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- PDB-3s2k: Structural basis of Wnt signaling inhibition by Dickkopf binding ... -

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Basic information

Entry
Database: PDB / ID: 3s2k
TitleStructural basis of Wnt signaling inhibition by Dickkopf binding to LRP5/6.
Components
  • Dickkopf-related protein 1
  • Low-density lipoprotein receptor-related protein 6
KeywordsSIGNALING PROTEIN / wnt co-receptor / beta-propeller / EGF domain / wnt signaling / wnt inhibitor / glycosylation
Function / homology
Function and homology information


negative regulation of mesodermal cell fate specification / regulation of endodermal cell fate specification / positive regulation of Wnt signaling pathway, calcium modulating pathway / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / negative regulation of presynapse assembly / Signaling by LRP5 mutants / Wnt signaling pathway involved in somitogenesis / regulation of dopaminergic neuron differentiation / negative regulation of cardiac muscle cell differentiation ...negative regulation of mesodermal cell fate specification / regulation of endodermal cell fate specification / positive regulation of Wnt signaling pathway, calcium modulating pathway / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / negative regulation of presynapse assembly / Signaling by LRP5 mutants / Wnt signaling pathway involved in somitogenesis / regulation of dopaminergic neuron differentiation / negative regulation of cardiac muscle cell differentiation / Wnt-Frizzled-LRP5/6 complex / motor learning / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / endoderm formation / synapse pruning / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / endocardial cushion development / regulation of receptor internalization / heart induction / receptor antagonist activity / kinase inhibitor activity / toxin transmembrane transporter activity / low-density lipoprotein particle receptor activity / co-receptor binding / Wnt receptor activity / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cellular response to cholesterol / midbrain dopaminergic neuron differentiation / Wnt-protein binding / negative regulation of protein serine/threonine kinase activity / dopaminergic neuron differentiation / heart valve development / frizzled binding / negative regulation of ossification / Wnt signalosome / neural crest cell differentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / embryonic limb morphogenesis / face morphogenesis / limb development / low-density lipoprotein particle receptor binding / negative regulation of SMAD protein signal transduction / negative regulation of Wnt signaling pathway / negative regulation of peptidyl-serine phosphorylation / negative regulation of smooth muscle cell apoptotic process / mesoderm formation / negative regulation of BMP signaling pathway / hair follicle development / canonical Wnt signaling pathway / coreceptor activity / positive regulation of cell cycle / regulation of neuron apoptotic process / response to retinoic acid / forebrain development / regulation of synaptic transmission, glutamatergic / Regulation of FZD by ubiquitination / negative regulation of protein binding / TCF dependent signaling in response to WNT / protein localization to plasma membrane / positive regulation of JNK cascade / growth factor activity / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / Wnt signaling pathway / response to peptide hormone / positive regulation of DNA-binding transcription factor activity / cell-cell adhesion / negative regulation of neuron projection development / early endosome membrane / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / chemical synaptic transmission / learning or memory / membrane raft / signaling receptor binding / neuronal cell body / synapse / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / : / : / : / Dickkopf-related protein 1/2/4, C-terminal subdomain 2 / Dickkopf-related protein 1/2/4, C-terminal subdomain 1 / Dickkopf, N-terminal cysteine-rich / Dickkopf-like protein / Dickkopf N-terminal cysteine-rich region / Lipase, subunit A ...: / : / : / : / Dickkopf-related protein 1/2/4, C-terminal subdomain 2 / Dickkopf-related protein 1/2/4, C-terminal subdomain 1 / Dickkopf, N-terminal cysteine-rich / Dickkopf-like protein / Dickkopf N-terminal cysteine-rich region / Lipase, subunit A / Lipase, subunit A / Low density lipoprotein receptor-related protein 5/6 / TolB, C-terminal domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat 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 / Coagulation Factor Xa inhibitory site / 6 Propeller / Neuraminidase / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 6 / Dickkopf-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsAhn, V.E. / Chu, M.L.-H. / Choi, H.-J. / Tran, D. / Abo, A. / Weis, W.I.
CitationJournal: Dev.Cell / Year: 2011
Title: Structural Basis of Wnt Signaling Inhibition by Dickkopf Binding to LRP5/6.
Authors: Ahn, V.E. / Chu, M.L. / Choi, H.J. / Tran, D. / Abo, A. / Weis, W.I.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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
A: Low-density lipoprotein receptor-related protein 6
B: Low-density lipoprotein receptor-related protein 6
C: Dickkopf-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,56715
Polymers154,0653
Non-polymers3,50112
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint30 kcal/mol
Surface area26630 Å2
Unit cell
Length a, b, c (Å)96.043, 108.014, 173.120
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, 3 molecules ABC

