Gene Ontology annotation through association of InterPro records with GO terms
Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity
Annotation inferences using phylogenetic trees
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
Protein-protein interactions between large proteins: two-hybrid screening using a functionally classified library composed of long cDNAs.
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The study used cytoplasmic domains of large transmembrane KIAA proteins as yeast-two-hybrid baits against a random-fragment library; the cached abstract does not identify the specific LRP4-WHRN pair.
"Cytoplasmic
domains of KIAA transmembrane proteins (>1000 amino acids) were used as bait for
yeast two-hybrid screening."
LRP promotes endocytosis and degradation, but not transcytosis, of the amyloid-beta peptide in a blood-brain barrier in vitro model.
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The paper's “mLRP4” is explicitly an engineered LRP mini-receptor in MDCK cells, not the LRP4 gene product O75096; its amyloid-beta result cannot support human LRP4 function.
"cells were stably transfected with Pgp or mLRP4, an LRP mini-receptor. When
compared to empty vector-transfected cells, MDCK-Pgp cells did not transcytose
radiolabeled Abeta in the basolateral-to-apical direction. MDCK-mLRP4 cells were
found to endocytose and degrade, but not to trasncytose intact radiolabeled
Abeta."
Lrp4 is a receptor for Agrin and forms a complex with MuSK.
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The foundational study reports that Lrp4 binds agrin, complexes with MuSK, and mediates agrin-dependent MuSK activation at neuromuscular synapses.
"Here, we report that Lrp4, a member of the LDLR family,
is a receptor for Agrin, forms a complex with MuSK, and mediates MuSK activation
by Agrin."
LRP4 serves as a coreceptor of agrin.
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An independent foundational study showed that LRP4 binds neuronal agrin, complexes with MuSK, is required for agrin-dependent MuSK phosphorylation and AChR clustering, and can reconstitute agrin responsiveness in heterologous cells.
"report that LRP4, a low-density lipoprotein receptor (LDLR)-related protein, is
expressed specifically in myotubes and binds to neuronal agrin. Its expression
enables agrin binding and MuSK signaling in cells that otherwise do not respond
to agrin. Suppression of LRP4 expression in muscle cells attenuates agrin
binding, agrin-induced MuSK tyrosine phosphorylation, and AChR clustering. LRP4
also forms a complex with MuSK in a manner that is stimulated by agrin."
Lrp4, a novel receptor for Dickkopf 1 and sclerostin, is expressed by osteoblasts and regulates bone growth and turnover in vivo.
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In vitro assays showed Lrp4 binding to Dkk1 and sclerostin, while Lrp4-deficient mice had altered bone dimensions, density, and turnover markers.
"Here we show that Lrp4 is expressed in
bone and cultured osteoblasts and binds Dkk1 and sclerostin in vitro. MicroCT
analysis of Lrp4 deficient mutant mice revealed shortened total femur length,
reduced cortical femoral perimeter, and reduced total femur bone mineral content
(BMC) and bone mineral density (BMD)."
The low-density lipoprotein receptor-related protein 10 is a negative regulator of the canonical Wnt/beta-catenin signaling pathway.
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This paper experimentally studies LRP10, a distinct LDLR-family protein, despite LRP10 also occurring as a historical synonym in the human LRP4 UniProt record.
"Here, we found that LRP10, a new member of the LDLR
gene family, inhibits the canonical Wnt/beta-catenin signaling pathway."
LRP4 mutations alter Wnt/beta-catenin signaling and cause limb and kidney malformations in Cenani-Lenz syndrome.
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Recessive human LRP4 variants were identified in 12 Cenani-Lenz syndrome families with limb and kidney malformations, and tested variants lost LRP4's antagonism of LRP6-mediated canonical Wnt activation.
"By sequencing candidate genes, we identified recessive
LRP4 mutations in 12 families with CLS. LRP4 belongs to the low-density
lipoprotein (LDL) receptor-related proteins (LRPs), which are essential for
various developmental processes. LRP4 is known to antagonize LRP6-mediated
activation of canonical Wnt signaling, a function that is lost by the identified
mutations."
Bone overgrowth-associated mutations in the LRP4 gene impair sclerostin facilitator function.
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Recombinant-protein assays established direct SOST-LRP4 binding, and perturbation experiments showed that LRP4 facilitates SOST inhibition of Wnt1/beta-catenin signaling.
"Biochemical assays with recombinant proteins
confirmed that sclerostin LRP4 interaction is direct. Interestingly, in vitro
overexpression and RNAi-mediated knockdown experiments revealed that LRP4
specifically facilitates the previously described inhibitory action of
sclerostin on Wnt1/β-catenin signaling."
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Human bone-overgrowth variants R1170W and W1186S impaired LRP4-SOST interaction and the SOST-facilitator effect.
"Notably,
we identified two mutations in LRP4 (R1170W and W1186S) in patients suffering
from bone overgrowth. We found that these mutations impair LRP4 interaction with
sclerostin and its concomitant sclerostin facilitator effect."
LRP4 third β-propeller domain mutations cause novel congenital myasthenia by compromising agrin-mediated MuSK signaling in a position-specific manner.
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Two heteroallelic human LRP4 variants in a congenital-myasthenia patient reduced binding to both MuSK and agrin; domain mutagenesis separated the MuSK-signaling edge from the Wnt-regulating central cavity of beta-propeller 3.
