molecular transducer activity signaling receptor activity enzyme binding protease binding molecular condensate scaffold activity protein-macromolecule adaptor activity ATP-dependent protein binding transmembrane transporter binding type 5 metabotropic glutamate receptor binding signaling receptor binding glutamate receptor binding G protein-coupled receptor binding G protein-coupled glutamate receptor binding molecular function activator activity molecular function regulator activity enzyme regulator activity molecular function inhibitor activity peptidase regulator activity enzyme inhibitor activity aspartic-type endopeptidase inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity lamin binding glycosaminoglycan binding carbohydrate derivative binding	negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling biological regulation cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation regulation of cell communication cellular process positive regulation of signaling regulation of calcium ion transport regulation of localization import into cell transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport calcium ion import into cytosol monoatomic cation transport regulation of metal ion transport regulation of calcium ion import calcium ion transmembrane import into cytosol regulation of transport regulation of monoatomic ion transport import across plasma membrane inorganic ion transmembrane transport establishment of localization inorganic cation import across plasma membrane inorganic cation transmembrane transport transmembrane transport regulation of transmembrane transport calcium ion import across plasma membrane regulation of calcium ion import across plasma membrane inorganic ion import across plasma membrane regulation of monoatomic cation transmembrane transport calcium ion import calcium ion transmembrane transport cellular response to stimulus positive regulation of signal transduction response to stimulus regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling positive regulation of calcium-mediated signaling signal transduction positive regulation of intracellular signal transduction regulation of response to stimulus calcium-mediated signaling multicellular organismal process negative regulation of interleukin-2 production regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of interleukin-2 production negative regulation of metabolic process interleukin-2 production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process protein destabilization regulation of protein stability inorganic ion homeostasis homeostatic process intracellular copper ion homeostasis copper ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis positive regulation of protein localization to plasma membrane protein localization cellular localization regulation of protein localization cellular macromolecule localization regulation of protein localization to membrane positive regulation of protein localization to cell periphery protein localization to cell periphery protein localization to plasma membrane positive regulation of protein localization to membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of protein localization to plasma membrane regulation of protein modification process regulation of protein phosphorylation peptidyl-tyrosine modification regulation of primary metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation primary metabolic process macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process peptidyl-tyrosine phosphorylation negative regulation of phosphate metabolic process negative regulation of protein modification process negative regulation of protein metabolic process negative regulation of protein phosphorylation negative regulation of phosphorus metabolic process negative regulation of phosphorylation neuron apoptotic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process positive regulation of neuron apoptotic process programmed cell death regulation of neuron apoptotic process immune response-regulating cell surface receptor signaling pathway negative regulation of signaling regulation of antigen receptor-mediated signaling pathway negative regulation of antigen receptor-mediated signaling pathway negative regulation of cell communication immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response negative regulation of response to stimulus regulation of T cell receptor signaling pathway T cell receptor signaling pathway negative regulation of signal transduction negative regulation of T cell receptor signaling pathway negative regulation of immune system process immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response amyloid precursor protein catabolic process regulation of amide metabolic process regulation of amyloid-beta formation regulation of amyloid precursor protein catabolic process negative regulation of amyloid precursor protein catabolic process amyloid-beta metabolic process amide metabolic process amyloid precursor protein metabolic process amyloid-beta formation negative regulation of amyloid-beta formation negative regulation of amide metabolic process regulation of type II interferon production type II interferon production negative regulation of type II interferon production regulation of cellular component organization dendritic spine maintenance cell projection organization cellular component maintenance regulation of dendritic spine maintenance cellular component organization regulation of synapse structure or activity cellular component organization or biogenesis synapse organization negative regulation of cell projection organization negative regulation of dendritic spine maintenance plasma membrane bounded cell projection organization dendritic spine organization postsynapse organization negative regulation of cellular component organization regulation of cell projection organization regulation of postsynapse organization regulation of synapse