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- PDB-4a0p: Crystal structure of LRP6P3E3P4E4 -

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Basic information

Entry
Database: PDB / ID: 4a0p
TitleCrystal structure of LRP6P3E3P4E4
ComponentsLOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6
KeywordsSIGNALING / LRP6 / WNT SIGNALLING / WNT3A / DKK1 / MESD
Function / homology
Function and homology information


Wnt signaling pathway involved in somitogenesis / Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / kinase inhibitor activity / Wnt receptor activity / low-density lipoprotein particle receptor activity / toxin transmembrane transporter activity ...Wnt signaling pathway involved in somitogenesis / Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / kinase inhibitor activity / Wnt receptor activity / low-density lipoprotein particle receptor activity / toxin transmembrane transporter activity / negative regulation of smooth muscle cell apoptotic process / Wnt-protein binding / cellular response to cholesterol / midbrain dopaminergic neuron differentiation / negative regulation of protein serine/threonine kinase activity / dopaminergic neuron differentiation / frizzled binding / neural crest cell differentiation / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / canonical Wnt signaling pathway / coreceptor activity / positive regulation of cell cycle / Regulation of FZD by ubiquitination / TCF dependent signaling in response to WNT / protein localization to plasma membrane / cell-cell adhesion / response to peptide hormone / Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / cytoplasmic vesicle / early endosome membrane / membrane raft / signaling receptor binding / neuronal cell body / synapse / positive regulation of DNA-templated transcription / cell surface / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Low density lipoprotein receptor-related protein 5/6 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / TolB, C-terminal 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-related protein 5/6 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / TolB, C-terminal 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 / Coagulation Factor Xa inhibitory site / 6 Propeller / Neuraminidase / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Mainly Beta
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, S. / Malinauskas, T. / Aricescu, A.R. / Siebold, C. / Jones, E.Y.
CitationJournal: Dev Cell / Year: 2011
Title: Structural and functional studies of LRP6 ectodomain reveal a platform for Wnt signaling.
Authors: Shuo Chen / Doryen Bubeck / Bryan T MacDonald / Wen-Xue Liang / Jian-Hua Mao / Tomas Malinauskas / Oscar Llorca / A Radu Aricescu / Christian Siebold / Xi He / E Yvonne Jones /
Abstract: LDL-receptor-related protein 6 (LRP6), alongside Frizzled receptors, transduces Wnt signaling across the plasma membrane. The LRP6 ectodomain comprises four tandem β-propeller-EGF-like domain (PE) ...LDL-receptor-related protein 6 (LRP6), alongside Frizzled receptors, transduces Wnt signaling across the plasma membrane. The LRP6 ectodomain comprises four tandem β-propeller-EGF-like domain (PE) pairs that harbor binding sites for Wnt morphogens and their antagonists including Dickkopf 1 (Dkk1). To understand how these multiple interactions are integrated, we combined crystallographic analysis of the third and fourth PE pairs with electron microscopy (EM) to determine the complete ectodomain structure. An extensive inter-pair interface, conserved for the first-to-second and third-to-fourth PE interactions, contributes to a compact platform-like architecture, which is disrupted by mutations implicated in developmental diseases. EM reconstruction of the LRP6 platform bound to chaperone Mesd exemplifies a binding mode spanning PE pairs. Cellular and binding assays identify overlapping Wnt3a- and Dkk1-binding surfaces on the third PE pair, consistent with steric competition, but also suggest a model in which the platform structure supports an interplay of ligands through multiple interaction sites.
History
DepositionSep 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,81213
Polymers71,1701
Non-polymers1,64212
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)169.815, 42.699, 119.879
Angle α, β, γ (deg.)90.00, 97.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6 / LRP6 / LRP-6


Mass: 71170.094 Da / Num. of mol.: 1 / Fragment: P3E3P4E4, RESIDUES 629-1244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: C0019 / Cell line (production host): HEK293S / Production host: HOMO SAPIENS (human) / References: UniProt: O75581

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 , 4 types, 445 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.37 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 66493 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / % possible all: 88.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IJQ