#1: Protein Low-density lipoprotein receptor-related protein 6 / LRP-6


Mass: 71475.383 Da / Num. of mol.: 2 / Fragment: ectodomain repeats 3, 4 UNP residues 630-1246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75581
#2: Protein Dickkopf-related protein 1 / Dickkopf-1 / Dkk-1 / hDkk-1 / SK


Mass: 11114.712 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 178-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKK1, UNQ492/PRO1008 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O94907

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Sugars , 3 types, 10 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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 , 2 types, 58 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS IS A NATURAL VARIANT

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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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10-15% PEG3350, 100 mM Tris-Cl (pH 8.5), 100 mM Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.0039 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0039 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 47525 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.75-2.853.40.627199.8
2.85-2.963.40.4591100
2.96-3.13.40.305199.9
3.1-3.263.40.2011100
3.26-3.463.40.1231100
3.46-3.733.40.0851100
3.73-4.113.40.061199.9
4.11-4.73.40.041100
4.7-5.923.30.043199.9
5.92-503.30.026197.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.8→45.82 Å / SU ML: 0.75 / σ(F): 0 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 2235 4.96 %
Rwork0.1938 --
obs0.1967 45023 99.85 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.742 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8856 Å20 Å2-0 Å2
2--3.8263 Å2-0 Å2
3----6.7119 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10329 0 228 56 10613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310803
X-RAY DIFFRACTIONf_angle_d0.69314630
X-RAY DIFFRACTIONf_dihedral_angle_d15.4674055
X-RAY DIFFRACTIONf_chiral_restr0.051632
X-RAY DIFFRACTIONf_plane_restr0.0021886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.86090.40051520.32052621X-RAY DIFFRACTION100
2.8609-2.92740.40331240.30922660X-RAY DIFFRACTION100
2.9274-3.00060.3831610.28182647X-RAY DIFFRACTION100
3.0006-3.08170.37371440.26422625X-RAY DIFFRACTION100
3.0817-3.17240.29221220.25062620X-RAY DIFFRACTION100
3.1724-3.27480.33921190.23532691X-RAY DIFFRACTION100
3.2748-3.39180.29981270.22192640X-RAY DIFFRACTION100
3.3918-3.52750.25771390.20822671X-RAY DIFFRACTION100
3.5275-3.6880.27281260.19632667X-RAY DIFFRACTION100
3.688-3.88230.27951490.18672662X-RAY DIFFRACTION100
3.8823-4.12540.24021530.17472658X-RAY DIFFRACTION100
4.1254-4.44370.20541500.14522656X-RAY DIFFRACTION100
4.4437-4.89040.17791460.12772696X-RAY DIFFRACTION100
4.8904-5.5970.19431370.14822712X-RAY DIFFRACTION100
5.597-7.04750.22621400.18452741X-RAY DIFFRACTION100
7.0475-45.82610.22261460.21472821X-RAY DIFFRACTION98
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)
11.92260.59610.87121.15580.38451.86620.2415-0.3298-0.21390.0646-0.0394-0.04260.27930.0305-0.11080.367-0.094-0.07510.33120.04910.273420.7079-12.2476-11.0574
21.3228-0.06840.44231.67580.70691.8255-0.12730.11520.0065-0.05650.0625-0.1197-0.09030.06450.05440.3626-0.13180.00030.4053-0.03860.37837.5463-15.4062-54.6411
31.2381-0.9612-0.35672.03010.49650.97290.14530.17680.0974-0.2584-0.0914-0.0343-0.07450.0594-0.05150.22710.0232-0.00110.23680.01480.24230.095529.7755-25.1372
42.02590.2262-0.04381.07320.51481.94030.0043-0.02340.12480.11680.0046-0.1382-0.16680.01610.02870.3242-0.0138-0.07040.23560.01050.320915.412753.540911.1318
52.12150.02210.87421.65560.04061.56210.1188-0.25090.10880.3191-0.06090.26470.3098-0.1120.01870.3186-0.06410.02610.4092-0.06170.395713.975114.084-11.8812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 630:932
2X-RAY DIFFRACTION2chain A and resid 933:1246
3X-RAY DIFFRACTION3chain B and resid 628:932
4X-RAY DIFFRACTION4chain B and resid 933:1246
5X-RAY DIFFRACTION5chain C

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