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- PDB-3v64: Crystal Structure of agrin and LRP4 -

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Basic information

Entry
Database: PDB / ID: 3v64
TitleCrystal Structure of agrin and LRP4
Components
  • Low-density lipoprotein receptor-related protein 4
  • agrin
KeywordsPROTEIN BINDING / beta propeller / laminin-G / signaling
Function / homology
Function and homology information


negative regulation of sodium ion export across plasma membrane / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / positive regulation of presynaptic membrane organization / positive regulation of protein geranylgeranylation / ECM proteoglycans / acetylcholine receptor regulator activity / regulation of axon guidance / regulation of synaptic activity ...negative regulation of sodium ion export across plasma membrane / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / positive regulation of presynaptic membrane organization / positive regulation of protein geranylgeranylation / ECM proteoglycans / acetylcholine receptor regulator activity / regulation of axon guidance / regulation of synaptic activity / Retinoid metabolism and transport / positive regulation of synaptic assembly at neuromuscular junction / postsynaptic membrane assembly / positive regulation of motor neuron apoptotic process / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / regulation of cardiac muscle cell membrane potential / BMP binding / presynaptic membrane assembly / sialic acid binding / plasma membrane organization / negative regulation of axonogenesis / proximal/distal pattern formation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / dystroglycan binding / amyloid-beta clearance by cellular catabolic process / ATPase inhibitor activity / heparan sulfate proteoglycan binding / anatomical structure development / transforming growth factor beta binding / negative regulation of ossification / synaptic assembly at neuromuscular junction / dorsal/ventral pattern formation / embryonic limb morphogenesis / dendrite morphogenesis / limb development / motor neuron apoptotic process / positive regulation of filopodium assembly / generation of neurons / embryonic digit morphogenesis / neuromuscular junction development / regulation of synapse organization / receptor clustering / enzyme-linked receptor protein signaling pathway / odontogenesis of dentin-containing tooth / positive regulation of Rac protein signal transduction / plasma membrane raft / apolipoprotein binding / basement membrane / hair follicle development / regulation of cardiac muscle contraction / synaptic cleft / coreceptor activity / axonal growth cone / regulation of microtubule cytoskeleton organization / synapse assembly / synaptic membrane / kidney development / synapse organization / regulation of protein phosphorylation / negative regulation of canonical Wnt signaling pathway / sarcolemma / neuromuscular junction / protein localization / receptor tyrosine kinase binding / Wnt signaling pathway / positive regulation of GTPase activity / endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / protein transport / chemical synaptic transmission / scaffold protein binding / collagen-containing extracellular matrix / transmembrane transporter binding / postsynaptic density / cell differentiation / receptor ligand activity / positive regulation of protein phosphorylation / dendrite / neuronal cell body / glutamatergic synapse / synapse / calcium ion binding / 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 / Complement Clr-like EGF domain / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin-type EGF-like (LE) domain profile. / Laminin G domain / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai ...Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / Complement Clr-like EGF domain / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin-type EGF-like (LE) domain profile. / Laminin G domain / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Complement Clr-like EGF-like / Kazal-type serine protease inhibitor domain / SEA domain superfamily / Laminin-type EGF domain / SEA domain profile. / Kazal-type serine protease inhibitor domain / SEA domain / SEA domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / Laminin G domain profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Kazal type serine protease inhibitors / TolB, C-terminal domain / Laminin G domain / Laminin G domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / 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 / Laminin / Laminin / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / 6 Propeller / Neuraminidase / 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 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Agrin / Low-density lipoprotein receptor-related protein 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsZong, Y. / Zhang, B. / Gu, S. / Lee, K. / Zhou, J. / Yao, G. / Figueiedo, D. / Perry, K. / Mei, L. / 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 1.1Mar 1, 2017Group: Structure summary
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,71915
Polymers120,6964
Non-polymers1,02311
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.460, 106.070, 112.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules CDAB

#1: Protein Low-density lipoprotein receptor-related protein 4


Mass: 39467.395 Da / Num. of mol.: 2 / Fragment: LG3 domain (unp residues 1759-1948)
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: Q9QYP1
#2: Protein agrin / / LRP-4 / Multiple epidermal growth factor-like domains 7


Mass: 20880.699 Da / Num. of mol.: 2 / Fragment: beta 1 propeller (unp residues 396-737)
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: P25304

