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- PDB-8dvn: Crystal structure of LRP6 E3E4 in complex with disulfide constrai... -

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Basic information

Entry
Database: PDB / ID: 8dvn
TitleCrystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.10
Components
  • E3.10 Disulfide constrained peptide
  • Low-density lipoprotein receptor-related protein 6
KeywordsSIGNALING PROTEIN / LRP6 / E3E4 / Wnt Signaling / Disulfide constrained peptide / Wnt agonism
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 / toxin transmembrane transporter activity / low-density lipoprotein particle receptor activity / Wnt receptor 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 / toxin transmembrane transporter activity / low-density lipoprotein particle receptor activity / Wnt receptor activity / cellular response to cholesterol / midbrain dopaminergic neuron differentiation / Wnt-protein binding / 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 / negative regulation of smooth muscle cell apoptotic process / 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 / Wnt signaling pathway / response to peptide hormone / positive regulation of DNA-binding transcription factor activity / cell-cell adhesion / early endosome membrane / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / chemical synaptic transmission / 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 / 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 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 / 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 / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsThakur, A.K. / Liau, N.P.D. / Sudhamsu, J. / Hannoush, R.N.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Synthetic Multivalent Disulfide-Constrained Peptide Agonists Potentiate Wnt1/ beta-Catenin Signaling via LRP6 Coreceptor Clustering.
Authors: Thakur, A.K. / Miller, S.E. / Liau, N.P.D. / Hwang, S. / Hansen, S. / de Sousa E Melo, F. / Sudhamsu, J. / Hannoush, R.N.
History
DepositionJul 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: E3.10 Disulfide constrained peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,65711
Polymers75,2702
Non-polymers2,3879
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.097, 116.783, 127.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 71774.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75581
#2: Protein/peptide E3.10 Disulfide constrained peptide


Mass: 3495.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 5 types, 5 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: 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: 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 , 2 types, 13 molecules

#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M KSCN

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.53→44.33 Å / Num. obs: 34563 / % possible obs: 99.91 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.03857 / Net I/σ(I): 15.13
Reflection shellResolution: 2.53→2.61 Å / Redundancy: 6.6 % / Num. unique obs: 22437 / CC1/2: 0.503 / Rpim(I) all: 0.8099 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX1.20rc3-4406_finalrefinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A0P

4a0p


Resolution: 2.53→44.33 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 3341 5.1 %
Rwork0.2093 62131 -
obs0.2112 34563 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.95 Å2 / Biso mean: 86.8793 Å2 / Biso min: 41.98 Å2
Refinement stepCycle: final / Resolution: 2.53→44.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5113 0 151 9 5273
Biso mean--122.35 68.08 -
Num. residues----644
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.53-2.560.42151330.4336251598
2.56-2.60.45711400.4172258599
2.6-2.640.39061500.3982257599
2.64-2.690.40971350.36652594100
2.69-2.730.3551240.3662608100
2.73-2.780.32791160.35192607100
2.78-2.830.39041570.32392591100
2.83-2.890.37661460.32252588100
2.89-2.960.42041370.32832601100
2.96-3.020.38311510.32152544100
3.02-3.10.36631360.30042640100
3.1-3.180.39881240.2612569100
3.18-3.280.30881440.24182593100
3.28-3.380.29971560.22682609100
3.38-3.50.27961270.22092576100
3.5-3.640.30391380.2282600100
3.64-3.810.24391240.19982608100
3.81-4.010.20911520.1732595100
4.01-4.260.20251340.15852584100
4.26-4.590.18861380.13712598100
4.59-5.050.14661420.14252595100
5.05-5.780.21361410.16392608100
5.78-7.280.1941410.18452575100
7.28-44.330.18841550.17762573100
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)
12.1845-1.2792-0.7746.0029-0.56483.0319-0.1712-0.31540.11310.71280.4103-0.0240.10020.0126-0.23850.47740.0155-0.00560.5712-0.01480.373712.37924.574517.5471
23.0448-0.6614-0.6913.57140.23062.4032-0.10280.0626-0.4251-0.0391-0.0799-0.22440.95110.13130.14740.99660.0714-0.03620.5322-0.01320.509734.5498-5.8476-7.6097
33.1837-2.48751.82312.7704-3.58428.3456-0.33841.98171.2458-0.5275-0.1693-0.6677-1.72630.14940.54960.9539-0.07210.10421.01180.17820.909816.774237.4973-2.5571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 630 through 920)A630 - 920
2X-RAY DIFFRACTION2chain 'A' and (resid 921 through 1245 )A921 - 1245
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 32 )B1 - 32

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