4J8R

Structure of an octapeptide repeat of the prion protein bound to the POM2 Fab antibody fragment

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	C1-set_4	e4j8rA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
A	V-set	e4j8rA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
D [auth C]	C1-set_4	e4j8rC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth C]	V-set	e4j8rC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
B	V-set_8	e4j8rB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B	C1-set_1	e4j8rB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
E [auth D]	V-set_8	e4j8rD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E [auth D]	C1-set_1	e4j8rD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth D]	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
A, D [auth C]	POM2 FAB	L-KAPPA	Mus musculus (house mouse)	IGKV6-2301, IGKJ101, IGKJ102, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202444-0)
B, E [auth D]	POM2 FAB	VH-CH1	Mus musculus (house mouse)	IGHV1-5403, IGHJ401, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202444-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D [auth C]	Light Chain	IGKV6	Kappa	major prion protein	SAbDab (2024-11-08)
B, E [auth D]	Heavy Chain	IGHV1	-	major prion protein	SAbDab (2024-11-08)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth C]	Light chain of POM2 Fab	-	-	-
B, E [auth D]	Heavy chain of POM2 Fab	-	-	-
C [auth I], F [auth J]	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 cellular biosynthetic process negative regulation of interleukin-2 production negative regulation of cellular metabolic process 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 cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process interleukin-2 production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular 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 localization within membrane regulation of protein localization to cell periphery 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 positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation positive regulation of phosphorus metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of molecular function positive regulation of protein modification process positive regulation of protein kinase activity positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity 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 response to copper ion response to metal ion 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 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 cellular response to metal ion cellular response to copper ion response to oxygen-containing compound response to nitrogen compound response to amyloid-beta behavior system process learning or memory nervous system process cognition regulation of potassium ion transport potassium ion transmembrane transport regulation of potassium ion transmembrane transport potassium ion transport 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 glutamate receptor signaling pathway regulation of glutamate receptor signaling pathway neuron projection maintenance cellular response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound positive regulation of peptidyl-tyrosine phosphorylation	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane cytoplasm membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection inclusion body side of membrane Golgi apparatus axon synapse axon terminus presynapse distal axon terminal bouton cell junction neuron projection terminus cell surface cell periphery plasma membrane membrane microdomain membrane raft postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth I], F [auth J]	IPR022416	Prion/Doppel protein, beta-ribbon domain	Domain
C [auth I], F [auth J]	IPR025860	Major prion protein N-terminal domain	Domain
C [auth I], F [auth J]	IPR036924	Prion/Doppel beta-ribbon domain superfamily	Homologous Superfamily
C [auth I], F [auth J]	IPR000817	Prion protein	Family

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.