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- PDB-3v65: Crystal structure of agrin and LRP4 complex -

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Basic information

Entry
Database: PDB / ID: 3v65
TitleCrystal structure of agrin and LRP4 complex
Components
  • Agrin
  • Low-density lipoprotein receptor-related protein 4
KeywordsPROTEIN BINDING / laminin-G / beta-propeller
Function / homology
Function and homology information


negative regulation of sodium ion export across plasma membrane / positive regulation of presynaptic membrane organization / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / Formation of the dystrophin-glycoprotein complex (DGC) / ECM proteoglycans / acetylcholine receptor regulator activity / regulation of synaptic activity / regulation of axon guidance ...negative regulation of sodium ion export across plasma membrane / positive regulation of presynaptic membrane organization / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / Formation of the dystrophin-glycoprotein complex (DGC) / ECM proteoglycans / acetylcholine receptor regulator activity / regulation of synaptic activity / regulation of axon guidance / Retinoid metabolism and transport / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / positive regulation of motor neuron apoptotic process / chondroitin sulfate binding / postsynaptic membrane assembly / regulation of cardiac muscle cell membrane potential / BMP binding / presynaptic membrane assembly / negative regulation of axonogenesis / sialic acid binding / positive regulation of skeletal muscle acetylcholine-gated channel clustering / plasma membrane organization / proximal/distal pattern formation / dystroglycan binding / amyloid-beta clearance by cellular catabolic process / ATPase inhibitor activity / heparan sulfate proteoglycan binding / dorsal/ventral pattern formation / transforming growth factor beta binding / synaptic assembly at neuromuscular junction / embryonic limb morphogenesis / limb development / negative regulation of ossification / motor neuron apoptotic process / positive regulation of filopodium assembly / dendrite morphogenesis / positive regulation of peptidyl-tyrosine phosphorylation / embryonic digit morphogenesis / neuromuscular junction development / generation of neurons / enzyme-linked receptor protein signaling pathway / regulation of synapse organization / receptor clustering / odontogenesis of dentin-containing tooth / positive regulation of Rac protein signal transduction / regulation of protein phosphorylation / basement membrane / regulation of postsynapse assembly / apolipoprotein binding / plasma membrane raft / hair follicle development / regulation of cardiac muscle contraction / axonal growth cone / synapse assembly / coreceptor activity / positive regulation of GTPase activity / regulation of microtubule cytoskeleton organization / kidney development / synaptic membrane / negative regulation of canonical Wnt signaling pathway / synapse organization / neuromuscular junction / sarcolemma / receptor tyrosine kinase binding / Wnt signaling pathway / circadian rhythm / endocytosis / intracellular protein localization / protein transport / positive regulation of protein phosphorylation / scaffold protein binding / : / chemical synaptic transmission / transmembrane transporter binding / cell differentiation / postsynaptic density / receptor ligand activity / neuronal cell body / synapse / dendrite / calcium ion binding / glutamatergic synapse / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
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 / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin EGF domain ...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 / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin EGF domain / : / Complement Clr-like EGF domain / Laminin-type EGF domain / SEA domain superfamily / Kazal-type serine protease inhibitor domain / Complement Clr-like EGF-like / Kazal-type serine protease inhibitor domain / SEA domain profile. / SEA domain / SEA domain / : / Laminin G domain profile. / Kazal type serine protease inhibitors / TolB, C-terminal domain / 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 / 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 / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / 6 Propeller / Neuraminidase / 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 / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Agrin / Low-density lipoprotein receptor-related protein 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZong, Y. / Jin, R.
CitationJournal: Genes Dev. / Year: 2012
Title: Structural basis of agrin-LRP4-MuSK signaling.
Authors: Zong, Y. / Zhang, B. / Gu, S. / Lee, K. / Zhou, J. / Yao, G. / Figueiredo, D. / Perry, K. / Mei, L. / Jin, R.
History
DepositionDec 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agrin
B: Low-density lipoprotein receptor-related protein 4
D: Low-density lipoprotein receptor-related protein 4
C: Agrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7656
Polymers128,6854
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.720, 110.230, 158.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.483318, -0.030238, -0.874922), (0.020579, -0.99952, 0.023176), (-0.875203, -0.006804, 0.483708)34.55657, 85.08112, 20.88902

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Components

#1: Protein Agrin


Mass: 20880.699 Da / Num. of mol.: 2 / Fragment: agrin LG3 (unp residues 353-737)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Agrn, Agrin / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25304
#2: Protein Low-density lipoprotein receptor-related protein 4 / LRP-4 / Multiple epidermal growth factor-like domains 7


Mass: 43461.734 Da / Num. of mol.: 2 / Fragment: LRP4 beta-1 (unp residues 1759-1948)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lrp4, Megf7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9QYP1
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY
Sequence detailsTHE CRYSTALLIZED SEQUENCES FOR CHAIN A/B ARE CORRESPONDING TO UNP P25304-4'S RESIDUE RANGE 1759-1948

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 293 K / Method: evaporation, recrystallization / pH: 8
Details: 20% PEG 3350, 0.2 M potassium phosphate dibasic, 0.15 M sodium chloride, 2 mM calcium chloride, pH 8.0, EVAPORATION, RECRYSTALLIZATION, temperature 293K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2011
RadiationMonochromator: single crystal side-bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.3→60 Å / Num. all: 21574 / Num. obs: 20688 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.3→3.48 Å / % possible all: 93

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→60 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.859 / SU B: 85.909 / SU ML: 0.607 / Cross valid method: THROUGHOUT / ESU R Free: 0.66 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29743 1095 5.1 %RANDOM
Rwork0.20237 ---
all0.20716 21574 --
obs0.20714 20342 94.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.627 Å2
Baniso -1Baniso -2Baniso -3
1-4.59 Å20 Å20 Å2
2--1.6 Å20 Å2
3----6.19 Å2
Refinement stepCycle: LAST / Resolution: 3.3→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8564 0 2 0 8566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198764
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9411919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.32851083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56723.396424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.295151426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8291577
X-RAY DIFFRACTIONr_chiral_restr0.1040.21302
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216751
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 67 -
Rwork0.337 1323 -
obs--89.68 %

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