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- PDB-3soq: The structure of the first YWTD beta propeller domain of LRP6 in ... -

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Basic information

Entry
Database: PDB / ID: 3soq
TitleThe structure of the first YWTD beta propeller domain of LRP6 in complex with a DKK1 peptide
Components
  • Dickkopf-related protein 1
  • Low-density lipoprotein receptor-related protein 6
KeywordsPROTEIN BINDING/Antagonist / beta propeller / PROTEIN BINDING-Antagonist complex
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 / Wnt signaling pathway involved in somitogenesis / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / Signaling by LRP5 mutants / regulation of dopaminergic neuron differentiation / Wnt-Frizzled-LRP5/6 complex / 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 / Wnt signaling pathway involved in somitogenesis / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / Signaling by LRP5 mutants / regulation of dopaminergic neuron differentiation / Wnt-Frizzled-LRP5/6 complex / negative regulation of cardiac muscle cell differentiation / endoderm formation / motor learning / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / synapse pruning / neural crest formation / Signaling by RNF43 mutants / endocardial cushion development / heart induction / negative regulation of protein serine/threonine kinase activity / receptor antagonist activity / regulation of receptor internalization / kinase inhibitor activity / toxin transmembrane transporter activity / Wnt receptor activity / co-receptor binding / low-density lipoprotein particle receptor activity / positive regulation of Wnt signaling pathway, planar cell polarity pathway / Wnt-protein binding / midbrain dopaminergic neuron differentiation / cellular response to cholesterol / heart valve development / dopaminergic neuron differentiation / frizzled binding / negative regulation of presynapse assembly / Wnt signalosome / embryonic limb morphogenesis / Disassembly of the destruction complex and recruitment of AXIN to the membrane / limb development / negative regulation of ossification / face morphogenesis / neural crest cell differentiation / low-density lipoprotein particle receptor binding / negative regulation of SMAD protein signal transduction / negative regulation of smooth muscle cell apoptotic process / negative regulation of Wnt signaling pathway / mesoderm formation / negative regulation of BMP signaling pathway / hair follicle development / canonical Wnt signaling pathway / response to retinoic acid / regulation of synaptic transmission, glutamatergic / forebrain development / coreceptor activity / regulation of neuron apoptotic process / positive regulation of cell cycle / negative regulation of protein binding / Regulation of FZD by ubiquitination / positive regulation of DNA-binding transcription factor activity / protein localization to plasma membrane / TCF dependent signaling in response to WNT / positive regulation of JNK cascade / growth factor activity / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cell-cell adhesion / response to peptide hormone / Wnt signaling pathway / endocytosis / nervous system development / negative regulation of neuron projection development / positive regulation of cytosolic calcium ion concentration / early endosome membrane / 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, N-terminal cysteine-rich / Dickkopf-like protein / : / : / Dickkopf N-terminal cysteine-rich region / Dickkopf-related protein 1/2/4, C-terminal subdomain 2 / Dickkopf-related protein 1/2/4, C-terminal subdomain 1 / Low density lipoprotein receptor-related protein 5/6 ...: / : / Dickkopf, N-terminal cysteine-rich / Dickkopf-like protein / : / : / Dickkopf N-terminal cysteine-rich region / Dickkopf-related protein 1/2/4, C-terminal subdomain 2 / Dickkopf-related protein 1/2/4, C-terminal subdomain 1 / 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 / Laminin / Laminin / 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
alpha-L-fucopyranose / Low-density lipoprotein receptor-related protein 6 / Dickkopf-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, W. / Bourhis, E. / Zhang, Y. / Rouge, L. / Wu, Y. / Franke, Y. / Cochran, A.G.
CitationJournal: Structure / Year: 2011
Title: Wnt antagonists bind through a short peptide to the first beta-propeller domain of LRP5/6.
Authors: Bourhis, E. / Wang, W. / Tam, C. / Hwang, J. / Zhang, Y. / Spittler, D. / Huang, O.W. / Gong, Y. / Estevez, A. / Zilberleyb, I. / Rouge, L. / Chiu, C. / Wu, Y. / Costa, M. / Hannoush, R.N. / ...Authors: Bourhis, E. / Wang, W. / Tam, C. / Hwang, J. / Zhang, Y. / Spittler, D. / Huang, O.W. / Gong, Y. / Estevez, A. / Zilberleyb, I. / Rouge, L. / Chiu, C. / Wu, Y. / Costa, M. / Hannoush, R.N. / Franke, Y. / Cochran, A.G.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
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_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.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.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_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
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Z: Dickkopf-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9886
Polymers36,4712
Non-polymers5184
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-4 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.320, 46.976, 68.722
Angle α, β, γ (deg.)90.00, 97.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AZ

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


Mass: 35685.926 Da / Num. of mol.: 1 / Fragment: UNP residues 20-335
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/peptide Dickkopf-related protein 1 / Dickkopf-1 / Dkk-1 / hDkk-1 / SK


Mass: 784.862 Da / Num. of mol.: 1 / Fragment: UNP residues 38-44 / Source method: obtained synthetically / Details: peptide D / Source: (synth.) Homo sapiens (human) / References: UniProt: O94907

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Sugars , 2 types, 2 molecules

#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#4: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 268 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M potassium thiocyanate and 30% (w/v) PEG MME 2000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 26003 / % possible obs: 98 % / Observed criterion σ(I): 2.3
Reflection shellResolution: 1.9→1.97 Å / % possible all: 82

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→23.044 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 1273 5 %5 percent
Rwork0.177 ---
obs0.1792 25483 97.87 %-
all-26003 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.31 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8836 Å20 Å2-1.4179 Å2
2--1.7669 Å2-0 Å2
3---2.1167 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 31 266 2765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042578
X-RAY DIFFRACTIONf_angle_d0.9253504
X-RAY DIFFRACTIONf_dihedral_angle_d14.589931
X-RAY DIFFRACTIONf_chiral_restr0.068385
X-RAY DIFFRACTIONf_plane_restr0.003451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.97530.29731170.25372248X-RAY DIFFRACTION83
1.9753-2.06510.25631530.1952676X-RAY DIFFRACTION99
2.0651-2.17390.2221350.17462747X-RAY DIFFRACTION100
2.1739-2.310.23531230.17132744X-RAY DIFFRACTION100
2.31-2.48810.23181490.1782755X-RAY DIFFRACTION100
2.4881-2.73820.23571550.18292727X-RAY DIFFRACTION100
2.7382-3.13350.23381450.18412757X-RAY DIFFRACTION100
3.1335-3.94470.20491680.16732706X-RAY DIFFRACTION100
3.9447-23.04540.19811280.16752850X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.296 Å / Origin y: -0.7198 Å / Origin z: -16.6998 Å
111213212223313233
T0.1218 Å20.0203 Å2-0.0007 Å2-0.0952 Å2-0.0139 Å2--0.1121 Å2
L1.2441 °2-0.3821 °20.2664 °2-0.6375 °2-0.2375 °2--1.0585 °2
S0.0814 Å °0.0393 Å °-0.0647 Å °-0.0462 Å °-0.0202 Å °0.0696 Å °0.0391 Å °-0.016 Å °-0.0006 Å °

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