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- PDB-8s9p: 1:1:1 agrin/LRP4/MuSK complex -

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Basic information

Entry
Database: PDB / ID: 8s9p
Title1:1:1 agrin/LRP4/MuSK complex
Components
  • Agrin
  • Low-density lipoprotein receptor-related protein 4
  • Muscle, skeletal receptor tyrosine-protein kinase
KeywordsSIGNALING PROTEIN / agrin / LRP4 / MuSK / NMJ / RTK
Function / homology
Function and homology information


positive regulation of presynaptic membrane organization / positive regulation of protein geranylgeranylation / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / positive regulation of synaptic assembly at neuromuscular junction / regulation of synaptic assembly at neuromuscular junction / clustering of voltage-gated sodium channels ...positive regulation of presynaptic membrane organization / positive regulation of protein geranylgeranylation / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / positive regulation of synaptic assembly at neuromuscular junction / regulation of synaptic assembly at neuromuscular junction / clustering of voltage-gated sodium channels / synaptic assembly at neuromuscular junction / chondroitin sulfate binding / skeletal muscle acetylcholine-gated channel clustering / Glycosaminoglycan-protein linkage region biosynthesis / HS-GAG biosynthesis / postsynaptic membrane assembly / presynaptic membrane assembly / HS-GAG degradation / sialic acid binding / negative regulation of axonogenesis / proximal/distal pattern formation / Wnt-protein binding / dystroglycan binding / amyloid-beta clearance by cellular catabolic process / positive regulation of skeletal muscle acetylcholine-gated channel clustering / Formation of the dystrophin-glycoprotein complex (DGC) / NCAM1 interactions / heparan sulfate proteoglycan binding / dorsal/ventral pattern formation / negative regulation of ossification / limb development / positive regulation of filopodium assembly / embryonic digit morphogenesis / dendrite morphogenesis / generation of neurons / enzyme-linked receptor protein signaling pathway / neuromuscular junction development / receptor clustering / RSV-host interactions / odontogenesis of dentin-containing tooth / positive regulation of Rac protein signal transduction / Respiratory syncytial virus (RSV) attachment and entry / basement membrane / Non-integrin membrane-ECM interactions / apolipoprotein binding / regulation of postsynapse assembly / plasma membrane raft / positive regulation of GTPase activity / hair follicle development / ECM proteoglycans / Integrin cell surface interactions / Retinoid metabolism and transport / coreceptor activity / laminin binding / transmembrane receptor protein tyrosine kinase activity / lysosomal lumen / cell surface receptor protein tyrosine kinase signaling pathway / synaptic membrane / neuromuscular junction / kidney development / negative regulation of canonical Wnt signaling pathway / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / synapse organization / structural constituent of cytoskeleton / Golgi lumen / memory / Wnt signaling pathway / positive regulation of protein phosphorylation / endocytosis / G protein-coupled acetylcholine receptor signaling pathway / : / protein autophosphorylation / protein tyrosine kinase activity / scaffold protein binding / postsynaptic membrane / Attachment and Entry / cell differentiation / receptor complex / postsynaptic density / neuronal cell body / calcium ion binding / synapse / dendrite / positive regulation of gene expression / cell surface / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. ...NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Domain found in sea urchin sperm protein, enterokinase, agrin / : / Complement Clr-like EGF domain / Laminin-type EGF domain / SEA domain superfamily / Complement Clr-like EGF-like / Kazal-type serine protease inhibitor domain / Kazal-type serine protease inhibitor domain / SEA domain profile. / SEA domain / SEA domain / : / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kazal type serine protease inhibitors / Laminin G domain profile. / Laminin G domain / Laminin G domain / Kazal domain superfamily / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / Kazal domain / Kazal domain profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-like domain / Immunoglobulin domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / : / EGF-like domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Concanavalin A-like lectin/glucanase domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Agrin / Muscle, skeletal receptor tyrosine-protein kinase / Low-density lipoprotein receptor-related protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsXie, T. / Xu, G.J. / Liu, Y. / Quade, B. / Lin, W.C. / Bai, X.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143158 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structural insights into the assembly of the agrin/LRP4/MuSK signaling complex.
Authors: Tian Xie / Guangjun Xu / Yun Liu / Bradley Quade / Weichun Lin / Xiao-Chen Bai /
Abstract: MuSK is a receptor tyrosine kinase (RTK) that plays essential roles in the formation and maintenance of the neuromuscular junction. Distinct from most members of RTK family, MuSK activation requires ...MuSK is a receptor tyrosine kinase (RTK) that plays essential roles in the formation and maintenance of the neuromuscular junction. Distinct from most members of RTK family, MuSK activation requires not only its cognate ligand agrin but also its coreceptors LRP4. However, how agrin and LRP4 coactivate MuSK remains unclear. 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. Our cryo-EM analyses therefore uncover the assembly mechanism of agrin/LRP4/MuSK signaling complex and reveal how MuSK receptor is activated by concurrent binding of agrin and LRP4.
History
DepositionMar 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agrin
B: Low-density lipoprotein receptor-related protein 4
C: Muscle, skeletal receptor tyrosine-protein kinase


Theoretical massNumber of molelcules
Total (without water)527,0043
Polymers527,0043
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Agrin


Mass: 217553.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGRN, AGRIN / Production host: Homo sapiens (human) / References: UniProt: O00468
#2: Protein Low-density lipoprotein receptor-related protein 4 / LRP-4 / Multiple epidermal growth factor-like domains 7


Mass: 212287.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP4, KIAA0816, LRP10, MEGF7 / Production host: Homo sapiens (human) / References: UniProt: O75096
#3: Protein Muscle, skeletal receptor tyrosine-protein kinase / Muscle-specific tyrosine-protein kinase receptor / MuSK / Muscle-specific kinase receptor


Mass: 97163.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUSK / Production host: Homo sapiens (human)
References: UniProt: O15146, receptor protein-tyrosine kinase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 1:1:1 agrin/LRP4/MuSK complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4 / Details: 25 mM HEPES pH 7.4, 150 mM NaCl, and 2 mM CaCl2
SpecimenConc.: 0.56 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2SerialEMimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2414116
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82511 / Symmetry type: POINT

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