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- PDB-3s8v: Crystal structure of LRP6-Dkk1 complex -

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Basic information

Entry
Database: PDB / ID: 3s8v
TitleCrystal structure of LRP6-Dkk1 complex
Components
  • Dickkopf-related protein 1
  • Low-density lipoprotein receptor-related protein 6
KeywordsSIGNALING PROTEIN / Wnt / receptor / LRP5 / LRP6 / LDL receptor-like protein / Dickkopf (Dkk) / YWTD b-propeller
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 / Lipase, subunit A ...: / : / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCheng, Z. / Xu, W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Crystal structures of the extracellular domain of LRP6 and its complex with DKK1.
Authors: Cheng, Z. / Biechele, T. / Wei, Z. / Morrone, S. / Moon, R.T. / Wang, L. / Xu, W.
History
DepositionMay 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
X: Dickkopf-related protein 1


Theoretical massNumber of molelcules
Total (without water)151,4343
Polymers151,4343
Non-polymers00
Water00
1
A: Low-density lipoprotein receptor-related protein 6
X: Dickkopf-related protein 1


Theoretical massNumber of molelcules
Total (without water)80,6052
Polymers80,6052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-10 kcal/mol
Surface area28990 Å2
MethodPISA
2
B: Low-density lipoprotein receptor-related protein 6


Theoretical massNumber of molelcules
Total (without water)70,8291
Polymers70,8291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.384, 105.050, 161.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A629 - 1243
2115B629 - 1243

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Components

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


Mass: 70828.742 Da / Num. of mol.: 2 / Fragment: E3E4, residues 629-1243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP6 / Plasmid: pAcGP67b / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75581
#2: Protein Dickkopf-related protein 1 / Dickkopf-1 / Dkk-1 / hDkk-1 / SK


Mass: 9776.192 Da / Num. of mol.: 1 / Fragment: Dkk1c, residues 184-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKK1, UNQ492/PRO1008 / Plasmid: pET32m / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: O94907
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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 20mM citric acid, 80mM Bis-tris propane pH 8.8, 19-20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.210.999
SYNCHROTRONALS 8.2.120.999
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 10, 2011
ADSC QUANTUM 315r2CCDApr 10, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9991
21
ReflectionResolution: 3.05→30 Å / Num. all: 30976 / Num. obs: 30419 / % possible obs: 98.2 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IJQ and 3S8Z

1ijq

3s8z


Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.866 / Occupancy max: 1 / Occupancy min: 1 / SU B: 26.364 / SU ML: 0.462 / Cross valid method: THROUGHOUT / ESU R Free: 0.562 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29248 1485 5.1 %RANDOM
Rwork0.24042 ---
obs0.24306 27740 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.121 Å2
Baniso -1Baniso -2Baniso -3
1--3.2 Å20 Å20 Å2
2---5.09 Å2-0 Å2
3---8.29 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10177 0 0 0 10177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02110403
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.94514105
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46251268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27423.658514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.467151786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8721593
X-RAY DIFFRACTIONr_chiral_restr0.0740.21545
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217927
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2388MEDIUM POSITIONAL0.590.5
2382LOOSE POSITIONAL0.825
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 83 -
Rwork0.324 1880 -
obs--91.47 %

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