1ijq


Resolution: 1.9→29.09 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.895 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21098 3378 5.1 %RANDOM
Rwork0.18135 ---
obs0.18284 63115 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.951 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20.07 Å2
2--0.38 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4848 0 98 437 5383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215052
X-RAY DIFFRACTIONr_bond_other_d0.0010.023424
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.9656860
X-RAY DIFFRACTIONr_angle_other_deg0.92838272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0875607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85923.821246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40615842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0841543
X-RAY DIFFRACTIONr_chiral_restr0.0680.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021033
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.75963025
X-RAY DIFFRACTIONr_mcbond_other0.31361238
X-RAY DIFFRACTIONr_mcangle_it3.149114883
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.282112027
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.483161977
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 204 -
Rwork0.306 3720 -
obs--78.91 %
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)
1-0.105-0.6146-0.29492.2301-0.23013.17680.0389-0.0708-0.04010.1003-0.01020.30150.0886-0.299-0.02870.2427-0.0279-0.05540.1814-0.0370.271975.16940.2745.141
23.0191-0.02710.36182.3663-0.64482.3290.06960.0214-0.0589-0.2615-0.0510.150.0632-0.0618-0.01850.23260.0382-0.08520.0402-0.02230.208478.54344.64133.151
32.0872-0.71320.48214.1140.22072.24470.15820.2308-0.0473-0.4989-0.2195-0.12630.09230.09380.06130.28410.0461-0.00470.0958-0.00180.20690.84142.07428.458
41.99830.87110.29875.60760.09772.54240.11760.0084-0.1167-0.1196-0.1603-0.68150.08310.22580.04270.19750.0262-0.02170.08580.01820.3173100.42537.44636.428
53.89121.16050.46564.0655-0.60613.2060.1224-0.2728-0.21840.2999-0.192-0.58040.20450.18140.06960.250.0065-0.11480.07680.03680.285597.93631.30648.177
63.0465-1.104-1.40051.54350.53334.1051-0.117-0.3028-0.07150.49090.0706-0.0141-0.11780.19470.04640.377-0.0423-0.07290.1250.02760.211185.59934.42953.582
71.46790.13580.64261.5337-0.07311.0387-0.0725-0.01130.379-0.081-0.1170.0979-0.1983-0.0610.18940.31650.0235-0.08380.0707-0.03130.312679.91958.19233.27
83.5843-1.6622-0.28425.1139-1.16361.6321-0.2675-0.70570.0470.85170.4485-0.0155-0.0207-0.0644-0.1810.42850.0911-0.12920.2506-0.02480.216251.29242.92230.153
93.2093-0.5679-0.16833.70260.46732.7508-0.0438-0.4552-0.18470.43790.17460.21650.155-0.2257-0.13080.2840.0226-0.03970.14280.05770.202638.94143.27824.541
101.1835-0.6021-0.59483.80751.00272.22770.0267-0.0456-0.18180.0587-0.06120.17740.1861-0.27410.03450.234-0.0177-0.07520.04730.0120.257437.30939.22410.552
112.0765-0.03011.41823.18750.53414.02670.05430.1017-0.0667-0.086-0.0021-0.10740.03170.0921-0.05220.21660.0191-0.05970.025-0.00540.194749.82337.7214.47
123.07720.13750.55696.3433-1.25744.47790.04890.3007-0.1117-0.3022-0.1191-0.60160.17210.64690.07030.24730.0398-0.06520.2049-0.01050.296461.8537.789.042
133.22120.69360.04632.2380.42361.5550.052-0.085-0.02340.1065-0.0374-0.23870.02780.2434-0.01460.29160.0369-0.15140.1179-0.00810.274562.59442.28222.366
143.2354-0.8319-0.25482.9343-0.4191.328-0.0063-0.18660.25110.20160.05510.111-0.2008-0.1397-0.04890.31740.03430.01490.0708-0.01950.270734.57158.00820.456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A661 - 704
2X-RAY DIFFRACTION2A705 - 746
3X-RAY DIFFRACTION3A747 - 790
4X-RAY DIFFRACTION4A791 - 833
5X-RAY DIFFRACTION5A834 - 874
6X-RAY DIFFRACTION6A630 - 660
7X-RAY DIFFRACTION6A875 - 882
8X-RAY DIFFRACTION7A883 - 933
9X-RAY DIFFRACTION8A965 - 1005
10X-RAY DIFFRACTION9A1013 - 1055
11X-RAY DIFFRACTION10A1056 - 1101
12X-RAY DIFFRACTION11A1102 - 1144
13X-RAY DIFFRACTION12A1145 - 1184
14X-RAY DIFFRACTION13A934 - 964
15X-RAY DIFFRACTION13A1185 - 1196
16X-RAY DIFFRACTION14A1197 - 1246

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