organization cell junction organization neuron projection organization regulation of plasma membrane bounded cell projection organization cellular response to chemical stimulus response to chemical cellular response to xenobiotic stimulus response to xenobiotic stimulus interleukin-17 production negative regulation of interleukin-17 production regulation of interleukin-17 production calcineurin-NFAT signaling cascade negative regulation of intracellular signal transduction negative regulation of calcineurin-NFAT signaling cascade regulation of calcineurin-mediated signaling regulation of calcineurin-NFAT signaling cascade negative regulation of calcium-mediated signaling negative regulation of calcineurin-mediated signaling calcineurin-mediated signaling establishment of protein localization protein targeting positive regulation of establishment of protein localization regulation of protein targeting to membrane establishment of protein localization to membrane regulation of establishment of protein localization protein targeting to membrane regulation of protein targeting positive regulation of protein targeting to membrane negative regulation of DNA-binding transcription factor activity RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of molecular function nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of molecular function regulation of DNA-binding transcription factor activity regulation of DNA-templated transcription negative regulation of lymphocyte proliferation regulation of leukocyte activation regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of leukocyte activation regulation of activated T cell proliferation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation activated T cell proliferation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of activated T cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation negative regulation of programmed cell death negative regulation of apoptotic process glutamate receptor signaling pathway positive regulation of glutamate receptor signaling pathway regulation of glutamate receptor signaling pathway behavior system process learning or memory long-term memory nervous system process cognition memory response to copper ion cellular response to metal ion response to metal ion cellular response to copper ion response to oxygen-containing compound response to nitrogen compound response to amyloid-beta regulation of protein maturation negative regulation of proteolysis negative regulation of protein maturation protein maturation regulation of proteolysis proteolysis regulation of protein processing protein processing negative regulation of protein processing regulation of potassium ion transport potassium ion transmembrane transport regulation of potassium ion transmembrane transport potassium ion transport cell cycle regulation of cell cycle response to cadmium ion response to oxidative stress response to stress cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization neuron projection maintenance cellular response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound positive regulation of phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation positive regulation of phosphorus metabolic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection inclusion body Golgi apparatus postsynapse synapse cell junction axon axon terminus presynapse distal axon terminal bouton neuron projection terminus membrane microdomain membrane raft extrinsic component of membrane postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse endoplasmic reticulum
B	Nanobody	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR022416	Prion/Doppel protein, beta-ribbon domain	Domain
A	IPR036924	Prion/Doppel beta-ribbon domain superfamily	Homologous Superfamily
A	IPR000817	Prion protein	Family
A	IPR025860	Major prion protein N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P04156	fatal familial insomnia Gerstmann-Straussler-Scheinker syndrome kuru Alzheimer disease progressive myoclonus epilepsy Creutzfeldt Jacob disease spongiform encephalopathy with neuropsychiatric features Wilson disease Huntington disease-like 1 scrapie prion disease inherited Creutzfeldt-Jakob disease Liver Cirrhosis, Experimental dentatorubral-pallidoluysian atrophy prostate cancer fatal familial insomnia Gerstmann-Straussler-Scheinker syndrome kuru Alzheimer disease progressive myoclonus epilepsy Creutzfeldt Jacob disease spongiform encephalopathy with neuropsychiatric features Wilson disease Huntington disease-like 1 scrapie prion disease inherited Creutzfeldt-Jakob disease Liver Cirrhosis, Experimental dentatorubral-pallidoluysian atrophy prostate cancer amyloidosis primitive neuroectodermal tumor Crohn disease malignant glioma Down syndrome malignant pancreatic neoplasm acquired metabolic disease exocrine pancreatic carcinoma akinetic mutism familial Alzheimer-like prion disease gastric cancer giardiasis ovarian cancer hereditary diffuse gastric adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia IgA glomerulonephritis plasma cell myeloma invasive ductal breast carcinoma kuru, susceptibility to rheumatoid arthritis cystic fibrosis lung cancer depressive disorder malignant mesothelioma Duchenne muscular dystrophy action myoclonus-renal failure syndrome facioscapulohumeral muscular dystrophy myopathy gastric neoplasm oligodendroglioma amyotrophic lateral sclerosis glioblastoma atypical teratoid rhabdoid tumor breast cancer Pick disease Charcot-Marie-Tooth disease inborn errors of metabolism juvenile dermatomyositis large cell medulloblastoma Riley-Day syndrome dementia malignant colon neoplasm ulcerative colitis dermatomyositis Emery-Dreifuss muscular dystrophy medulloblastoma neurodegenerative disease osteosarcoma pancreatic intraductal papillary-mucinous carcinoma B-cell chronic lymphocytic leukemia breast carcinoma pityriasis rubra pilaris

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.