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Sugars , 1 types, 2 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 119 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.77 %
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: Dec 2, 2010
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: 2.85→50 Å / Num. all: 28058 / Num. obs: 27778 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.116
Reflection shellResolution: 2.85→3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.446 / Num. unique all: 4058 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→50 Å / SU ML: 0.85 / σ(F): 1.35 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 1382 4.96 %Random
Rwork0.2032 ---
obs0.2056 27778 98.46 %-
all-28098 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.786 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.9476 Å2-0 Å2-0 Å2
2---2.1478 Å2-0 Å2
3----7.7998 Å2
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8308 0 53 110 8471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088548
X-RAY DIFFRACTIONf_angle_d1.32611607
X-RAY DIFFRACTIONf_dihedral_angle_d18.33111
X-RAY DIFFRACTIONf_chiral_restr0.0911276
X-RAY DIFFRACTIONf_plane_restr0.0061509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.95190.33751310.2742609X-RAY DIFFRACTION99
2.9519-3.07010.26181330.24052608X-RAY DIFFRACTION99
3.0701-3.20980.30141370.22232662X-RAY DIFFRACTION99
3.2098-3.37910.27731290.20792631X-RAY DIFFRACTION99
3.3791-3.59080.2671480.19112638X-RAY DIFFRACTION99
3.5908-3.8680.30661570.18372639X-RAY DIFFRACTION99
3.868-4.25720.25781400.17952656X-RAY DIFFRACTION99
4.2572-4.87320.22051330.16052661X-RAY DIFFRACTION98
4.8732-6.13930.25611400.18342669X-RAY DIFFRACTION98
6.1393-77.06150.29671340.20982730X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4999-2.93010.76137.4755-3.2313.2146-0.27420.6402-0.0527-0.41590.23770.5582-0.5795-0.39110.06180.44980.0055-0.15330.4952-0.0940.2779-23.5283-12.0958-35.2039
21.9827-2.77291.45154.1225-1.26381.597-0.0840.29220.4002-0.1738-0.0162-0.4835-0.37860.19670.0740.3518-0.06920.04310.4116-0.05230.3008-18.7017-3.6224-30.8686
33.20461.43180.65693.95491.39082.879-0.07640.03270.12350.1277-0.0381-0.0962-0.11870.06880.1050.2551-0.0060.00630.27110.02120.1553-13.1993-7.6901-21.9683
46.2034-2.96111.44245.85540.4666.8704-0.20330.11440.1492-0.72120.16010.0686-0.08850.2852-0.00130.33790.0228-0.01010.3383-0.02710.3929-20.185-14.2872-32.7781
55.9639-2.72013.94774.6078-0.9322.8838-0.14840.74330.73630.792-0.08740.60570.10710.22240.26380.8081-0.05290.17230.63370.16090.5744-38.78561.2243-4.4139
67.9192-2.26573.10221.0786-1.81442.8275-0.33390.34710.63380.14110.0530.1642-0.3841-0.06980.20660.49820.08370.03240.3876-0.06530.4731-31.71017.347-9.3417
75.12331.59980.43574.93590.36094.4267-0.37010.07270.1793-0.62710.40340.4058-0.46550.2041-0.09430.5976-0.01890.00270.4244-0.00640.4591-36.631712.0833-19.4834
83.87340.15380.68064.6927-0.52473.67170.2743-0.7438-0.15541.5342-0.09911.08310.3193-0.3382-0.21840.9354-0.00160.20710.90190.09530.5592-41.42964.2721-6.9588
97.2261-8.67371.34282.0066-1.60220.2560.4509-1.28931.15960.6515-0.3144-1.5476-0.53510.8944-0.23140.7457-0.20250.04820.7329-0.12381.014620.7461-4.97121.7618
105.8714-0.59162.15782.6445-0.40793.2446-0.0305-0.6113-0.03820.82010.1413-0.1299-0.4679-0.1347-0.16640.6188-0.06850.07830.1642-0.06060.2759-0.621311.08114.2784
112.52591.3036-0.17873.433-0.63572.56020.09450.057-0.0120.2146-0.0709-0.1910.0690.1967-0.01180.1990.02980.01830.1685-0.0190.15421.35982.7822.9521
120.69770.3011-0.5431.7336-2.37177.36940.01960.07740.06090.1865-0.3866-0.3818-0.44320.79390.35190.3905-0.1312-0.01760.34580.10240.344912.722919.2743-7.0881
132.6395-1.87630.82432.0661-2.31694.3699-0.647-0.03331.2370.03250.10960.2342-0.8046-0.49370.38791.5544-0.0831-0.06490.7152-0.12990.7717-41.539341.0266-63.0524
141.36190.46351.47054.472-2.69593.8935-0.58470.63630.8292-1.0348-0.13491.041-1.4784-0.7261-0.07452.0835-0.338-0.1393-0.03790.74140.2667-30.832538.0901-65.7423
152.45381.1475-0.06913.03740.37331.71630.0655-0.03140.11990.07810.0364-0.3092-0.53980.4278-0.08330.4809-0.16540.00430.3145-0.05150.2544-25.377327.9844-42.5795
162.38150.91020.08882.51940.23111.99440.25250.29590.2350.1579-0.0931-0.189-0.97110.6284-0.05160.6729-0.27980.02660.12120.01960.1945-24.771831.9934-44.4861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1758:1778)
2X-RAY DIFFRACTION2(chain A and resid 1779:1819)
3X-RAY DIFFRACTION3(chain A and resid 1820:1899)
4X-RAY DIFFRACTION4(chain A and resid 1900:1948)
5X-RAY DIFFRACTION5(chain B and resid 1759:1778)
6X-RAY DIFFRACTION6(chain B and resid 1779:1818)
7X-RAY DIFFRACTION7(chain B and resid 1819:1891)
8X-RAY DIFFRACTION8(chain B and resid 1892:1948)
9X-RAY DIFFRACTION9(chain C and resid 403:416)
10X-RAY DIFFRACTION10(chain C and resid 417:495)
11X-RAY DIFFRACTION11(chain C and resid 496:687)
12X-RAY DIFFRACTION12(chain C and resid 688:745)
13X-RAY DIFFRACTION13(chain D and resid 404:416)
14X-RAY DIFFRACTION14(chain D and resid 417:442)
15X-RAY DIFFRACTION15(chain D and resid 443:638)
16X-RAY DIFFRACTION16(chain D and resid 639:742)

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