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- PDB-7nam: LRP6_E1 in complex with Lr-EET-3.5 -

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Basic information

Entry
Database: PDB / ID: 7nam
TitleLRP6_E1 in complex with Lr-EET-3.5
Components
  • Low-density lipoprotein receptor-related protein 6
  • Trypsin inhibitor 2
KeywordsSIGNALING PROTEIN / LRP6 / Wnt signaling / cystine knot peptide
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: 1.6 Å
AuthorsHansen, S. / Hannoush, R.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Directed evolution identifies high-affinity cystine-knot peptide agonists and antagonists of Wnt/ beta-catenin signaling.
Authors: Hansen, S. / Zhang, Y. / Hwang, S. / Nabhan, A. / Li, W. / Fuhrmann, J. / Kschonsak, Y. / Zhou, L. / Nile, A.H. / Gao, X. / Piskol, R. / de Sousa E Melo, F. / de Sauvage, F.J. / Hannoush, R.N.
History
DepositionJun 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Trypsin inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7896
Polymers38,9862
Non-polymers1,8044
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint12 kcal/mol
Surface area14790 Å2
Unit cell
Length a, b, c (Å)108.890, 46.940, 87.790
Angle α, β, γ (deg.)90.000, 124.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-577-

HOH

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Components

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


Mass: 35614.844 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 Trypsin inhibitor 2


Mass: 3370.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1a_1-5]/1-2-1-3-2/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 3350, 0.2 M Na malate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→42.121 Å / Num. obs: 91673 / % possible obs: 96.5 % / Redundancy: 3.397 % / Biso Wilson estimate: 26.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.059 / Χ2: 1.163 / Net I/σ(I): 10.54 / Num. measured all: 311416 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.643.5591.0451.2624409696568590.6361.23198.5
1.64-1.693.5430.8721.5124216693968340.6931.02998.5
1.69-1.743.5050.652222804663865060.8080.77198
1.74-1.793.4750.4842.6221786645362690.8710.57397.1
1.79-1.853.3550.363.4420367626260700.9160.42996.9
1.85-1.913.2610.2744.2219066612358470.9440.32995.5
1.91-1.983.5450.2285.4819953580656290.9650.26997
1.98-2.073.4660.167.3318800562354240.980.1996.5
2.07-2.163.4140.1228.917468535051170.9870.14595.6
2.16-2.263.3430.110.3416730521450050.990.11996
2.26-2.393.1010.07912.0514147491545620.9910.09692.8
2.39-2.533.30.07113.6514610461844270.9940.08495.9
2.53-2.73.3740.0616.0514291440242350.9950.07196.2
2.7-2.923.2970.0518.912845403938960.9960.05996.5
2.92-3.23.2390.04321.8511494372935490.9960.05195.2
3.2-3.583.0080.03724.959358339431110.9970.04491.7
3.58-4.133.4870.03430.6210205298529270.9980.03998.1
4.13-5.063.5080.02935.298700252224800.9980.03498.3
5.06-7.163.2830.02736.056136194918690.9990.03295.9
7.16-42.1213.8140.02244.774031108410570.9990.02597.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SOV

3sov


Resolution: 1.6→42.121 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1926 2431 5.13 %
Rwork0.1702 44999 -
obs0.1713 47430 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.13 Å2 / Biso mean: 40.6893 Å2 / Biso min: 17.81 Å2
Refinement stepCycle: final / Resolution: 1.6→42.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 234 228 3118
Biso mean--69.85 41.48 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012942
X-RAY DIFFRACTIONf_angle_d1.1543974
X-RAY DIFFRACTIONf_chiral_restr0.046449
X-RAY DIFFRACTIONf_plane_restr0.006505
X-RAY DIFFRACTIONf_dihedral_angle_d14.3921085
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.63270.29011530.2941264799
1.6327-1.66820.3231560.297262699
1.6682-1.7070.27341560.2699265499
1.707-1.74960.27241430.2608266198
1.7496-1.7970.26391320.2404266798
1.797-1.84980.25771570.2325257197
1.8498-1.90950.20821510.2177261896
1.9095-1.97780.27071380.2231264098
1.9778-2.0570.24821430.2064262697
2.057-2.15060.22161180.2072263697
2.1506-2.2640.23141350.1985266098
2.264-2.40580.21951630.181252595
2.4058-2.59150.23451330.1863269098
2.5915-2.85230.20131260.1766267398
2.8523-3.26490.19091740.161263697
3.2649-4.11280.15711360.1337265897
4.1128-42.1210.12041170.1299281198
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)
11.4878-0.7373-0.57671.62060.03042.37690.0465-0.0355-0.2806-0.17350.03070.44970.3365-0.33250.00040.2375-0.0481-0.04010.23190.02370.330414.6633-9.506423.8329
21.6172-0.09590.27161.1503-0.0451.97320.01730.06940.1402-0.19020.0127-0.0845-0.15130.307100.209-0.01740.04080.2226-0.0150.209830.73982.346820.1449
31.30240.56510.30081.5126-0.4042.06430.02920.44680.1579-0.59680.02980.3777-0.1434-0.1263-0.00010.37730.0271-0.07850.30360.03830.28415.92624.52017.9014
40.6562-0.02470.83661.45340.01521.98680.09630.2962-0.3197-0.36660.01240.08860.33440.30980.04450.2910.07240.0030.2402-0.04260.225828.6462-9.762715.33
50.81460.8136-0.532.273-0.1560.44670.11350.1112-0.170.0614-0.2876-0.47260.38660.7296-0.07750.22970.14410.07380.5201-0.03450.329247.6636-8.49425.7237
60.53960.1233-0.02350.3565-0.12950.13270.229-0.27690.29560.4148-0.03840.5125-0.3603-0.3211-00.34190.06910.10920.3744-0.02020.46278.008112.25731.5734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 98 )A19 - 98
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 183 )A99 - 183
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 262 )A184 - 262
4X-RAY DIFFRACTION4chain 'A' and (resid 263 through 305 )A263 - 305
5X-RAY DIFFRACTION5chain 'A' and (resid 306 through 325 )A306 - 325
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 32 )B1 - 32

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