"The
identified mutations in LRP4 are located at the edge of its 3rd beta-propeller
domain and decrease binding affinity of LRP4 for both MuSK and agrin. Mutations
in the LRP4 3rd beta-propeller domain were previously reported to impair Wnt
signaling and cause bone diseases including Cenani-Lenz syndactyly syndrome and
sclerosteosis-2. By analyzing naturally occurring and artificially introduced
mutations in the LRP4 3rd beta-propeller domain, we show that the edge of the
domain regulates the MuSK signaling whereas its central cavity governs Wnt
signaling."
Architecture of the human interactome defines protein communities and disease networks.
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BioPlex 2.0 used affinity-purification mass spectrometry in a proteome-scale human co-complex survey; candidate co-associations are discovery evidence rather than proof of direct binding.
"Here we present BioPlex 2.0
(Biophysical Interactions of ORFeome-derived complexes), which uses robust
affinity purification-mass spectrometry methodology to elucidate protein
interaction networks and co-complexes nucleated by more than 25% of
protein-coding genes from the human genome"
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
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BioPlex 3.0 and its HCT116 companion network are cell-line-specific AP-MS interaction maps, so an LRP4 co-association is not automatically direct or physiologically general.
"Through affinity-purification
mass spectrometry, we have created two proteome-scale, cell-line-specific
interaction networks. The first, BioPlex 3.0, results from affinity purification
of 10,128 human proteins-half the proteome-in 293T cells and includes 118,162
interactions among 14,586 proteins. The second results from 5,522
immunoprecipitations in HCT116 cells."
Quantitative fragmentomics allow affinity mapping of interactomes.
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The study measured a large human PDZ-domain/PDZ-binding-motif interaction panel, providing fragment-level affinity evidence rather than evidence that every pair forms a physiological full-length complex.
"Here, we measure the affinities of 65,000 interactions involving PDZ
domains and their target PDZ-binding motifs (PBM) within a human interactome
region particularly relevant for viral infection and cancer."
Structural insights into the assembly of the agrin/LRP4/MuSK signaling complex.
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A 3.8-A cryo-EM reconstruction showed a 1:1:1 extracellular agrin-LRP4-MuSK complex in which LRP4 simultaneously recruits agrin and MuSK.
"Here, we report the cryo-EM structure of the extracellular
ternary complex of agrin/LRP4/MuSK in a stoichiometry of 1:1:1. This structure
reveals that arc-shaped LRP4 simultaneously recruits both agrin and MuSK to its
central cavity, thereby promoting a direct interaction between agrin and MuSK."
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The structure used human proteins but only an LRP4 extracellular fragment (residues 21-1350); LDLa repeats and several MuSK domains were unresolved, so PDB 8S9P is not a fully observed full-length LRP4 structure.
"The human MuSK-ECD and agrin-ECD were individually expressed by the Bac-to-Bac expression system. The human LRP4-ECD was expressed through the BacMam expression system. The MuSK-ECD (24-495aa) was subcloned into a pFastBac vector with a gp67 signaling sequence and N-terminal His tag for protein expression and secretion in Sf9 insect cells. Similarly, the agrin-ECD (1329-2068aa, Δ1897-1907aa) was subcloned into a pFastBac vector with a gp67 signaling sequence and C-terminal His tag for protein expression and secretion in sf9 cells. The LRP4-ECD (21-1350aa) was subcloned into a pACEMam1 vector with the LRP4 signaling sequence and a C-terminal Flag tag for protein expression and secretion in HEK293F cells."
Multiple LDLR family members act as entry receptors for yellow fever virus.
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Human-cell perturbations identified LRP4 as one of several LDLR-family proteins that can mediate yellow-fever-virus entry through its LDLa region; this is pathogen exploitation, not an endogenous core function.
"Here, using a surface protein-targeted CRISPR-Cas9 screen, we identified LRP4, a
low-density lipoprotein receptor (LDLR) family member, as a candidate entry
receptor for YFV. Genetic ablation of LRP4 impaired YFV infection of cells and,
reciprocally, complementation or ectopic expression of LRP4 increased infection.
Related viruses in the YFV antigenic complex also showed LRP4-dependent
infection. LRP4 promoted YFV entry into cells through LDLR type A (LA) domain
binding to domain III of the YFV envelope protein."
UniProtKB entry O75096 (LRP4_HUMAN)
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The reviewed human product is a 1905-aa type-I membrane protein with signal peptide 1-20, extracellular region 21-1725, transmembrane helix 1726-1746, and cytoplasmic tail 1747-1905.
"FT SIGNAL 1..20
FT /evidence="ECO:0000255"
FT CHAIN 21..1905
FT /note="Low-density lipoprotein receptor-related protein 4"
FT /id="PRO_0000017325"
FT TOPO_DOM 21..1725
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 1726..1746
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 1747..1905
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255""
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The reviewed record maps LRP4 to PANTHER subfamily PTHR22722:SF15; manual feature-table counting gives 8 LDL-receptor class-A domains, 20 class-B repeats, and 3 explicitly annotated EGF-like domains.
"DR PANTHER; PTHR22722:SF15; LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED; 1."
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The record has one RefSeq protein and no curated UniProt alternative-products block; therefore no reviewed isoform-specific function can be asserted.
"DR RefSeq; NP_002325.2; NM_002334.4."